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LabChip GX/GXII User Manual

1. 108 LAS a x 177 Laser Safety aaa ess 9 Last Peak Time 206 Layout Options Window 142 Leading Edge 133 Line Voltage 182 Location barcode label 34 LOIS Rise does ss 208 Log ba 44 ARN AA KA KAHA toi 124 Lower marker 208 M Main window 83 Maintenance and Service 184 Cleaning the Chip Cartridge 185 198 Manual export 79 Manual peak 53 Manually exporting data 75 Marker 36 124 aligning 55 ASSICONING 244204044004 assis 36 Assignments 124 concentration 124 Drift Tolerance 133 Marker well 178 Not detected 36 UM and LM for DNA 55 P N 128682 Rev 00 LabChip Dx User Manual Index 226 Maximum Graphs per Page 103 Mechanical safety 11 Menu 84 85 86 87 88 89 Analysis menu 86 Collection Menu 86 File menu 85 Help menu 89 Instrument menu 87 Menu Bar 84 Tools menu 87 Validation menu 88 View menu 88 Window menu 89 Workspace Menu 85 Merging two peaks 54 Microfluidics
2. 10 USE pee tear eae ereeees ham LG 11 instrument 7 laser nce siens ss ses trim 9 mechanical 11 power cord wawa pawang KAKA 11 training required 7 Sample 22 36 43 103 133 PCE ne hs oe ede eR EEA 36 Calculating size 36 LOGO is 0x04 NGA KARA 2 22 36 NAME 262052544042 ose 103 Name template 43 Sample Color 103 Sample Peak Quantitation 133 Sample Saver 22 Sample Name Editor Window 161 Save 30 Saving and Exporting Assays 57 Saving Plate Data Files 30 Saving Workspace Files 31 Save Workspace As Window 163 Scale Gel Contrast 105 Searching for Events in the Events Tab 191 Select a Data File Window 164 Selected in Gel 114 Selecting the Wells in a Collection 42 Sale SPA 184 Service PIANS ua wk AK AA KG 3 Shortcuts 201 Show all peaks 114 Show Data Points 103 Show EP Legend 108 P N 128682 Rev 00 LabChip Dx User Manual Index 228 Show Expected Peaks 108 Show Legend in Gel 108 Show Peak Baselines 103 Showing views 60 Sip Height 32 120 Sipper location 178 DIZ esse se sa das kA kahe LA 182 Sleep mode 5 NADA AA sc 199 Slope Threshold
3. 210 Microplate 32 181 Microplate carrier 181 Migration Time 36 Min Peak Width 36 210 Minimum peak height 125 210 Minimum Peak Width 125 Minimum Sip Height 32 Modifying Analysis Parameters 51 Molarity 36 210 Molecular Separation Techniques 211 Monitoring the Run 27 Mouse shortcuts 201 Move Timeout Error 195 SDS a a AGANG 8 N New assay 57 New Collection Window 144 New plate 32 New workspace 39 O Only Annotate Expected Peaks 103 Opening a Data File 40 Opening a New Workspace 39 Operating Humidity 182 Operating Temperature 182 ODNET tama rod en 177 jo Me D ane ie ee 5 188 OQ running 190 Orientation 103 Caliper Life Sciences Inc C AA AA 179 Output Tab Start Run Window 168 Overlay Electropherogram printing 69 Overlay Electropherograms Tab 101 Overlaying well graphs 58 P Pane width adjusting 60 PEAK 4 36 53 210 211 212 eee pA PE 53 PCG taka bb a6 oe Ene AAP 110 Baseline 36 125 133 211 changing Peak Find parameters 52 excluding 53 NAGINOG es E 76 Heights eeeceed eee vs 210 211 identifying peaks
4. 77 125 216 Software Disconnects 199 Software IQ Window 141 Software Reference 82 Software Troubleshooting 199 Sort within each well 114 Specifications 32 182 instrument 182 DAS ea ETE 32 Standard curve 36 124 216 Na A da te 20 22 217 Monitoring the Run 27 Running the assay 22 Start button 22 Slall PO Maa 4 sms raie 217 Starting a Run 22 Start Run Window 165 Start Time 125 changing 54 Status light 175 Stop Button 22 28 90 Storage Temperature 182 Support plans 3 Supported Barcode Types 182 System Components Test 187 System Diagnostics Window 172 System log 208 System Peak Exclusion 124 System Status 90 T Temperature Range 182 Templates 43 Text orientation 103 Thermal Limit Switch 182 Time changing analysis time 54 Tools Meny 244045654444 e085405 87 Training required 7 Transient Overvoltages 182 Caliper Life Sciences Inc Troubleshooting 28 186 198 Abortingarun 28 Chip has Expired 196 Chip Temperature Warnin
5. ll rights reserved LabChip Dx User Manual ma i Y Ca Copyright Trademarks Content Preface 2 Preface This manual is published by Caliper Life Sciences Inc 68 Elm Street Hopkinton MA 01748 USA Copyright 2008 2011 Caliper Life Sciences Inc All rights reserved Reproduction by any means or in any form of this manual or the products it describes is prohibited Caliper Life Sciences Inc LabChip and the LabChip logo are registered trademarks of Caliper Life Sciences Inc The Caliper logo and DataViewer are trademarks of Caliper Life Sciences Inc Microsoft Windows and Windows NT are either registered trademarks or trademarks of Microsoft Corporation in the United States and or other countries All other trademarks and registered trademarks are the property of their respective holders The information in this manual may contain typographical errors or technical inaccuracies and is subject to change without notice Modifications may also be made to the product described in this manual at any time Proper Equipment Operation Contact Us WARNINGS e To reduce the risk of electric shock do not remove the cover No user serviceable parts inside Refer to qualified service personnel if help is required e Use this product only in the manner described in this manual If the equipment is used in a manner not specified by the manufacturer the protection provided by the equipment may be impaired
6. 81 212 merging peaks 54 Peak Find Settings 125 Peak Find Tab 125 Peak integration mode 133 Peak Size Calibration Point 133 Peak Table View 110 Show Peak Baseline 103 Valley to Valley Baseline 133 Peak Find Tab 125 Peak Table 110 eXporting sms sure 72 printing 71 Properties 114 Plate Capacity 182 Plate Carrier Motion Blocked Error 194 Plate compatibility 32 Plate Height 32 120 Plate Information Window 145 Plate Name 120 Plate Orientation 182 Plate Sensor Test 189 Plate Type 120 Plate View or Plate List 93 Plate adding new 32 Point to point fit 124 212 Pollution Degree 182 Polynomial 36 125 205 213 HI US 213 HIGOP APA 124 Oe 45404 ee PK 125 205 213 P N 128682 Rev 00 LabChip Dx User Manual Index 227 Position barcode label 34 Power button 175 Power cable 176 Power cord selection 11 Power Input Specification 182 Power Options 199 Preparing and Running An Assay 22 PICSSULC manabanaaga aaa a 177 Pressure Leak Detected Error 195 Pressure Leak Test 188 Pressu
7. Selected in Gel If selected only the gel lanes selected in the Gel View display To select multiple wells Ctrl click on the lanes in the Gel view Entire If selected all wells in all plates that are included in the collection Collection are displayed Pin icon In the top right corner used to lock in place or unlock the Properties tab If locked in place the Peak Table display panel is resized to accommodate the tab P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 115 Filter View The Filter view in the Collection Pane is used to define criteria to select wells for a collection automatically The filter types available depend on the type of assay that was used to create the data Each filter can be assigned a different color to determine which filter applies to each well See Example Expected Peaks Filter for an example of a filter Figure 45 Filter View One or more filters can be defined independently by selecting the appropriate filter type range mode and range values and then clicking the Add button The Available Filters list box displays all of the filters that are part of the current collection The check box next to each filter in the list is used to include or exclude that filter from the analysis The Filter Options selection determines how multiple filters are logically combined The options available are OR AND Peak and AND Well e OR Selects any well
8. Pona Kasa Saves the selected settings in a run file with the specified name xml Import Imports the settings from an existing run file xml into the Run File Editor window Closes the Run File Editor window without saving the settings P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 160 Run Info Window Use the Run Info window to view information about the run options for the selected plate data file To open the Run Info window select View gt Run Info on the LabChip Dx Main Window or right click on the name of the data file above the plate diagram and select Run Info Rua Info Demo ONA 5k 2009 05 14 09 40 0P HT DHA HT DNA 5K 202600 SPE 0 17318 CAT LABCHIPONE genw iC Peya bes Colina Lie Sona Lahi ao Data Dens DHA NG GG a Papas Fes PCR Seated Sp Miche 5 DO immi it OS 40 05 Ab AZ AJ MAS AG AT AE AS AUD ATI Al ET 82 69 84 05 86 87 BE 655 810 011 812 True 4 bi li ti a w F Pard Pre Part ris Figure 78 Run Info Window The information in this window is view only and cannot be changed The Run Info tab displays assay information and run information The Event Log tab displays the events that occurred during the run The Run Info window contains the following buttons Print Opens the Print Preview window to view the run information before Preview printing Opens the Print window to print the run informati
9. on page 20 If necessary create a new assay See Creating a New Assay on page 21 See Adding a New Plate on page 32 if the plate you are using is not in the list of defined plates See Placing the Barcode on the Plate on page 34 if using barcodes on the sample plates Clean the electrodes and the O Rings as directed in the LabChip Dx Assay User Guide Prepare the chip for the assay as directed in the LabChip Dx Assay Quick Guide Prepare the plate for the assay as directed in the LabChip Dx Assay Quick Guide Run the assay See Running an Assay on page 22 If desired choose to export copies of gels or graphs see Selecting the Auto Export Settings on page 25 or to export copies of the data files see Automatically Exporting Copies of Data Files on page 26 Monitor the run see Monitoring the Run on page 27 If necessary stop the run see Stopping a Run on page 28 Opening the LabChip Dx Software To open the LabChip Dx software 1 P N 128682 Rev 00 Double click on the LabChip Dx icon on the Windows desktop The LabChip Dx Main Window opens See Creating a New Assay on page 21 or Running an Assay on page 22 LabChip Dx User Manual Caliper Life Sciences Inc Operation 21 Creating a New Assay The LabChip Dx software enables you to create a new assay by opening and editing an existing assay and then saving the assay with a new name
10. 3 Cannot save a file 199 Cartridge 179 Center Calibration Point 133 Center point 202 Changing sample name 22 43 Changing the View of the Results 58 Chemical Safety 8 CMY 4 amce he eee aS PEREST 178 Chip button 175 Chip cartridge 179 cleaning the chip cartridge 185 Chip Expiration 90 Chip focusing 177 Chip has Expired Warning 196 Chip Interface Test 187 Chip Pressure system 117 Caliper Life Sciences Inc Chip SUS ss KAKA creuse 90 Chip Temperature Test 188 Chip Temperature Warning 197 Chromatography Data Interchange Format Ta 79 Cleaning the Chip Cartridge 185 198 Clipboard 203 Collection 41 86 96 204 adding to workspace 41 Collection Menu 86 Collection pane 96 Selecting the Wells in a Collection 42 Color gel 105 Compare results 58 Compatible plates 32 Compute Resources Test 187 Computer Power Options 199 Computer Software Lock Ups 200 Concentration 17 124 Continuing a Run 29 COMMAS 4 Rad ES 105 Goo EP ETE E E 65 CODY Gel earar AKEN suc AKA 65 Copy Graph 65 Copy Lane
11. P N 128682 Rev 00 Size Specifies the size of the excluded peaks in BP Window Specifies the tolerance window as a percent of the size of the peak to allow for small variations in peak size Color Displays the color to use to mark the peak in the Graph View or the Gel View Name Specifies a name to display in the Type description for the peak LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 132 Excluded Peaks Tab Continued e Apply to Wells Specifies the wells that the excluded peak is applied to lt All gt specifies that the excluded peak applies to all wells Clicking on the column opens the Select Wells window to choose the specific wells to apply the excluded peak to Import button Opens the Import Excluded Peaks window to select an Excluded Peak File gep to import The gep file is created by exporting excluded peaks from another assay Clear button Deletes all Excluded Peaks from the table Restore button Restores the settings to the last saved settings for excluded peaks Export button Opens the Export Excluded Peaks window to create an Excluded Peaks File gep from the current settings in the tab Import the gep file into another assay to use the same excluded peaks in another assay P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 133 Advanced Tab Use the Advanced tab on the Assay Analysis Window to select the Qu
12. Tools Menu The Instrument menu contains the following commands Start Run Opens the Start Run Window to begin running a sample plate See the Assay User Guide for chip and sample prep instructions Start Wash Begins a sequence of steps to wash the chip See the Assay User Guide for chip prep instructions NOTE The Instrument menu does not display if the software was installed in Reviewer mode The Tools menu contains the following commands Run File Editor Opens the Run File Editor window to create Run files Run files contain the settings to run an assay using Caliper s automation control software such as iLink Pro Sample Name Editor Opens the Sample Name Editor Window to change import or export the sample names assigned to the wells of the plate Assay Editor Opens the Select Assay To Edit window Selecting an assay opens the Assay Analysis Window to make changes to the selected assay Teaching Utility Opens the Robot Teaching Wizard to teach the correct reference location Reteach the robot if the sipper is not accessing the plate properly Also includes a plate puncture test to verify the taught location Plate Editor Opens the Plate Information Window to add edit or delete plates from the LabChip DX software P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc View Menu Software Reference 88 The View menu contains the following commands Event Viewer Opens the Event V
13. When you choose Standard Curve from the Analysis menu for a DNA assay a window similar to Figure 102 opens The standard curve is drawn from the values obtained for the DNA ladder It is a plot of the size of the ladder peaks vs time with a point to point fit For each sample peak the apex is interpolated from the Standard Curve to determine the peak size in base pairs BP THE NE Figure 102 DNA Assay Standard Curve For more information about the use of the standard curve during analysis see How the Software Analyzes DNA Data on page 36 P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Glossary of Terms 217 Start Point The peak find algorithm analyzes the data from time zero looking for a slope greater than the Slope Threshold The point where the slope is greater than the slope threshold specified in the Peak Find Tab is marked as the start point of a peak Start Time This setting determines the time after the start of a run when peaks will be detected Any peaks appearing before this time are ignored Upper Marker An internal standard that is added to a DNA sample in a well to assist in determining size and concentration of the sample The marker is the same as the last peak in the DNA ladder Workspace Use a workspace file to view the plate data from a run Multiple plate data files can be opened in the same workspace to enable comparison between data from differe
14. respectively 100 Drift Tolerance 10 Drift 1 ree ipa Tolerance Figure 98 Marker Drift Tolerance P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Glossary of Terms 210 As the drift tolerance is reduced the acceptable deviation from the ladder marker migration time is reduced causing the analysis to reject nearby peaks preceding the true marker The marker drift tolerance is selected on the Advanced Tab of the Assay Analysis Window see page 133 Microfluidics The miniaturization of chemical processes generally pertaining to systems involved in the control of fluid flow This includes pumps valves jets and microchannels Minimum Peak Height The Minimum Peak Height value determines the height limit below which a peak will not be detected For each peak the difference between the peak start time and the peak apex must be greater than the Minimum Peak Height value The Minimum Peak Height is specified on the Peak Find Tab of the Assay Analysis Window Minimum Peak Width The Min Peak Width value determines the width in seconds under which a peak will not be detected For each peak the difference between the peak start time and the peak end time must be greater than the Minimum Peak Width value The Minimum Peak Width is specified on the Peak Find Tab of the Assay Analysis Window Molarity Molarity Concentration 106 660 Size nmol l where molarity is measured in nanomo
15. 4 5 65 Create daily subdirectories 39 Current Calibration Test 189 Current Leakage Check Failed Warning 197 Current Leakage Test 188 Curve fit 124 212 Customer Support plans 3 D Data smoothing 76 Data Analysis 39 36 How the Software Analyzes DNA DANA 6 AKA OY 36 Data File 40 58 204 206 automatically exporting 26 evaluation 58 OB RIT Se mn a core de 40 reanalyzing 66 reverting to revision 67 Data Flle Version Window 136 Data filtering 36 205 P N 128682 Rev 00 LabChip Dx User Manual Index 224 Data points 204 Data Range 124 Detection Wavelength 182 DECO ss ss sr 177 Device Disconnected Error 194 Diagnostics 186 running tests 186 Dilution Ratio 124 Disconnected Device Error 194 Disconnected software 199 DNA Assay Analysis 205 WOO 4s eed KAMA eR eee eee 174 DXD file 40 E Eject button 175 Electrical safety 10 Electrode wells 178 PICCUIOUES AA de eee ne 179 Electrokinetic Forces 205 Electroosmotic Flow 205 Electropherogram Graph View Properties 103 PNUM PR ET Ae oe 4 69
16. Ki ak acum sa B ma DT Sama baa h are La ine aaa a ma wa Sama Er a oom rx mh etma ina MES ma Wa m aa Tae Ai la Cane ha iwa Dm wa ke hpi D mAh 5 Paa acer DY CRT ka tao D Mans E ma aaa Hm aa 2 We ua Nama lags ba nik el le Baa pen Bi a kya 4a lamg Tha a nhia ma pe kk CTET a Tein Ti Ta EK B Pl Es a wa wik eee AA Li Bin 8 ELI rhs NG CRC wa im baga te Pa 8 Cita LE wa a Turon Pia la aie pal ma rn asi hai Taea th Na Pai i hi TET wa Dita DAA D EE ake hi CTET DT Kama bng ta bets LT Laos a T a Lama ra di ai a Les Lame r ya iya mn FE NG aoe Baca hi ki h Dr Ten TA Ta BEC mai Tina Wi a aya DT sasa Paa ta HA Bier ai Let Lu ma sos a ws ua Dmu A ka kka Heni Ty ina hi wa iya Tama D la ih h bem hi hi Tate Mik Ta SF BE uD i 5 DT ae DA DER SERIE o E WG am itt Mili Fa Mama a nal Ak caret ane cp Paga tote iam Bara HG ses la Figure 22 Printed Well Table P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 71 Peak Table Choosing this option prints the columns displayed in the Peak Table View To change the columns that are printed or the order of the columns change the columns in the Peak Table View e Selecting the Exclude Marker check box removes all markers from the printout e Selecting the Add Border check box prints the table with a border around each cell in the table e Selecting the Add Well Name as Header check box prints
17. On the Assay Analysis Window click the Export as Assay button specify a name and location for the assay file and click the Save button 4 When running the next plate select the new assay file in the Start Run window The procedure above can also be used to automatically include a set of expected peaks in the assay P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 58 Changing the View of the Results The views in the LabChip Dx Main Window can be customized to display data according to the preferences of the user These options do not change the raw data but provide different means of displaying the data To change the view in the main window see e Viewing Gels on page 58 e Viewing Zero Baselines on page 59 e Adjust Pane Widths on page 60 e Show or Hide Views on page 60 e Zoom In and Zoom Out on page 60 e Viewing Graphs in the Overlay Electropherograms Tab on page 62 e Viewing Graphs in the Electropherograms Tab on page 63 e Viewing Multiple Properties in the Well Table View on page 64 Viewing Gels To compare the gels generated by the instrument view the gels in the Gel View Figure 14 Gel View The color width and contrast of the gels can be changed using the Gel View Properties To rearrange gels click on the column header well name and drag the well to the desired location To hide a well select the well and then
18. aaa mop o pep pe ee eee eee ae mao ee egg Seed Figure 26 Filtering Examples P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Understanding Peak Finding 77 Because peaks tend to broaden as time progresses use a short filter width initially and then switch to a wider filter near the end of the signal for this type of signal The High Size filter on the Peak Find Tab can be used to smooth the tail of the upper marker without affecting the earlier peaks Ultimately some noise may have to be tolerated to avoid distorting the peak shape Filter Width 0 5 sec High Size Filtering Width 1 2 sec Transition 45 sec Figure 27 High Size Filtering Peak Detection Slope Threshold Peak baseline and Peak detection are controlled primarily through the Slope Threshold property on the Peak Find Tab The signal slope increases rapidly at the start of the peak becomes negative after crossing the peak apex and then returns to a small value at the end of the peak The slope threshold is the slope value used to identify the start and end of the peak The regions outside the zone where the absolute value of the slope exceeds the slope threshold are deemed baseline The slope threshold determines the peak start point and end point e The first point with local derivative above the slope threshold indicates the Start Point of a peak e The first point where the negative slope on the falling edge of the peak drops
19. the peak Property Displayed in Well Table Specifies the content of a column added to the well table for each expected peak Apply to Wells Specifies the wells that the expected peak is applied to lt All gt specifies that the expected peak applies to all wells Clicking on the column opens the Select Wells window to choose the specific wells to apply the expected peak to Import button Opens the Import Expected Fragments Table window to select an Expected Peak File gep to import The gep file is created by exporting expected peaks from another assay Clear button Deletes all Expected Peaks from the table Restore button Restores the settings to the last saved settings for expected peaks Export button Opens the Export Expected Fragments window to create an Expected Peak File gep from the current settings in the tab Import the gep file into another assay to use the same expected peaks in another assay P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 131 Excluded Peaks Tab Use the Excluded Peaks tab on the Assay Analysis Window to enter Excluded Fragments for DNA assays After the data is analyzed any peaks matching the excluded peaks are excluded from the analysis Figure 56 Assay Tea Window Excluded Peaks Tab The Excluded Peaks tab contains the following options and buttons Excluded Peak Table Lists the excluded peaks for the assay analysis
20. 3 AZ Blank AU AU SL U S 5 4 AA Ladder 200 300 10 5 5 A5 Phixl74 Bisufl 200 300 10 5 6 AB Blank 20 300 10 5 AT Ladder 200 300 105 5 AH PRATA Boul 00 300 105 a Ca Ar STE CU ANT ing ri 4 b bi Sampieyames FA 4 Figure 9 Sample Name CSV File A Sample Name CSV file must use the following format Column A The well label A1 to P24 The wells labels can be entered in any order and do not need to cover the entire plate Column B The desired sample name for each well Column C A user comment to be added to the well properties Column D A list of Expected Peak sizes for the well This list is separated by semi colons P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 45 Column E The search window size for each Expected Peak in column D as a 10 10 of Expected Peak size If all Expected Peaks use the same window size enter a single value otherwise enter unique values as a semicolon separated list If fewer windows than EPs are entered the last window applies to all remaining EPs in the list Column F Any higher columns are ignored Applying Different Window Values to Expected Peaks of the Same Size in Different Wells Only one Expected Peak of a particular size can exist in the assay analysis settings If the same Expected Peak size with a different Expected Peak window is entered in the Sample Name Editor window only the first Expected Peak is created A
21. 411 1 1Lad gd 2J hgned Time sec Figure 29 Slope Values Although it is obvious that the region before 23 sec is baseline the slope ranges between 15 sec Setting the slope threshold much below 15 sec causes the analysis to detect these noise bumps as peaks These bumps will not actually be identified as peaks because they will not meet the Minimum Height and or Minimum Width thresholds but the analysis will run much slower as it carefully explores each bump Also the analysis will have difficulty finding baseline regions of qualifying width P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Understanding Peak Finding 80 Peak Splitting Inflection Threshold In situations where peaks overlap the signal does not return to the baseline and the slope may or may not change sign depending on the how close the peaks are to each other Two peaks with a valley in the middle is normally split into two peaks but if a peak appears as a shoulder on another peak splitting does not normally occur A shoulder is recognized in the analysis as an inflection point The slope reverses direction but does not change sign The slope trace shows peaks and valleys the valleys being the location of the inflection points The peak in Figure 30 is normally identified as a single peak although the orange slope trace shows three distinct inflection points Inflection points in signal valley in slope Figure 30 Sin
22. 5 800 600 400 200 Aligned Time sec Figure 5 Ladder Graph DNA P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 37 How the Software Analyzes DNA Data Continued 5 The ladder is analyzed see Ladder Analysis on page 208 and P N 128682 Rev 00 a standard curve of migration time versus DNA size is plotted from the DNA ladder by interpolation between the individual DNA fragment size migration points The standard curve derived from the data of the ladder well should resemble Figure 6 3 BN a a Paa yqjyjitit a a maa aaa THE HC Two markers are run with each of the samples bracketing the DNA sizing range The Lower Marker and Upper Marker are internal standards used to align the ladder data with data from the sample wells Figure 7 shows an example of assigned marker peaks LM and UM in a sample well Figure 7 Markers DNA LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 38 How the Software Analyzes DNA Data Continued 7 The standard curve and the markers are used to calculate DNA fragment sizes for each well from the migration times measured 8 To calculate the concentration of the individual DNA fragments in all sample wells the upper marker in conjunction with a calibration curve plotting assay specific concentration against base pair size is applied to the individual sample peaks in all sample we
23. 65 C 70 C Fluorescence Detection Detection Wavelength Bandpass 670 725 nm 20 30 40 50 60 80 100 and 120 Hz Light Source Red laser diode Barcode Reader Barcode Engine Microscan MS3CCD Supported Barcode Code 39 Code 93 Code 128 Types P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Maintenance and Service 184 Maintenance and Service Cleaning the O rings and chip interface prevents pressure leaks and current leaks The O rings should be cleaned daily with a more thorough cleaning of the O rings and chip interface monthly See Cleaning the Chip Cartridge The LabChip Dx Assay User Guides contain LabChip Kit Essential Practices and instructions for preparing reagents and plates Make sure to follow the instructions to ensure the optimum performance of your instrument The current version of the Assay User Guides can be accessed on the Caliper web site at http www caliperls com support reference library data sheets labchip systems data sheets htm The cleaning and maintenance procedures are reviewed during the standard customer training provided with the initial instrument installation If you have any questions concerning maintenance or require additional training please contact Caliper Technical Support see page 2 WARNING A Laser maintenance and service should be performed only by a qualified Caliper representative P N 128682 Rev 00 LabChip Dx User Manual Calip
24. 7 are not included P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 73 Raw Data ASCII text file that contains the signal data from the run as one file per well or multiple wells in the same file Note that data that is exported has been smoothed using the polynomial filter In addition to exporting time and value information you can choose to export Size information This information is determined based on aligned data and is used to correlate the peaks across different runs or from one row to another When Include Size Data is not checked and only time and values are exported the state of the analysis function peaks aligned or not aligned with the ladder data determines whether or not data that is exported is or is not aligned The same is true for the Zero Baseline function if enabled data that is exported is also zeroed to the baseline Below is an example of part of a raw data file exported from a DNA assay header not included and data truncated in this example DATA Time Size Value 0 000 158 365 0 80 0 017 158 269 0 86 0 033 158 173 0 53 0 050 158 077 0 63 0 067 157 981 0 45 0 083 157 885 0 28 0 100 157 788 0 24 0 117 157 692 0 05 0 133 157 596 0 38 0 150 157 500 0 66 0 167 157 404 1 06 0 183 157 308 1 45 0 200 157 212 1 70 Raw data can also be exported in a Chromatography Data Interchange Format formerly AIA format which is used by some graphical
25. AVERTISSEMENTS AA e Pour r duire le risque de choc lectrique ne pas retirer le couvercle Ce produit ne contient aucune pi ce pouvant tre reparee par l utilisateur Au besoin confier l appareil un r parateur qualifi e Ce produit ne doit tre utilis que comme d crit dans ce manuel Si cet appareil est utilis d une mani re autre que celle sp cifi e par le fabricant la protection fournie par l appareil peut tre entrav e If you have a question about a product that is not answered in this manual or online Help or if you need assistance with this product contact the Caliper Technical Support Center from 8 00 A M to 8 00 P M Eastern Time Monday through Friday Phone 508 435 9761 1 877 LabChip for LabChip products only Fax 508 435 0950 Email techsupport caliperLS com Internet www caliperLS com P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Preface 3 For support in Europe contact Caliper Life Sciences LTD Runcorn UK 44 1928 711448 or fax 44 1928 791228 For more information contact your local Caliper representative Before you call you should have the following information available for the technical representative e Product serial number e Software version found by choosing About from the main Help menu e If applicable the error number shown on the product s LCD display in the product software or in the log file Product Service and Customer Supp
26. Add Expected Peak aj Add New Expected Peak O O a Size BP Window Color _ Name Property Displayed in Well Table Apply to Wells EP52 Pad B1 Cancel Figure 49 Add New Expected Peak Window Size Specifies the expected size of the peak in BP The default size is the size of the peak that was selected Window Specifies the tolerance window as a percent of the expected size for the fragment to allow for small variations in expected peak size Color Displays the color to use to mark the peak in the Graph View or the Gel View Specifies a name to display in the Type description for the peak Property Specifies the content of a column added to the well table for each Displayedin expected peak Well Table Specifies the wells that the expected peak is applied to lt All gt specifies that the expected peak applies to all wells Clicking on the column opens the Select Wells window to choose the specific wells to apply the expected peak to P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 120 Add Plate Window Use the Add Plate window to add new plates to the system To open the Add Plate window click the Add Plate button on the Plate Information Window Les Ada Plate PAA m E460 or Ex Cana ti wel Figure 50 Add Plate Window The Add Plate window contains the following settings Plate Name Specifies the plate name that displays in the Start Ru
27. Apply button to display the new columns in the Well Table Duplicate properties in the table will be removed when the settings are applied to the plate LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 65 Copying Information The Edit menu and some of the right click pop up menus offer the following choices for copying information from the LabChip Dx software for use with other applications depending on the selection e Copy Gel e Copy Lane e Copy Graph e Copy Rows to Clipboard e Copy Column to Clipboard Choosing any of these commands places a copy of the selected item on the computer s clipboard You can then paste the item into a word processing graphics or other program Choosing Copy Gel copies all of the wells displayed in the Gel View with the labels as part of the graphic To copy a gel right click in the Gel View and choose Copy Gel Choosing Copy Lane copies the selected well in the Gel View with the labels as part of the graphic To copy a gel for a single well right click in the Gel View and choose Copy Lane Choosing Copy Graph copies the graph displayed in the Graph View The size of the image that is placed on the clipboard when copying a graph is the same size as the graph displayed in the software Copying rows from the Peak Table View or the Well Table View places ASCII information from the selected row or rows on the clipboard To copy a row or multiple rows select the desired rows in
28. Caliper Customer shall prepay shipping charges for equipment returned to Caliper and Caliper will pay for return shipment to Customer A Returned Material Authorization RMA must be obtained for any equipment being returned to Caliper Contact the Caliper Technical Support Center by telephone at 508 435 9761 or via the Internet at techsupport caliperls com or by fax at 508 435 0950 before returning any equipment to Caliper Customer must complete a Caliper Chemical Questionnaire prior to the issuance of an RMA All equipment returned to Caliper must first be decontaminated to meet Caliper and United States Department of Transportation procedures and standards for the safety of Caliper personnel F Hazardous Limitation Statement At no time will Caliper personnel perform service on unsafe equipment perform service in unsafe environments or decontaminate equipment to make it safe Prior to performing any service work Caliper personnel will evaluate the condition of the equipment and the environment in which the equipment is located If Caliper determines that the equipment and or the environment could be hazardous to Caliper personnel Caliper reserves the right to refuse to service the equipment Il MICROFLUIDIC CHIPS Caliper warrants that microfluidic chips each a Chip purchased from Caliper by Customer will be free from defects in material and workmanship for a period of sixty 60 days from the date of shipment the Warrant
29. Caliper Life Sciences Inc Preface 4 NOTE Changes or modifications to this equipment not expressly approved by the party responsible for compliance could void the user s authority to operate the equipment REMARQUE Tout changement ou modification apporte a cet instrument non expressement approuv par l entit responsable de la conformit peut annuler l autorisation d op rer l appareil accord e l utilisateur Table of Symbols Table 1 contains symbols that identify particularly important information and alert you to the presence of hazards These symbols may appear in this manual and or on the product it describes Table 1 Important Symbols Symbol Description Symbole Description DANGER An imminently hazardous situation which if not avoided will result in death or serious injury DANGER Situation presentant un danger imminent qui siil n est pas limin peut entra ner des blessures graves voire la mort WARNING Caution risk of danger Refer to the User s documentation AVERTISSEMENT Attention danger potentiel Se reporter a la documentation de l utilisateur NOTE cautionary statement an operating tip or maintenance suggestion may result in instrument damage if not followed REMARQUE nonc indiquant une pr caution prendre un conseil de fonctionnement ou une suggestion d entretien son non respect peut provoquer des dommages l instrument Hazardous voltage risk of shock inj
30. Electropherograms tab 63 102 Electrophoresis 17 206 ENG POI rer do NPA KALA 206 ENG IN 36 125 206 changing 54 Entire collection 114 Error Messages 193 194 195 196 197 Chip has Expired Warning 196 Chip Temperature Warning 197 Current Leakage Check Failed Warning 197 Device Disconnected Error 194 Error Message Area 92 Focus Failed Error 194 195 HV Check Failed Warning 196 Move Timeout Error 195 Plate Carrier Motion Blocked Error 194 Pressure Leak Detected Error 195 Event Viewer Window 137 Searching for Events in the Events PAP PEE RAE 191 Caliper Life Sciences Inc Viewing Current Events in the Events LENA AA PAA 192 Viewing Past Events in the Events FAG sagana the ce pe sears 192 Excluded fragments 131 Excluded Peaks Tab 131 Excluding a peak 36 53 Expected Fragments 46 Expected Fragments Tab 129 Expected Peaks Credne EP eo he RES 46 exporting 47 else No si era 47 IMDOMING saa son Od 47 viewing in Gel View 49 viewing in Peak Table View 50 viewing in Well Table View 49 Expected Peaks only 114 Export 43 72 129 131 134 138 Auto Export window 134 Automatically 25 Excluded Peaks button 131 Expect
31. Files If selected the selected gels are each exported to a separate image file Contrast Lane Specifies the gel lane to use to set the minimum and maximum RFU values for all lanes in the collection or selected wells before exporting the gels All exported gels are set to the minimum and maximum RFU values in the selected well Height Specifies the desired height in pixels of the gel graphic Image Format for Gel and Electropherogram Select the desired format for the exported image files P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 141 Installation Qualification Window Use the Installation Qualification Window to perform the IQ test The IQ test verifies proper installation of the LabChip Dx software and verifies no unauthorized changes have been made to the software To open the Installation Qualification Window select Validation gt Software IQ on the LabChip Dx Main Window So lmware Installation Quafication Software hasse Gualfcabon Appicabon hiomaton Directory Siructure r Fiss Summary Poges Previous Pang Figure 62 Installation Qualification Window The Installation Qualification Window contains the following information Application Verifies that the LabChip Dx Registry Entries exist If all expected Information registry entries are found displays Passed If any problems are found displays Failed Directory Verifies that all folders exist
32. GEP has been exported you can import the settings into another plate or workspace 3 With the plate open in a workspace in the Expected Fragments Tab click the Import button at the bottom of the window The Import Expected Fragments Table window opens 4 Navigate to the location of the file select the name of the file to import and then click the Open button The expected peak settings are imported into the tab 5 To apply the EFs to the active plate click the Apply button 6 To apply the EFs to all plates in the workspace click the Apply Global button Forcing Expected Peaks If there are multiple peaks in the tolerance range the largest peak is labeled as the expected peak even if it is not the exact size specified If a different nearby peak should have been selected as the expected peak you can manually specify which peak is labeled the expected peak 1 Inthe Graph View right click on the peak that should be labeled as the expected peak 2 Onthe shortcut menu select Force Expected Peak and then select the desired peak from the menu To clear a forced peak and revert to the default expected peak right click on the forced expected peak and select Clear Forced EP P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 48 Viewing the EFs in the Graph View Expected Fragments are identified in the electropherogram by open triangles over the peaks The triangles are the same color a
33. Gel view are also selected in the Well Table View and are displayed in the Overlay Electropherograms Tab LE POON RE ANN AN NG NG NG NG NG ANG NG ANG AG AN AA Cc mami cm Ga CA a eU 4 3 Figure 39 Gel View Moving the cursor over a band in the Gel view displays a tool tip that includes the same information about the peak as the Peak Table View Changing the columns displayed in the Peak Table will change the contents of the tool tip in the Gel view The upper and lower markers of all wells are aligned to the upper and lower markers of the first well in the gel view Figure 40 Gel Headers P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 106 Gel View Continued A colored column header indicates that the well is selected by a filter Click the Filter View to view the color of each filter A red exclamation point under the header indicates an analysis error occurred in the well A yellow exclamation point under the header indicates an analysis warning occurred in the well A gray header indicates a normal well To change the size of the gel header click on the border between the header and the well and drag the header to the desired size Expected Peaks are indicated on the gel by colored horizontal lines The graphs displayed in the Graph View are synchronized with the lanes selected in the Gel tab You can drag and drop the gel lanes to change the order of the wells for co
34. If all expected folders exist displays Structure Passed If any folders are not found displays Failed Files Verifies that all files that were installed by the LabChip Dx software still exist If all file exist displays Passed If any files are not found displays Failed Summary Displays Passed if all tests passed Displays Failed if any of the IQ tests failed Displays a progress bar while the IQ test is running View Details Displays the detailed results of the current IQ Only displays after Button the IQ has been completed Previous Result Displays the results of the last IQ that was completed Only button available before another IQ test is run Save As button Saves the results of the IQ in an xml file Start IQ button Begins running the IQ Close button Closes the Installation Qualification Window P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 142 Layout Options Window Use the Layout Options window to change the location of the views in a collection To open the Layout Options window select Collection gt Layout on the LabChip Dx Main Window Layout Options a Fersi io Ta Appa l Factory Delai Carl Figure 63 Layout Options Window Viewer Lists the viewers available to display in the Collection Pane Left If selected the view displays on the right side of the Collection pane The view displays at the top if any view is selecte
35. Plate Information window select Tools gt Plate Editor on the LabChip DX Main Window or click the View Plate Info button on the Verify a Plate Window in the Robot Teaching Wizard Pa Plus bhai A Cum Poses EL EPS marmi mu a EE a e TE EE IL Albin Mae Plate inna ed Spee K Mars T iar Hat Hasti eed Cnh Le Hashi E PCR Sad Sa Renan HS 11 24 15 14 PCR Shine Sin Mais 4 tal HE 11 24 15 Ta LU PTR Shortie Sep Bomar vent Plate Figure 65 Plate Information Window The Plate Information window contains the following tabs e Predefined Plates Displays Caliper defined plates These plates are read only and cannot be edited or deleted e Custom Plates Displays all user created plates Plates can be added deleted and modified The Plate Information window contains the following options and buttons Plate Information Displays the plate information for each plate defined for use in table the system See Add Plate Window on page 120 for a description of each column Delete Selected Deletes the selected plate from the system Only available Plate when the Custom Plates tab is selected Add Plate Opens the Add Plate Window to enter information for a new plate Only available when the Custom Plates tab is selected Modify Selected Opens the Add Plate Window to edit information for the selected Plate plate Only available when the Custom Plates tab is selected Verify
36. Specifications This section lists the technical specifications for the LabChip Dx instruments Technical specifications are subject to change without notice General Size HxWxD 18 75in SC x 19 25 in 49cm x 25 375in 64cm Plate Plate Capacity one 96 a Or a well Lone 96 well or 384 well microplate Kh o 3 77 mm minimum space a around instrument for proper air flow Environmental Operating Temperature 65 to 78 F 18 to 26 C Operating Humidity 20 to 0 relative humidity noncondensing Storage Temperature 50 to 104 F 10 to 40 C Transient Overvoltages Installation Category II Overvoltage Pollution Pollution Degree 2 Electrical Power Input 3 0A max at 100 127Vac 50 60HZz 10 1 5A max at 200 240Vac 50 60HZz 41096 Line Voltage 100 127 200 240V nominal 90 264V maximum operating range Total Heat Emission 800W No customer replaceable fuses in system Contact Caliper Technical Support see page 2 if blown fuses are suspected Through the power cord Computer Interface USB 2 0 P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc LabChip Dx Instrument Description 183 Assay Voltage Minimum Voltage Current 100V limited by current Maximum Voltage Current 3000V limited by current Chip Pressure Pressure Range 50 to 5 psig Chip Temperature Control Temperature Range Ambient 5 C to 40 C no active cooling Thermal limit switch
37. Viewer window tabs contain the following columns Column Title Description The data and time the event or error occurred The system component that generated the event or error Event Code The event error ID number used by Caliper to troubleshoot errors Text describing the event or error Click the OK button to close the Event Viewer window P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 138 Export Window Use the Export window to export data manually To open the Export window select File gt Export on the main Menu Bar Use the Auto Export Window to automatically export data at the end of each run Peak Tables and Well Tables are exported to CSV files which can be imported into a spreadsheet program such as Microsoft Excel Raw Data can be exported to either a CSV file or to a Chromatography Data Interchange Format file formerly AIA which is used by some graphical analysis software tools Electropherogram and Gel data are exported to the selected image format See Exporting Data Manually on page 75 for instructions E LabChip Dx Export ej M ap M C i Pga Flea apar Lie Scences Late mm El Fock Tae a anG DHA SK SE mada Peak Table o c Smelo Des y FE Wal Tabie a VAT a EN o Croce Flan Cato Lite Scenes Lab KI BA Fam Data DOC Der Otis Desa DAG EK 96 vou cay Mam Data Optora eet the dala n Yo mgt sih can be mported Fi Becivoherogram Ces Data Dem
38. Window Use the Auto Export window to export data automatically at the end of a run To open the Auto Export window click the Settings button next to Automatic Export in the Output Tab on the Start Run Window See Selecting the Auto Export Settings on page 25 for instructions The Peak Table Well Table and Raw Data files are automatically exported to the data file location in formats that are compatible with the Seegene Viewer The export path cannot be changed The Include Size Data and Export Single Table options for Raw Data are always selected and cannot be cleared LabChig Dx Export a Epot M ka M C Program Fes Cainer Lie Serena FE 1 bA Bedmphemgam Ayipada Cainer MAWADLEYL 20 Program les Caliper Life Scene LabChp A Ge K Daai 10027 Cac MAWADLEYLZ 20110 Cortal Lara Figure 58 Auto Export Window Electropherogram If selected the graph displayed in the Graph View is exported to the specified folder in the selected image format Click the Browse button to specify the desired path for the image file The file names are lt plate name gt _Gel_ lt well number gt The Entire Collection is always exported when automatically exporting electropherograms P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 135 Auto Export Window Continued Gel If selected the gels displayed in the Gel View are exported to the specified folder in the sel
39. Window The log file maintains a running record of all events that occur with the instrument while it is online with the software and records all events that occur in the software Each event specifies the date and time of the event source of the event the event code and a description of the event P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Glossary of Terms 209 Marker Drift Tolerance Isolating the markers in the sample is key to alignment and sizing The markers in the sample appear similar in size and migration time to the markers in the ladder Markers are discriminated from nearby peaks through a weighing scheme which attributes a numerical value to the migration time similarity and area similarity This approach is usually successful as long as the first peak is the marker but when there is a peak of similar size arriving just before the true marker the first marker is likely to be confused with the marker When the primary differentiator between the two peaks is the migration time the marker drift tolerance can be used to narrow the acceptable range for the migration time by increasing the importance of the similarity between the sample and ladder marker peak times The marker drift tolerance specifies the accepted range as a percentage of the ladder migration time The blue and yellow triangles shown in the figure below represent the weight assigned to a peaks migration time for a tolerance of 100 and 10
40. a well header plate name well name and sample name before the peaks in each well e Selecting the Per Page or Per Well option for the Column Header specifies whether the Peak Table column headers are printed only at the top of each page default or if the headers are also printed at the beginning of each new well table e Selecting both the Well Table and the Peak Table prints each well on a separate page with the Well Table row at the top of the page and the Peak Table for the well below it aai Fin Liimi as Dons EU far Con aga Ee Aga Sur Dami Casim na a ie DEEE ii GENE FRANS CRT Sims cesesamene COCCECEEEE LALALAAYA fable chen ta Heute FEE Figure 23 Printed Peak Table P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 72 Exporting Data Data from a Peak Table Well Table Gel or Graph can be exported automatically and or manually Options selected for automatic export do not affect manual export options and vice versa e To automatically export data during the run select the desired settings in the Start Run Window as described in Selecting the Auto Export Settings on page 25 e To manually export data see Exporting Data Manually on page 75 Peak Tables Well Tables and Raw Data are exported to CSV files which can be imported into a spreadsheet program such as Microsoft Excel Gel and Graph data is exported to the selected i
41. a specific microplate A graphical representation of the microplate displays Data files have a DXD extension Export Opens the Export Window to choose the type of data to export Exports a Peak Table Well Table Gel Single Graph or all open graphs in the current Collection to a file depending on the options selected Print Opens the Print Window to choose the data to print Save Workspace Saves the current workspace Save Workspace As Saves the current workspace with a new filename Exit Closes the LabChip Dx software Workspace Menu The Workspace menu contains the following commands Remove Plate Removes the selected plate data file from the workspace Save Plate Saves the plate data file dxd Changes to the analysis settings in the Assay Analysis Window are saved at the end of the plate data file Previous analysis settings are not overwritten enabling you to use the Restore Plate button on the Assay Analysis Window to go back to any previously saved settings Plate data files are automatically saved when the Workspace is saved P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 86 Collection Menu The Collection menu contains the following commands Undo Undoes changes to the collection view settings and filter settings Changes made in pop up windows such as analysis settings export settings etc are not affected by this Undo New Collection Open
42. analysis settings using the Restore Plate button in the Assay Analysis window Updated analysis settings are saved when the plate data file is saved To save the data file either e select Workspace gt Save Plate on the Menu Bar e right click on the plate name in the Plate View or Plate List and select Save Plate or e select File gt Save Workspace or File gt Save Workspace As on the Menu Bar See Saving Workspace Files for more information NOTE Changing the analysis settings and saving the plate data file does not change the raw data from the run Only the display of the data is changed If you change the analysis settings without saving the new settings and then try to close the workspace exit the software or acquire new data you are prompted to save the changes Selecting Yes opens the Save Workspace As Window P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Operation 31 Saving Workspace Files When viewing plate data in the LabChip Dx main window you view the selected data files in a Workspace When a new run starts a new blank workspace opens which contains the data file for the plate in the run After the run is complete saving the workspace saves the data file with the current analysis settings See Saving Data Files for more information on the contents of the data files The Data Files are not saved in the Workspace file The workspace file contains links to the revision of
43. e Home Timeout e Move Timeout e Pressure Leak Detected e Focus Failed Chip Warnings e Chip has Expired LabChip Dx Warnings e HV Check Failed e Current Leakage Check Failed e Chip Temperature Warning P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 194 Device lt Name gt is Disconnected This error message indicates that there is no communication between the software and the specified device Possible Causes Recommended Actions 1 Cable between computer Verify that the USB communication cable is secure and instrument unplugged pugg Verify the power cord is plugged in 2 Instrument power loss 3 Computer went into hibernation Press the Power button on the LabChip Dx instrument See page 175 Restart the LabChip Dx software If the problem is not resolved contact Caliper Technical Support see page 2 Plate Carrier Motion Blocked Error Message Plate carrier motion blocked Make sure tray movement is not obstructed Possible Causes Recommended Actions 1 Something is blocking Remove the blockage the door from opening Restart the instrument 2 Something may have fallen inside and is blocking f the problem is not resolved contact Caliper Technical the robot motion Support see page 2 Home Timeout Error Message Home Timeout Possible Causes Recommended Actions 1 Something is obstructing Check for a
44. entered the same value applies to all expected peaks If multiple vales are entered separated by semi colons each expected peak will use the corresponding Window value If more expected peaks are entered than Window values the last Window applies to all remaining expected peaks in the list 5 Click the Export button navigate to the desired location for the file type the desired name for the file and click the Save button P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 44 To import the sample names into a data file 1 Open the data file in an open workspace in the LabChip Dx Main Window 2 Select Tools gt Sample Name Editor on the LabChip Dx Main Window The Sample Name Editor Window opens 3 Click the Import button navigate to the file location select the name of the csv file that contains the sample names and click the Open button 4 Click the Apply button in the Sample Name Editor window to apply the sample names to the active plate Format of Sample Name File CSV Format The Sample Names created in the Sample Name Editor Window can be exported to a CSV file A CSV file can also be created in Microsoft Excel or generated automatically with a LIMS to import the Sample Names into the data file Figure 9 shows a Sample Names file open in Microsoft Excel 5ampheHames csv O XX B C D E F Ei Ladder 200 300 40 10 5 5 2 2 Phata Buki 200 AN 105
45. for each version change To open a different version of the data file click the Restore Plate button in the Assay Analysis Window The Data File Version Window contains the following options List of Displays the list of all saved data file versions Versions Displays the details of the changes Print All Versions If selected version information and Options details for all data versions is printed Selected Version If selected version information and details for only the selected version is printed Print Opens the Print Preview window to preview the Preview printed version information Print Opens the Print window to print the data file version information Closes the Data File Version window P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 137 Event Viewer Window Use the Event Viewer window to view events and errors that occur during the current run or during a previous run To open the Event Viewer window select View gt Event Viewer on the LabChip Dx Main Window Hah otage mad Cotes a Press ray Ers Figure 60 Event Viewer Window The Event Viewer window contains the following tabs Current Events tab Displays the events that occurred during the current session Past Events tab Displays all events from previous sessions Search Results tab Enables you to search for specified text in past events current events or all events The Event
46. ladder at the beginning of the row e Align Well Groups to Specified Ladders If selected each row is aligned with the ladder selected in the table The Markers panel displays which markers are being used for alignment This setting is determined by the assay type and cannot be modified To turn off alignment select Turn Off Analysis on the Analysis menu P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 124 Analysis Tab Use the Analysis tab on the Assay Analysis Window to view the Upper and or Lower marker peak designation this setting cannot be changed or to view or change the Ladder Sizes Ladder Concentration Standard Curve Data Range and Marker Concentration Peak nd pected Fragmerts Excluded Fragments Advanced a Ae Cnceiato pr RERO Gave knaen FL Conc ng ul Size BP 4 Pori to Point Ladder 1 00 ng l 1 CPobromial Ft Upper Data Panga WelEnd sec Figure 53 Assay Analysis Window Analysis Tab Ladder Sizes A table showing the sizes in base pairs of the ladder peaks Click in the Size column and type the desired size to change the ladder size Ladder Concentration The concentration in ng uL for the ladder peaks Standard Curve Determines whether the fit for the standard curve used to calibrate migration time to size will be done on a point to point or Polynomial fit of the ladder DNA assays are set to point to point curv
47. lala Overall Progress ra Fregreii BE Ik Ji Ee Th Hg ig i u tO L r Use the System Diagnostics window to run the diagnostics tests on the LabChip Dx instrument All tests should be run periodically to verify proper operation of the instrument To verify proper operation of a particular function you can select specific tests to run To open the System Diagnostics window select Validation gt Diagnostics Lends Repo Part Tip Figure 86 System Diagnostics Window The left side of the window displays the tests to run on the instrument Expand each section to view all of the tests in each section Tests selected with a green check mark will run To skip a test click on the check box to clear the selection Click on a section check box to select or clear all of the tests in the section P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 173 System Diagnostics Window Continued The right side of the window displays the results of the tests The Icon color indicates the status of each test e Blue The test is in progress e Yellow The test was skipped e Green The test passed e Red The test failed or was aborted Run Tests button Runs the selected tests marked with a green check mark After all tests are complete the Test Report Generation section at the bottom of the right side of the window displays the date and time when
48. manner described in this manual If the equipment is used in a manner not specified by the manufacturer the protection provided by the equipment may be impaired P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Instrument Safety 8 Chemical Safety WARNING NA Some chemicals used with the LabChip Dx are potentially hazardous and can cause illness e Read and understand the material safety data sheet MSDS provided by the chemical manufacturer before you store handle or work with any chemical or hazardous material e Minimize contact with and inhalation of chemicals and chemical wastes Wear appropriate personal protective equipment when handling chemicals e g safety glasses gloves or clothing For additional safety guidelines consult the MSDS e Do not leave chemical containers open Use only with adequate ventilation including a fume hood if necessary e Check regularly for chemical leaks or spills If a leak or spill occurs follow the manufacturer s cleanup procedures as recommended on the MSDS e Dispose of waste in accordance with good laboratory practices and local state provincial or national environmental and health regulations e After emptying waste containers seal them appropriately e Comply with all local state provincial or national laws and regulations related to chemical storage handling and disposal P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Scienc
49. minus the parallelogram of the local baseline down to absolute zero Data points are 0 05 seconds apart Aligned Area If the sample has been aligned the area of the aligned peaks is reported Size BP The size of the peak based on the ladder sizes specified in the assay Conc ng uL The concentration calculated relative to the ladder and marker peak concentrations The ladder concentration is displayed in the Analysis Tab of the Assay Analysis Window Expected Fragment BP Displays the size of the Expected Fragments Type Displays the type of peak for markers or expected peaks Comment Displays any comments associated with the well either from the Sample Name File selected in the Advanced Tab on the Start Run Window or from the Sample Name Editor Window P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 113 Peak Table View Continued Signal Noise The statistical standard deviation of 1 second of data just before the Peak Find Start Time Baseline The center average height of the peak baseline measured in RFUs FWHM The width of the peak Full Width at Half Maximum measured in seconds Molarity nmol l Displays the molarity of the peak Peak Table View Shortcut Menus Right click on a peak in the peak table to display a shortcut menu containing the following commands e Exclude Peak e Include Peak for excluded peaks or peaks of type e Force Lower Mar
50. on page 57 To reanalyze a data file 1 Open the workspace that contains the plate data see page 39 2 Change the analysis parameters see list above as needed 3 When you click the Apply Apply Global or OK buttons in the Assay Analysis Window the data is automatically re analyzed and the updated information is displayed 4 To view previous analysis settings click the Restore Plate button at the bottom of the Assay Analysis window and select the version to view P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 67 Reverting to a Specific Data File Revision Each time a data file is changed a new version of the data file is created and saved The LabChip Dx software enables you to revert to a previous version of a data file To revert to a previous data file version 1 On the LabChip Dx Main Window select Analysis gt Analysis Settings on the main menu The Assay Analysis Window opens 2 Click the Restore Plate button at the bottom of the window The Restore Plate Settings to Version window opens 3 Select the data file version that you want to restore to 4 Click the OK button The Assay Analysis Window displays the settings for the selected data file version 5 Click the OK button to display the data file with the selected settings P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 68 Printing Workspace Information Choosing File gt
51. or for thirty 30 days from time of replacement whichever is longer Such replacement parts may at Caliper s option be new or remanufactured All parts removed from warranted equipment become the property of Caliper Caliper reserves the right to satisfy its warranty obligations in full by refunding the purchase price of any non conforming product minus any service validation or travel charges B Customer Responsibilities In order for a product to be covered under this Warranty Customer must comply with the following terms e The equipment must be used under normal installation and application conditions as described in the product s User Manual e The equipment must be maintained as described in the User Manual e Only water or DMSO at a maximum concentration of 65 may be used as a system fluid in the Sciclone inL10 Any other system fluid must be approved by Caliper before use in the inL10 e When Caliper provides telephone fax or email support Customer is responsible for completing any necessary documentation of the service e If Customer maintains a change control validation logbook as a permanent record then Customer is responsible for entering all service documentation into such logbook e Customer must perform the appropriate level of revalidation required as a result of the maintenance or service provided C Exclusions e Failure to comply with any of the Customer Responsibilities listed above will void this Warranty
52. photodiode detectors for fluorescence detection and autofocus Fluorescence data can be acquired and stored at rates from 20 to 120 Hz Optical Train The fluorescence excitation fluorescence detection and autofocus optical trains contain several lenses and high efficiency interference filters The optical trains are factory aligned and do not require adjustment Chip Pressure System The pressure pump applies pressure or vacuum to the wells on the chip to move liquid through the chip The Pressure Pump is located inside the LabChip Dx instrument O Rings on the Chip Cartridge seal the chip wells and maintain the pressure Barcode Reader The LabChip Dx instrument is equipped with an internal Barcode Reader The Barcode Reader reads the customer applied barcode on the short portrait edge of the microplate Proper selection and placement of barcode labels is critical for successful reading See Placing the Barcode on the Plate on page 34 for specifications The barcode reader is internal to the system and cannot be viewed from the outside P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc LabChip Dx Instrument Description 178 DNA Chips The figures below show the format and parts of the microfluidic chips used in the LabChip Dx instruments to perform DNA sizing and quantitation Optical Window Waste Well Electrode E Wells Electrode Wells Marker Well at Sipper Unus
53. run specific assays on the LabChip Dx The Assay Kits include the reagents and consumables required to run the specific assay Assay User Guides Assay User Guides provide information about the assay Instructions for preparing the chip the plate the ladder vial and the buffer vial are included in the LabChip Dx Assay User Guide for the specific assay that you are running Detailed information about the assays including Specifications Safety Warnings Preparation Procedures Expected Results Troubleshooting LabChip Kit Essential Practices and Reordering Information is also located in the LabChip Dx Assay User Guide for the specific assay that you are running Assay Quick Guides Assay Quick Guides are included with each Assay Kit and include instructions for preparing the chip to run an assay P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Introduction 17 Principles of Operation The LabChip Dx assays are based on traditional gel electrophoresis principles that have been transferred to a chip format The chip format dramatically reduces separation time and provides automated sizing and quantitation information in a digital format The chip contains an interconnected set of microchannels that join the separation channel and buffer wells One of the microchannels is connected to a short capillary that extends from the bottom of the chip at a 90 degree angle The capillary sips sample from the wells of a m
54. see page 2 Optics TestChipA Tests Optics motion Optics Motor failure axes X Y and Z Contact Caliper Technical Support see page 2 Focus Laser Detector Incorrect initial starting position due to crash or contact of optics block with an object Laser or detector failed Laser power too low Contact Caliper Technical Support see page 2 Laser On Off Signal level difference between On and Off states too low may indicate laser burned out or detector failure Contact Caliper Technical Support see page 2 Chip TestChipA Set temp to 30 C then Initial chip temperature not Temperature raise to 35 C achieved in time Temperature ramp time not within spec may indicate heater disconnected or burned out Contact Caliper Technical Support see page 2 Current TestChipA For each pin apply Source current too high or Leakage 3000V to pin and sum of sink currents too 100 to all others Sum high Clean or replace the up currents O rings see page 185 and clean the chip cartridge P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 189 Chip Voltage TestChipB For each pin apply Voltage out of calibration Calibration 1000V while setting Pin not connected to power other nodes to 0 0 UA supply Ensure each node reaches applied voltage Current TestChipB For each pin source Current out of calibration Calibration 10 uA into sink at Pin no
55. selected and Well Table is not selected e If Per Page is selected the column header is printed only at the top of each page e If Per Well is selected the column header is printed at the top of each page and at the start of each new well P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 148 Print Validation Reports Window Use the Print Validation Reports Window to print the results after performing Installation Qualification IQ or Operational Qualification OQ OQ is performed in the System Diagnostics Window To open the Print Validation Reports Window select Validation gt Reports on the LabChip Dx Main Window Print Validation Re ports 6 Report Options _ __ _ Diagnostics Report f Software 1Q Report Faded Tesis Orly Report Period From Tuesday January 11 2011 Lil To Thursday February 10 2011 Mg Print Close Figure 67 Print Validation Reports Window The Print Validation Reports Window contains Option Button Diagnostics Report lf selected the results of Hardware OQ tests are printed Software IQ Report If selected the results of Software IQ tests are printed Failed Tests Only If selected only tests that have failed are printed If not selected both passed and failed tests are printed Report Period Specifies the dates when the tests were run Tests performed between the From and To dates inclusive are printed Print
56. that contains a peak that matches any of the filters selected in the Available Filters list e AND Peak Selects any well that contains a single peak that matches all of the filters selected in the Available Filters list e AND Well Selects any well that contains peaks that match all of the filters selected in the Available Filters list Different peaks in the same well can match different filters as long as all filter conditions are met in the same well P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 116 Filter View Continued The Quadrant Select panel specifies which quadrants of all plates in the collection will have the specified filters applied to them Selecting a quadrant check box applies the specified filters to that quadrant Clearing a quadrant check box excludes that quadrant from the specified filters Example Expected Peaks Filter In the example below the sizes 100 10 300 10 and 500 10 are selected with each expected peak size identified by a different color This filter will select any wells that contain all three expected peaks 100 300 AND 500 Note that the filter is selected checked under Available Filters indicating that the filter is being applied to the data AT f niai To select wells that contain any of the three peaks create a separate filter for each peak and select OR as shown below NGA Expect
57. the Well drop down list The well list includes all the wells on the current plate that are selected The Plate and Well Name fields are read only and cannot be changed from the Peak Find Tab P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 126 Peak Find Tab Continued This window contains the following options Table 1 Plate Peak Find Settings Plate Settings Minimum Specifies the height limit below which a peak is not detected For Peak Height each peak the difference between the peak start time and the peak apex must be greater than the Min Peak Height value Minimum Specifies the limit in seconds for the peak width Peaks narrower in Peak Width time than this value are not detected Slope Represents the amount of change in absorbance units over time Threshold required to indicate that a peak has occurred This setting is used to detect the start and end of a peak Increasing this setting may cause broad rolling bumps to be ignored or merge multiple bumps into a single peak Decreasing this setting will broaden the peaks width and potentially pick up broad bumps as peaks See Understanding Peak Finding on page 76 for more information Inflection Represents the value that the slope minimum must be below to Threshold trigger a splitting of the peak As the threshold is increased more peak splitting occurs See Understanding Peak Finding on page 76 for more i
58. the data file that was last open in the collection If a Workspace file is moved to another folder or computer the data files must be moved with the Workspace file The data files must be in the same location relative to the Workspace file as they were otherwise you are prompted to find the missing data files when you open the Workspace file It is a good practice to save the workspace files in the same location as the data files that are included in the workspace Saving a Workspace file automatically saves any changes to the data files that are open in the workspace and the settings for each collection in the workspace P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Operation 32 Adding a New Plate When using a plate other than the plates specified in the Start Run Window you must create a new plate in the Plate Information Window Use caution adding new plates Entering wrong values in the Add Plate Window can result in damaged chips and broken sippers It is best to use the plate specifications provided by the plate manufacturer If the specifications are not available measure the plate with a caliper Many plates have a large variation in the Z axis location of the well bottom Make sure the Sip Height has enough margin to accommodate this variation e Minimum Sip Height is 2 5mm e Maximum Sip Height depends on the sample volume e Sip Height of 4mm is probably safe To add a new plate 1 Sele
59. the folder where you want to save the exported copies of the data files Click the OK button to choose the selected folder The path displays in the Copy To text box on the Output Tab To continue setting the assay options in the Start Run Window see Running an Assay on page 22 LabChip Dx User Manual Caliper Life Sciences Inc Operation 27 Monitoring the Run The following occurs after a run is started in the LabChip Dx software 1 7 The priming and warming steps are performed e The priming step fills the channels of the chip with reagent Only performed if the chip holder has been opened since the last run e The warming step allows the heater plate located in the chip holder to regulate chip temperature to 30 C e Data collection begins after the warming and priming steps are completed After the run begins the Start button on the LabChip Dx main window changes to Stop The Active Data Tab displays the electropherogram of the well currently being read Data is saved to a file with the name shown above the plate diagram after each well is completed To view the results for individual wells as data is acquired or after the run is finished click a well in the Plate View or Plate List a sample name in the Well Table View or a lane in the Gel View Data from the selected well displays in the Overlay Electropherograms Tab and the Peak Table View For more information on data analysis see Data Analy
60. the table right click on one of the selected rows and select Copy Rows to Clipboard Copying columns from the Well Table View is only available for certain columns in the table To copy a column select a single cell in the column right click on the cell and select Copy Column to Clipboard P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 66 Reanalyzing a Data File Occasionally you may need to open and view or reanalyze a data file that was run and saved previously The raw data values are saved in the plate data file along with the original analysis settings that were chosen for the run and any changed analysis settings This enables you to reanalyze the data with new settings or to view previously saved settings The following analysis parameters can be changed e Plate peak find settings and Well peak find settings see Changing the Peak Find Parameters on page 52 e Sample names and comments see Using Sample Name Files on page 43 e Adda Peak see Adding a Peak on page 53 e Exclude peaks from analysis see Excluding a Peak on page 53 e Reassign upper lower markers see Upper and Lower Marker Peaks for DNA Assays on page 55 e Alignment or no alignment with ladder peaks see Aligning or Unaligning the Marker Peaks on page 55 e Assay you can save the changed settings under a new assay name if desired see Saving and Exporting Assays
61. time setting You can change the Baseline Start time on the Analysis Tab After the overall baseline is established a local baseline is calculated for each peak to compensate for baseline drift To select the desired baseline algorithm for all of the samples in the plate choose the desired option on the Peak Find Tab No Baseline Zero Baseline or Baseline Subtraction See Zero Baseline on page 218 for more information about the Zero Baseline option Baseline Subtraction can use either Spline fit or Rolling Ball fit for the baseline curve algorithm e Spline Creates a smooth line fit to the baseline data points and subtracts this smooth fit from the data The Threshold determines how much the baseline fit follows changes in the data Lowering the Threshold below the default value of 20 allows the baseline fit to ignore regions that are slow changes of real signal peaks and not baseline drift This spline curve is not constrained to remain below the signal and may produce negative signal values when subtracted from the signal e Rolling Ball Generates a smooth baseline curve by mathematically rolling a ball under the sample signal keeping it in contact with the closest signal point without crossing into the signal Time Diameter and Signal Diameter determine the smoothness of the curve in the Time and Signal axes and determine how closely the curve follows the signal The ball is P N 128682 Rev 00 LabChip Dx User Manual Cali
62. ussi les tests de s curit pour la mise la terre le courant transitoire de ligne d alimentation et la perte de courant Input Ol Entr e P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Preface 6 Table 1 Important Symbols Continued Symbol Description Symbole Description Output io Sortie Equipment Caution risk of danger labels are color Stop coded Mandatory action Les tiquettes Safe condition or information de l appareil Attention danger potentiel sont cod es Arr ter couleur Intervention obligatoire Condition s re ou informations de s curit Helpful hints additional information Conseils utiles informations supplementaires P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Instrument Safety 7 Instrument Safety The following safety information about the LabChip Dx is included in this section Read and review all safety information before operating the LabChip Dx e Required Training e Chemical Safety on page 8 e Laser Safety on page 9 e Electrical Safety on page 10 e Mechanical Safety on page 11 Required Training Ensure that all personnel involved with the operation of the instrument have e Received instruction in general safety practices for laboratories e Received instruction in specific safety practices for the instrument e Read and understood all related MSDSs WARNING Use this product only in the
63. wells are identified by dashed outlines around the selected gel lanes in the Gel view light blue wells in the Plate view and dark gray rows in the Well Table view and Peak Table view To remove a specific sample from the graph Ctrl click on the sample that you want to remove in the Plate View or Plate List Gel View Well Table View or Peak Table View To display only one sample in the Overlay Electropherograms tab click on one sample in the Plate View or Plate List Gel View Well Table View or Peak Table View P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 63 Viewing Graphs in the Electropherograms Tab If the Electropherograms Tab is not open select Collection gt Layout on the LabChip Dx Main Window select the location where you want to display the Electropherograms tab and click the Apply button The Electropherograms tab opens i Overlay Bectropherogram LIM 37278 18 EP194234 271110 EP503 i LM Le 18 EP184 2347271110 Figure 18 Electropherograms Tab with Multiple Graphs Data from multiple wells can be displayed in the same tab for visual comparison separate graph for each well in the collection is displayed in the Electropherograms tab The data file name and well name display at the top of each graph Use the scroll bar on the right side of the tab to scroll through the wells in the collection Zooming in or out on one graph zooms all of the gr
64. with the terms of this License Agreement In the event of a breach the Licensor reserves the right to seek equitable relief License Fees The license fees paid by you in connection with the purchase of the associated product s are paid in consideration of the licenses granted under this License Agreement Term This License Agreement is effective upon your opening of this package and shall continue until terminated You may terminate this License Agreement at any time by returning the Program and all copies thereof and extracts therefrom to Licensor Licensor may terminate this License Agreement upon the breach by you of any term hereof Upon such termination by Licensor you agree to return to Licensor the Program and all copies and portions thereof Limited Warranty Licensor warrants for your benefit alone for a period of 90 days from the date of the commencement of this License Agreement referred to as the Warranty Period that the Software Media in which the Software is contained are free from defects in material and workmanship If during the Warranty Period a defect in the Software Media arises you may return the Program to Licensor for either replacement or if so elected by Licensor refund of amounts paid by you under this License Agreement You agree that the foregoing constitutes your sole and exclusive remedy for breach by Licensor of any warranties made under this License Agreement EXCEPT FOR THE WARRANTIES SET FORTH ABO
65. 1 Labels each peak in the graph with the peak property selected from the drop down list Default is Type The Annotations available depend on the columns selected in the Peak Table View Text Orientation Specifies the orientation of the text for the annotation horizontal A button vertical up or vertical down P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 104 Set Font button Opens the Font window to choose the font style and size of the text for all annotations Annotation 2 Labels each peak in the graph with a peak property selected from the drop down list Default is None Peak Annotation If selected the types of the annotations display in the upper left Legend corner of the graph Well Annotation Displays the selected well property outside the graph Well Annotation The location of the well annotation Click the button to change to Location Button location upper right upper left lower left or lower right arrow Show Data Points If selected displays a dot on the graph at the location of each data point Show Peak If selected displays the baseline for each peak on the graph Baselines Only Annotate If selected only the peaks that are labeled as Expected Expected Peaks Fragments display the annotations If not selected all peaks display the annotations Graph Selected If selected only the wells selected in the Gel View or Well Table Gels Onl
66. 118 color is red Any well that meets both filter criteria are orange red yellow az 4 F A A D E E G be 24 Figure 46 Filter Plate Diagram P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 118 Filter View Continued SEE 2 ka ee ee ee Figure 47 Gel with Filters Applied The gel in Figure 47 shows the expected peaks marked with colored lines on the Gel view The well header is yellow if the well meets the filter criteria for the first filter red if it meets the filter criteria for the second filter and orange yellow red if it meets the filter criteria for both the first and second filters About LabChip Dx Window The About LabChip Dx window displays the software and firmware versions Select About LabChip Dx on the Help Menu to open this window P N 128682 Rev 00 About LabChip Ox a Lebi hip Dir Sofware Version 10 806 0 Pamana Veron 10177 00 Copmont 7009 2010 Cape lle boscar inc Al apii reserved No pan of tha katwan Say be moded in any fom or incorponsied in any system wilhout the written pemesson of the copyright owner Ex Figure 48 About LabChip Dx Window LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 119 Add New Expected Peak Window Use the Add New Expected Peak Window to add an expected peak to specific wells To open this window right click near a peak in the Graph View and select
67. 38 Installation Qualification Window 7 7 7 727 aaa 141 Layout Options WINDOW 7NA Naa GG 142 New Collection WINDOW aLam chica aed tacvbeoivieiacdeee ut ei nites 144 Plate Intormation WINGOW 100 sanan naaa NING GG Ga LA GAGA a BAG aaa 145 PANANONG ma Ata ma a a net a D met CA 146 Print Validation Reports Window ccccccceceeeceeececeececeeeeseeeeseseeseseesesesenses 148 Rename Collection Window iii 149 FOOL WUC NG VV IZ Ii aaa Sd dei 150 Welcome VV IMO OW nakadaan cues NAA Aa eee dede ani en Le 151 Teach RODOL WINGO W nce doesn Aa dani ous Re phan kata ha Seiad Oats 152 Teach the X Y and Z Reference Positions Window eee eeeeees 153 Verniy a Plate WING OW maa aaa AA AN isan NA Na 154 Verily POSIONS WINDOW a RA eau Rede NAA p LA AA ienaduaates 155 Finished WINQOW E SR a a de de PR Ad Ain ain 156 Verify All Target Positions Window UV 157 Verify All Target Positions Correct Window 158 RUN RICE GION VV ING OW ER sn ae ea eee le RL 159 RUNINO VIA COW tt tete NG aan e ad da et a te a tan dc aies 160 sample Name Editon WINDOW naaa ds es tes cc distant 161 Save Workspace As WINDOW Laan kas naaa LAAL Dna 163 Selecta Datla File WINDOW Gn a TANGA UA AA ANA 164 Slan RUN VV INGO WW is boats vee ah cst r anda AA a le at 165 AA 166 OUTDO UU TAD ane na ne nee eee ee te 168 AVANCE SE et 170 System Diagnostics WINDOW sniper UA ANAN 172 LabChip Dx Instrument Description aasa awan
68. 8 Viewing the EFs in the Gel View 49 Viewing the EFs in the Well Table aa 49 Viewing the EFs in the Peak Table VU 50 MOGITYING Analysis Parameters aaa ANA AA AA 51 P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Table of Contents 13 Changing the Peak Find Parameters VV 52 Adding a PEAR amba BAET daa DN etre ANA AG BNG TAN AA 53 Excluding a OAK aaa ANA AN nana a ena 53 Merging TWO Peaks aiai ANAN 54 Changing the Time Window for Analysis 54 Aligning or Unaligning the Marker Peaks ccccceceeeeeeeeeeeeeeeeeeeeeeeeeeeeees 55 Saving And EXOOnMinG ASSAYS Le nan a 57 Changing the View of the Results 58 VIEWING GEIS errestan TE 58 VIEWING Zero Baselines 222 59 Adut Rane VWWIGUAS serseri andsa EE NGA 60 SNOW Or TIDE NEWS ENE Aa a 60 ZOOM nand ZOOM O UV av Less a a a a 60 Viewing Graphs in the Overlay Electropherograms Tab 62 Viewing Graphs in the Electropherograms Tab ccccceceeeeeceeeeeeeeeeeeeeees 63 Viewing Multiple Properties in the Well Table View 64 CGopying INTO MANO aka AE kaaa Sn M dti a eai 65 heanalyzing a Data PIS in Rd node 66 Reverting to a Specific Data File Revision 67 Printing Workspace Information 68 Expono DATES Se Re ele ile tue 72 Exporting Data IMANUAINY AA AA 75 Understanding Peak Finding ss KEN AUKN NEN N KEANNA KNA NAAN N ANAKAN ANNA NA 76 Data SMOOMING SES RS YN
69. A ta or NMN 2 i JM H k K J AA oo JI Ek H H K NA H H A W X E PM HJQQO QD CAHAAAKXKAKAHAKAKK MJ 100000000008 s MOK NAK e668 66 6 le ey re AG ni H H WD a JM M H L LR oul i Ti Sapang ids ei frenis Tium mase ii ke Cancel Figure 82 Start Run Window The Start Run window opens when you click the Start button above the plate icon To begin the run select the desired settings on each tab and then click the Start button The Start Run Window contains the following tabs e Run Tab e Output Tab e Advanced Tab The following buttons are located at the bottom of the Start Run window ee ka Starts the run using the options specified in the tabs on the Start Run window Use the Run File Editor Window to create a run file Cancel Closes the Start Run window without saving any changes and without Starting the run Imports the settings from a run file xml into the Start Run window P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 166 Run Tab Use the Run tab in the Start Run Window to specify the assay type operator name plate type barcode option sample wells and sipping order for the run pea Operator Pinta Name SPCR Sted So Made CXA AAO DOC a WO WOOD WO ie ce an OOH K JO d A KA SOC JO ID UDODODG sa wf H OOC OK 00000 muk f Tangang nie A Paa oi Win T Gi ke Cancel Figure 83 Start Ru
70. Analysis Window to change the analysis settings P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 99 Graph View Continued Right Click Menu near a peak Right click above or below a peak in the graph to display a shortcut menu containing the following commands Exclude Peak Excludes the peak from the analysis The Peak Type label displays X Include Peak Includes an excluded peak in the analysis Only available when the selected peak is already excluded or is type System Peak or Including the peak will compute the peak properties populate the peak table and include the peak in the area total used for the Purity calculation Force Lower Marker Defines the selected peak as the Lower Marker The Peak Type label displays LM Clear Forced Lower Marker Allows the analysis to determine the lower marker The Peak Type label for the calculated lower marker displays LM Only available when the selected peak is a Forced Lower Marker Force Upper Marker Defines the selected peak as the Upper Marker The Peak Type label displays UM Clear Forced Upper Marker Allows the analysis to determine the upper marker The Peak Type label for the calculated upper marker displays UM Only available when the selected peak is a Forced Upper Marker Add Expected Peak Opens the Add New Expected Peak Window to add a new Expected Peak to the specified wells Force Expected P
71. Assay Analysis window are used to save apply or cancel changes Apply Apply setting changes and re analyze the plate but keep the Assay Analysis window open Apply Applies the selected analysis settings to all plates in the open Global workspace Export As Opens the Export Assay Settings from Plate to Assay file window to specify a name and location for a new assay file asy Clicking Save creates a new assay file with the settings in the Assay Analysis Window Restore Restores the analysis settings for the plate to the settings selected in Plate the Restore Plate Settings window Print Opens the Print Preview window to view the analysis settings before Preview printing Opens the Print window to print the analysis settings Cancel Restores the settings that were selected when the window was opened or when the last Apply was performed No re analysis is performed OK Apply changes in the Assay Analysis window and re analyze the plate with these new settings because the settings were used for the last analysis performed P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 122 Assay Information Tab The Assay Information tab on the Assay Analysis Window displays the header information for the current plate The information displayed was specified when the assay was run and cannot be changed D Akgnment Analyses Peak Find Expected Frag Pagay Class Kama Tila Comm
72. Button power is still supplied to the power supply fans when the power switch is in the Standby position Turning the instrument on reloads the system firmware and homes the robot P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc LabChip Dx Instrument Description 176 Rear Connectors The rear connectors are used to connect the LabChip Dx instrument to the computer and power supply USE Cable Power Cable Figure 89 Rear Connectors The following connectors are located on the back of the instrument Plug the power cord into this connector and a power outlet Cable WARNING AA Appliance inlet is disconnecting device Place device or equipment in a manner so that disconnecting device is accessible at all times USB Cable Connects the LabChip Dx instrument to the computer P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc LabChip Dx Instrument Description 177 Optics The LabChip Dx optics provide fluorescence detection red excitation and red emission for DNA chips and assays Red Laser The LabChip Dx instrument includes a high intensity long life red diode laser to excite fluorescence on microfluidic chips It is expected to have a lifetime of tens of thousands of operating hours Focusing and Alignment The LabChip Dx instrument uses back reflected red diode laser light for automatic chip focusing Photodiode Detectors The LabChip Dx uses two silicon
73. Continued Sample Saver If selected the selected wells are run the specified number of times Each well is samples once then the entire run repeats The data from all wells is combined in the same data file Sample Names File Specifies the file that will supply the names of the samples in the assay Click the Browse button next to Sample Names File select the name of the CSV file that contains the sample names and click the Open button The path and name of the file displays in the text box Use the Sample Name Editor Window to create Sample Name files Expected Peaks File Specifies the file that will supply the Expected Peaks for the assay Click the Browse button next to Expected Peaks File select the name of the GEP file that contains the expected peaks and click the Open button The path and name of the file displays in the text box See Using Expected Fragments on page 46 for more information Use the Expected Fragments Tab on the Assay Analysis Window to create the Expected Peaks file Excluded Peaks File Specifies the file that will supply the Excluded Peaks for the assay Click the Browse button next to Excluded Peaks File select the name of the GEP file that contains the excluded peaks and click the Open button The path and name of the file displays in the text box P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 172 System Diagnostics Window Statue
74. D THE ACCOMPANYING USER DOCUMENTATION COLLECTIVELY REFERRED TO HEREIN AS THE PROGRAM THE PROGRAM IS COPYRIGHTED AND LICENSED NOT SOLD BY OPENING THE PACKAGE CONTAINING THE PROGRAM YOU ARE ACCEPTING AND AGREEING TO THE TERMS OF THIS LICENSE AGREEMENT IF YOU ARE NOT WILLING TO BE BOUND BY THE TERMS OF THIS LICENSE AGREEMENT YOU SHOULD PROMPTLY RETURN THE PROGRAM IN UNOPENED FORM AND YOU WILL RECEIVE A REFUND THIS LICENSE AGREEMENT REPRESENTS THE ENTIRE AGREEMENT CONCERNING THE PROGRAM BETWEEN YOU AND CALIPER LIFE SCIENCES INC REFERRED TO AS LICENSOR AND IT SUPERSEDES ANY PRIOR PROPOSAL REPRESENTATION OR UNDERSTANDING BETWEEN YOU AND LICENSOR 1 License Grant Licensor hereby grants to you and you accept a nonexclusive license to use the Program only as authorized in this License Agreement The software included in the Program the Software may be used only on a single computer owned leased or otherwise controlled by you or in the event of the inoperability of that computer on a backup computer selected by you If the Software is an applications package you may use it on a single local system controller Neither concurrent use on two or more computers nor use in a local area network or other network is permitted without written authorization from licensor and the payment of additional license fees You agree that you will not assign sublicense transfer pledge lease rent or share your rights under this Licens
75. Front View Figure 87 shows the front view of the LabChip Dx and identifies the parts on the front of the instrument Front Panel Front Door Figure 87 Front View Front Panel Buttons and indicator light See Front Panel on page 175 Front Door Opens automatically to provide access to the microplate chip buffer vial and ladder vial P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc LabChip Dx Instrument Description 175 Front Panel The controls on the front panel open the front door eject the chip cartridge and indicate the status of the instrument s Status Light Chip Button Eject Button Figure 88 Front Panel The front panel contains the following parts Status Indicates the state of the instrument Light Dark not lit Power is off Solid green Power is on and instrument is idle Flashing green Running a plate Red Power is on cannot communicate with software Flashing Red Error detected Chip Moves the robot to open the door and releases the chip cartridge to button access the chip This button is illuminated when this function is available and flashes when movement is in progress Eject Moves the robot and opens the door to access the plate in the button microplate carrier This button is illuminated when this function is available and flashes when movement is in progress Power Turns the LabChip Dx instrument On Run or Off Standby Note that
76. Gray Wells were not read Blue Wells are included in the open collection Any Other Color Wells are selected by a Filter See the Filter View to determine which color represents each filter If a well is selected by multiple filters the colors are combined in the well Black Outline Wells are selected in the Gel View and Well Table View Red Exclamation Point in Well An analysis error has occurred in the well such as no lower marker detected Yellow Exclamation Point in Well An analysis warning has occurred in the well P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 95 List View The List View displays a list of all the wells in the currently open data files Select the List tab at the bottom of the Workspace pane to see the List view e Black wells are not included in the open collection e Dark Blue wells are included in the open collection e Light Blue wells are selected in the Gel View and Well Table View e Red wells have an analysis error Figure 33 List View P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 96 Collection Pane The Collection Pane in the LabChip Dx Main Window displays a tab for each collection in the workspace Each collection displays the information from the data files that are open in the Plate View or Plate List The Collection Tabs each contain the following views Graph View Gel Vi
77. MITY TO ANY DESCRIPTION OR REPRESENTATION THE EXISTENCE OF ANY LATENT OR PATENT DEFECTS AND IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE IN NO EVENT WILL CALIPER BE LIABLE WHETHER ARISING IN CONTRACT TORT INCLUDING NEGLIGENCE STRICT LIABILITY OR OTHERWISE FOR ANY LOSS OF PROFIT OR ANY OTHER COMMERCIAL DAMAGES INCLUDING BUT NOT LIMITED TO SPECIAL INCIDENTAL CONSEQUENTIAL OR OTHER AND IN NO EVENT SHALL CALIPER S LIABILITY EXCEED THE PURCHASE PRICE OF THE PRODUCT THERE ARE NO ORAL STATEMENTS PROMISES REPRESENTATIONS OR OTHER WARRANTIES COLLATERAL TO OR AFFECTING THIS WARRANTY THIS WARRANTY EXTENDS TO BUYER ONLY AND NOT TO PURCHASERS OR USERS OF BUYER S PRODUCTS No agent employee or representative of Caliper has any authority to bind Caliper to any affirmation representation or warranty concerning a Caliper product that is not contained in Caliper s printed product literature or this Warranty Any such affirmation representation or warranty made by any agent employee or representative of Caliper will not be binding on Caliper P N 113642 Rev 03 Caliper Life Sciences Inc Caliper Life Sciences Inc Software License Agreement 221 Caliper Life Sciences Inc Software License Agreement Thank you for purchasing our products PLEASE READ THE TERMS AND CONDITIONS OF THIS LICENSE AGREEMENT CAREFULLY BEFORE OPENING THE PACKAGE CONTAINING THE SOFTWARE MEDIA THE COMPUTER SOFTWARE CONTAINED THEREIN AN
78. N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 90 Chip Status and Run Status The Chip Status and Run Status areas on the LabChip Dx Main Window display the status of the system information about the Chip in the instrument and information about the assay that is currently running NOTE If the software was installed in Reviewer mode this status area does not display Wash Chip Status Asam Seeplex 400 Chip Reagent Status M A Ch boron danm I 23000 1 Che le Status 381 Samples 20 Primes Left Run Status Run Time Left 00 37 42 Piste Name 96 PCR Shorted Sap dde mio Bpo Yes Barcode N A Cycles 1 1 Status Running pate 00 37 42 System Status Displays the status of the system Displays Ready when the system is ready to run an assay While an assay is running each stage of the assay displays Priming Warming Running etc Run Button Opens the Start Run Window to begin to run an assay See the Assay User Guide for chip preparation instructions While an assay is running the Run button changes to a Stop button as shown above Click the Stop button to stop a running assay Assays that have been stopped cannot automatically be continued See Continuing a Stopped Run on page 29 for details on restarting a stopped assay Wash Button Begins a sequence of steps to wash the chip See the Assay User Guide for chip preparation instru
79. NA NAGA AA ANNA siees ace 76 Peak Detection Slope Threshold Vs 77 Peak Splitting Inflection Threshold 4 80 Pedak IASHITICATION sr as dada AE na AA AA 81 Software Referente uma ANAN AA 82 Lab Ginip DX Maini WINdOW nas a cocina ANS A Red a seen 83 MEONUDAN sam oare rcdunteetansts E ten IT KAN NGANGA A GANG 84 Chip Status and Run STATUS Rene NANANA AL 90 Eror Message AT Aa UA san 92 Piate VIEW or Hale MIS Aa de en antenne Ala 93 OMS C TON PANG ne ne sad dec 96 CD OVI NS tee Re ne a ALAGANG 97 Graph View Proper IOS usa naaa ad rss animent codes ee die see 103 Gel NEN aa AA GAO atte oes eee cu 105 Gel VIEW PIOD CCS a GG masa a AD 108 Well Table VIEW Gn Sn ner aa dette tie 109 Peak ADI VIN nee ee eee merde 110 Peak Table PrOD TUES ama a tn 114 FIET VIEW PR ANA 115 ADOUL LaDC MP DX WINDOW ama na le encre mme bee 118 Add New Expected Peak Window 119 Ada PIE WINGOW ereraa MP 120 ASSAN ANAIMSIS NIMES A AA NANA NANA AN AA NAAN 121 P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Table of Contents 14 AssayInlonmalon kapi nt BAG 122 Aligament TAO r a kalan 123 Analysis PAPE NAA T eis Ae E OE E anes 124 AG ri Ma areenaa a e EA HA 125 Expected Fragments I AD Re ii E 129 Excluded Peaks Aban a D a ans 131 Advanced TaD esera ra aeea 133 AUO EXPO WINDOW iseina a a a E 134 Hata File Version WINDOW Laden eens SE RETO 136 Event Viewer WINDOW SSSR a endl nana encoder 137 EXPOKWINTOM saaan sa a NANANA AN NAAN net ere Een 1
80. Plate Opens the Verify Plate window to perform a puncture test using the selected plate information Follow the instructions in the Verify Plate window to test the settings for the selected plate Close button Closes the Plate Information window P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 146 Print Window Use the Print window to print information from the currently open workspace If the workspace contains multiple collections information from the active selected collection is printed To open the Print window select File gt Print on the LabChip Dx Main Window LabChip Dx Prong a gt Prt Selling 2 Gel Page Option Table Option a Poist Add Border Bactrapheragram fet Landscape Peak Table nl Add Well Nama Well Tabie RE Con Ae Header 5 BA Peak Table Entire Colection Cohen Header Excksis Haka heen Par Page _ Selected Padis Par Wal Fre ven Fin Figure 66 Print Window The Print window provides the following options for printing e Print All Selects all of the options e Gel Prints a graphic of the gel for either all wells in the collection or all selected wells e Electropherogram Prints a graph of either all wells in the collection or all selected wells e Overlay Electropherogram Prints a graphic of all electropherograms either all selected or all in the collection over laid onto the same grap
81. Preview Displays a preview of the report and enables you to print or button export the results Print button Opens the Print window to print the report Close button Closes the window P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 149 Rename Collection Window Use the Rename Collection window to rename the currently selected collection The collection name displays on the Collection tab at the top of the LabChip Dx Main Window To open the Rename Collection window select Collection 3 Rename Collection on the LabChip Dx Main Window Rename Collection A Name Colecion 1 OK Figure 68 Rename Collection Window Name Type the desired name for the selected collection P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 150 Robot Teaching Wizard Use the Robot Teaching Wizard to teach the correct reference location Reteach the robot if the sipper is not accessing the plate properly Also includes a plate puncture test to verify the taught location and a Restore Defaults options to restore the original factory default positions to the robot To open the Robot Teaching Wizard select Tools gt Teaching Utility on the LabChip Dx Main Window The Robot Teaching Wizard consists of the following windows e Welcome Window on page 151 e Teach Robot Window on page 152 e Teach the X Y and Z Reference Positions Wind
82. Print opens the Print Window to select the information to print from the open workspace If the workspace contains multiple collections information from the active selected collection is printed The header of each printout contains the workspace name the collection name and the page number The Footer of each printout contains the LabChip Dx software version the date that the workspace was modified and the print date The following information can be printed for the open workspace e Print All e Gel e Electropherogram e Overlay Electropherogram e Well Table e Peak Table See below for descriptions of each option Print All This option prints the results of the assay in all of the available formats The page layout depends on the options selected in Print Settings Gel Choosing this option prints a gel image with the lanes marked by the sample name ofa jal la lattes ist RE Little ata a AA PEE ee plp BE BEBE eee a ea ee AK NE Figure 19 Printed Gel P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 69 Electropherogram Choosing this option prints an individual electropherogram of each of the selected wells ms gh Lem mhi Pagi La sms a L EUR apanan a i wrie Let a ma Aa were maana beara CA Liked mr HC Figure 20 Printed Electropherogram Overlay Electropherogram Choosing this option prints one graph with the electropherograms for all of the se
83. Show EPs If selected expected peaks are indicated in the gel by colored horizontal lines Show EP Displays a legend of the band colors and expected peak sizes in Legend the Gel view Click and drag to move the legend Show Filter Displays a legend of the colors assigned to each filter Click and Legend drag to move the legend Only displays if at least one filter is defined in the Filter tab Pin icon In the top right corner this is used to lock in place or unlock the Properties tab If locked in place the Gel display panel is resized to accommodate the tab P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 109 Well Table View The Well Table view in the Collection Pane contains a summary of analysis results for the wells selected from the microplates in the collection To view or hide columns in the Well Table view right click on a column header in the table The following columns are required by the Seegene Viewer and cannot be hidden Plate Number Plate Name Instrument Name Well Label and Sample Name The Select Well Table Columns window displays all available columns with the current selections in the Selected Columns list Show or hide columns in the well table by moving the column names between the Available Columns list and the Selected Columns list in the Select Well Table Columns window Drag and drop the column names in the Selected Columns list to change the order of the col
84. To create a new assay 1 On the LabChip Dx Main Window select Tools Edit Assay The Select Assay To Edit window opens 2 Select the name of the Assay file that you want to edit and click the OK button The Assay Analysis Window opens and displays the settings for the open assay 3 Modify the settings as necessary for the new assay See Modifying Analysis Parameters or Reanalyzing a Data File for information on setting or changing analysis parameters 4 Click the Save Assay button at the bottom of the Assay Analysis window specify the desired name for the new assay file and click the Save button P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Running an Operation 22 Assay To start an assay to read a plate 1 10 P N 128682 Rev 00 Click the Run button on the LabChip Dx Main Window see page 83 to open the Start Run Window lf the maximum number of samples for the chip have already been run or if the chip was last primed for a different assay a message displays instructions for resolving the problem Click the Run tab in the Start Run window Select the type of assay you want to run in the Assay Type drop down list Type the operator s name in the Operator Name text box Select the name of the plate in the Plate Name drop down list To use a plate that is not listed in the Plate Name list see Adding a New Plate on page 32 To read the plate barcode select the Use Barco
85. VE THE PROGRAM IS LICENSED AS IS AND THE LICENSOR DISCLAIMS ANY AND ALL OTHER WARRANTIES WHETHER EXPRESS OR IMPLIED INCLUDING WITHOUT LIMITATION ANY IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE Limitation of Liability Licensor s cumulative liability to you or any other party for any loss or damages resulting from any claims demands or actions arising out of or relating to this License Agreement shall not exceed the license fee paid to Licensor for the use of the Program In no event shall Licensor be liable for any indirect incidental consequential special or exemplary damages or lost profits even if Licensor has been advised of the possibility of such damages SOME STATES DO NOT ALLOW THE LIMITATION OR EXCLUSION OF LIABILITY FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES SO THE ABOVE LIMITATION OR EXCLUSION MAY NOT APPLY TO YOU P N 104954 Rev 3 Caliper Life Sciences Inc Caliper Life Sciences Inc Software License Agreement 222 7 Software Updates Licensor periodically creates Software updates which will be made available to you at no charge Thereafter Licensor shall not be responsible for your use of and shall not warrant or repair superseded or outdated versions of Software 8 Governing Law This License Agreement shall be construed and governed in accordance with the laws of the Commonwealth of Massachusetts Any dispute will be resolved in the state and federal courts of the Commonwealth of Ma
86. Zero Baseline Offsets all graphs to zero baseline but does not affect analysis e Baseline Subtraction A dynamic subtraction of the baseline that corrects for drifting Baseline Select the desired method for generating the baseline curve Spline Creates a smooth line fit to the baseline data points and subtracts this smooth fit from the data The Threshold determines how much the baseline fit follows changes in the data Rolling Ball Generates a smooth baseline curve by mathematically rolling a ball under the sample signal keeping it in contact with the closest signal point without crossing into the signal Time Diameter and Signal Diameter determine the smoothness of the curve in the Time and Signal axes High Size If selected a second larger filter is applied to the data after the Filtering specified time This is useful for assays where the peaks are narrow at the start of the assay and become broad and noisy for larger sizes of DNA If not selected the same size filter is used for all data e Filter Width sec The width of the second filter to be applied after the specified transition time Filter Width must be greater than the Sample Well Filter width and less than or equal to 3 0 seconds e Transition Time sec The time at which to transition to the larger filter size Transition time must be greater than the Baseline Time on the Analysis tab and less than the Well End time Table 2 Well Peak Find Set
87. a naanakan NANANA A AKN KA KNA KANAN 174 BONI VIEW a ha a GA nabahala nn aaa ABA aka AGA 174 FONERA AA AA APA 175 Rear 10 010 16 0 maana ka ANAND AGANG NADA Dn LGA NANA a ALINA GA 176 So e AA AA A PAA 177 GAD Pressure SYA ana akan kaha du teas 177 ae aa CA 177 DNA CHIPS a de eh delete AG AGA 178 CAP Ganga aa AA AA ie ND ad 179 High Voltage INterldcE aa ma Na NANANA 180 P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Table of Contents 15 Microplate Gama teen 181 SDECIIIC AMONNS maana GN rene ete les ado ae ie AA ADA 182 GENE Al aman NAA GAGA Pense a AA del der clean 182 ENVITOMMONUGl akan RS aha ete a ee 182 EICC Aldama Rene eer aera eee haha en AG Ba 182 AS SAN WOM ACG aa NAA TA Eau 183 CID Pros SU oain Ge AA 183 Chip Temperature GORIO aaa Naa kaha NAA kA 183 FIMOFESCENCE D CIECTION maa ANNA ANAKAN 183 Light Source Red laser diode 1 2 183 BArCOUS ROAD NA Se NAA PA 183 Maintenance and Servik ka ANAN 184 Cleaning the Chip Cang aNG nA ei DR de 185 Troubleshooting and DiagnostiCS sana ma naaawaawa nma KKA KA NKKAKAA KAN KA ANAN NAA nna 186 DIGNOS Saan CR Ne ANA AA AA 186 RUNNING the Diagnostics TESIS aaa NA AA 186 Description of Diagnostic TESIS AGANG 187 astallanon Qualification 1O senses aaae 190 Running Operational Qualification OQ eee eee ee eee nese eee eeees 190 Searching for Events in the Events Tab 191 Viewing Current Events in
88. aa Figure 75 Verify All Target Positions Window The Verify All Target Positions Window contains the following options and buttons Option Button Plate Name list Displays the names of the plates that have been created for use in the instrument View Plate Info Opens the Plate Information Window to view existing plates or button to add new plates Back button Displays the Welcome Window Next button Displays the Verify All Target Positions Correct Window Cancel button Closes the Robot Teach Wizard without saving changes to any positions P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 158 Verify All Target Positions Correct Window Use the Verify All Target Positions Correct Window to verify the plate buffer vial and ladder vial were all punctured correctly ny Poko fearing Piccard ry AA Ap AR ligt Firin a Diet bo we if al he hangat pira hares men panga pomery PN de Dendi Mes cp jea l orgues aaa tapar bee sore re Mig Pa ua oral Che Gees byer lune Sear Gay ia Lu Figure 76 Verify All Target Positions Correct Window The Verify All Target Positions Correct Window contains the following options and buttons pronen nan Positions Correct Select the check box if all positions were punctured in the check box center Clear the check box if any of the positions need to be corrected Back button Displays the Verify All Target Positions Window Next button If th
89. able options are not available with AIA Format e Select Include Size Data to align the data to the well s ladder for one file per well or to the first well for a single data file and include the size data in the exported data e Select Export Single Table to export the data for all wells in the plate to one CSV file If not selected the data from each well is exported to a separate CSV file lf Electropherogram is selected select either Entire Collection to export a separate graph for each well in the collection or select Selected Wells to export a separate graph for only the selected wells If Gel is selected choose the desired export options e Select either Entire Collection to export all of the wells in the collection or select Selected Wells to export only the wells that are selected in the Gel view e Select either Single File to include gels for all wells in the same image file or select Separate Files to export each gel to a separate image file e If desired change the height of the exported graphic in the Height text box If either Electropherogram or Gel is selected choose the desired format for the image files Click OK to export the data to the specified location LabChip Dx User Manual Caliper Life Sciences Inc Understanding Peak Finding 76 Understanding Peak Finding Peak finding is the complex data analysis process of converting the raw data signal into a list of meaningful peaks It involves smo
90. ains Option Button Function S Back button Displays the Welcome Window Next button Displays the Teach the X Y and Z Reference Positions Window Follow the instructions in the window before clicking the Next button Cancel button Closes the Robot Teach Wizard without saving changes to any positions P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 153 Teach the X Y and Z Reference Positions Window Use the Teach X Y and Z Reference Positions Window to align the sipper at the reference position save the reference position and test the alignment pts Ketan Teacher Mirae Teach The 2 7 and Referee Poti E Ge tn i M Aw bhe cote Le rates ro Se mata ar peop tte de Gen se Ds Parce Et D Share plahi aba i degr s an thee left cie ci kaaga Tha sal maba bas NG hope Ba opga rot hee isahan 2 Aa Shes ha etes renee on bad wa ad de red maling ood et ba gape 1 ng a aha meea uni Pa ppe ieee a a Pa ere ad ka NAA d Jeg che parahin up a baa unli Pa apes ima ee Pa honda kuaaia Cc iha Tar baitan fo nai ba paawa poi Cd Ghee Tar aa kg aly a ih paper nan ga Bagh e pated bode cay i Ba ppe A ge cag ee mobs candy aa Pa ICT paahon coca CRC De ang Pao chk Tea agar 2 Mega end iha upper si Bragh ais chauds WY meer Z enter ap Lie mnie 00 mm _ Sem Timm _ Sia BIL Eea Figure 71 Teach the X Y and Z Reference Positions Window The Teach the X Y and Z Reference Positions Wind
91. analysis software tools The Include Size Data and Export Single Table options are not available with Chromatography Data Interchange Format P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Gel Data Analysis 74 Exports the selected gel s in the selected image format Options are available to export the entire collection or only the selected gels Gels can be exported into the same image file or into separate files for each gel Figure 25 shows multiple selected gels exported to the same image file P N 128682 Rev 00 Blank PhiX17 L PhiK1T PhIK17 Figure 25 Exported Gel LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 8 75 Exporting Data Manually If the workspace contains multiple collections the data exported is from the active selected collection 1 2 P N 128682 Rev 00 Open the file that you want to export the data from Select Export from the File menu The Export Window opens Select the check boxes next to the views to export Selecting Export All selects all check boxes For each selected view to change the location for the files click the Browse button and select the desired location If Raw Data is selected choose the desired export options e Select the AIA Format check box to export in Chromatography Data Interchange Format which is used by some graphical analysis software tools The Include Size Data and Export Single T
92. anges to the plate information when you exit the Plate Information Window If you click the Yes button the plate information is saved even if you click the Cancel button in the Robot Teach Wizard Probe Teaching Hrag Lie AA Pangalanan a kaa mah ayh Pa maa Figure 74 Finished Window The Finished Window contains the following options and buttons Option Button Back button Displays the Verify Positions Window Finish button Saves the changes to the reference position and closes the Robot Teach Wizard Cancel button Closes the Robot Teach Wizard without saving changes to any positions P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 157 Verify All Target Positions Window Use the Verify All Target Positions Window to skip teaching the reference positions and verify the plate buffer vial and ladder vial positions Select the Verify Target Positions Only check box on the Welcome Window and click the Next button to open the Verify All Target Positions Window by Naba beaten Var ry Lan A a lang Fa I a ee ll be ps Fi kia Les Maha Haras Fiia iimm HT iei ES ai Pasa the Tag kumar an a parak ol Pa erred NG kaa Ba CANTINE 3 laan ache Ba cape aral ie thet naig bani nia ba ua ares dette lain plaka aa Ko pdala kakita Ces a Mas hano Ed Ba pala kls pois fe er ha habang laka D Drem te a ag ai p SU ha e hang Ka Dres dha laan gr mali paa hin ce ahas Pahang pa I Ci P
93. antification Peak Size Calibration point Concentration Size Correction Peak Integration Mode and Marker Find settings Figure 57 Assay Analysis Window Advanced Tab Quantification Determines whether the upper marker lower marker or a sample peak is used for quantification Selecting Sample Peak uses the peak size and concentration of the User Standard instead of the default ladder settings Peak Size Calibration Point Specifies which part of the peak is used as the size calibration point e Leading Edge If selected uses the start of the peak May be better for data where sample peaks are broader than ladder peaks e Center If selected uses the top of the peak May be better for data where leading edge is not well defined Peak Integration Mode Specifies the mode for determining the baseline e Peak Baseline A global peak baseline is used as the baseline for all peaks This baseline is determined by stitching together regions of low variance across the data signal e Valley to Valley Each peak is assigned a baseline by drawing a line under the peak joining the start and end of the peak at the data signal values Marker Find The Marker Drift Tolerance specifies a percent of migration time to use when determining the correct marker peak See Marker Drift Tolerance on page 209 for details P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 134 Auto Export
94. aphs in the tab to the same z00m level To only display the wells selected in the Gel View or Well Table View select the Graph Selected Gels Only check box in the Graph View Properties To move the graphs in the tab in the Gel View click and drag the well to the desired position To change the number of graphs displayed in the tab select the desired Maximum Graphs per Page value in the Graph View Properties P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 64 Viewing Multiple Properties in the Well Table View Properties for Expected Peaks display in the Well Table View When entering the settings in the Expected Fragments Tab on the Assay Analysis Window the property to display in the well table is specified in the Property Displayed in Well Table column To display multiple properties for the same Expected Peak in the Well Table 1 P N 128682 Rev 00 In the Expected Fragments Tab enter the properties for the expected peak selecting one of the desired properties in the Property Displayed in Well Table column Click in the next row and type the same name as an existing EP in the Name field of the table The row will automatically update with the same entries as the original row The only field that can be changed is the Property Displayed in Well Table column Change the Property to the desired selection Repeat until all desired properties have been added to the table Click the
95. ar from the date of installation or 8 000 hours of use e The use in a Sciclone inL10 of DMSO above 65 concentration or any other system fluid not sanctioned for use by Caliper will invalidate this warranty as it relates to the pipetting head assembly LabChip XT and Twister are not eligible for on site service and must be returned to Caliper s Repair Depot for warranty service pursuant to the process set forth in Section E below P N 113642 Rev 03 Caliper Life Sciences Inc Caliper Life Sciences Inc Product Warranty 220 If Caliper performs service on equipment and determines that any of the exclusions set forth in this Warranty apply then Caliper shall charge Customer its then current current list prices for parts labor and travel D Limited Life Parts Limited Life Parts are any parts that are exposed to solvents reagents or samples Such parts include but are not limited to syringes valves seals and fittings A pre defined list of Limited Life Parts are routinely replaced by Caliper Field Service Engineers during an Extended Warranty or Service Contract Preventative Maintenance visit or during Caliper Repair Depot servicing Otherwise these parts are available from Caliper at current list prices and are designed for replacement by Customer E Equipment Return Policy In servicing situations requiring the return of equipment to Caliper equipment must be returned to Hopkinton MA USA or another facility designated by
96. ation for electropherograms or gels click the Browse button and select the desired location Peak Table Well Table and Raw Data files are automatically exported to the data file location If Gel is selected a Select either Single File to include gels for all wells in the run in the same image file or select Separate Files to export each gel to a separate image file b To adjust the contrast minimum and maximum values for all gels to a specific lane in the gel choose the desired well in the Contrast Lane drop down list Only available after the sample wells have been selected on the Run tab c f desired change the height in pixels of the exported gel graphics in the Height text box If either Electropherogram or Gel is selected choose the desired format for the image files Click OK to save the Auto Export settings The specified files will be exported at the end of the run LabChip Dx User Manual Caliper Life Sciences Inc Operation 26 Automatically Exporting Copies of Data Files The LabChip Dx software provides the option of automatically exporting a copy of the data file dxd to another location The data file is copied to the specified folder after the run is complete To automatically export a copy of each data file 1 P N 128682 Rev 00 On the Output Tab on the Start Run Window select the Copy To check box Click the Browse button The Browse for Folder Window opens Navigate to
97. bee ra Mako eds d iiy Eo Diere ka Ben Piia eaters ka oria Gaan Punimi Pp we of en Piar Porter i ady Dube Poor E eds Laii Pintan Figure 73 Verify Positions Window The Verify Positions window contains the following options and buttons Option Button Verify Plate If selected the plate holder moves so that the sipper pierces Position the tape in the well each corner of the plate If the well is not pierced in the center of each well click the Back button and adjust the Plate Information Verify Buffer If selected the plate holder moves so that the sipper pierces Position the tape over the buffer vial If the buffer vial is not pierced in the center verify and adjust the Reference Position Verify Ladder If selected the plate holder moves so that the sipper pierces Position the tape over the ladder vial If the ladder vial is not pierced in the center verify and adjust the Reference Position Test button Moves the plate holder to test the selected positions Back button Displays the Verify a Plate Window Next button Displays the Finished Window Cancel button Closes the Robot Teach Wizard without saving changes to any positions P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 156 Finished Window The Finish Window is the last window to display in the Robot Teach Wizard Click the Finish button to save changes to the Reference position The software prompts you to save ch
98. below the slope threshold indicates the End Point of a peak A baseline is drawn under each peak region using a signal average in the baseline regions on each side of the peak P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Understanding Peak Finding 78 The Baseline Plateau property defines the minimum length of baseline region needed for computation of this average Often the region between peaks may not be long enough to qualify as baseline in which case the baseline is drawn from the nearest qualifying baseline region on each side of the peaks In Figure 28 the orange trace shows the signal slope superimposed over the data The light blue traces are the peak baseline The scale for the slope is the same as for the data but with units of sec For these well defined peaks a threshold of 15 sec clearly extracts the full peak signal Fluorescence 45 46 5 7 475 48 48 s Aligned T irra 8 c Figure 28 Slope Threshold The Slope Threshold is used to distinguish between baseline and peak regions so it should be set with care A common mistake is to set the threshold too low making it difficult for the analysis to find the baseline On the same data signal near the lower marker there is sufficient noise to create variation in the slope values as shown in Figure 29 on page 79 P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Understanding Peak Finding 79 Demo UNA 126
99. ciences Inc Glossary of Terms 204 Collection Use a collection to view the plate data A workspace can contain multiple collections to supply different views of the same data Each collection specifies e the wells selected for view in each plate data file e the layout of each Collection tab and e the display properties for each view in each collection Data Files While running an assay the raw data received from the instrument is automatically saved to the plate data file dxd As the data from each single well is received it is saved to the data file The name of the data file is specified in the Start Run Window If a run is stopped before the run is complete the data file contains the data for the completed wells After a run is complete the data is analyzed using the analysis settings in the assay The analysis settings are saved in the data file dxd After the run you can change the analysis settings using the Assay Analysis Window When the new settings are applied the data is reanalyzed and the updated results are displayed Changes to the analysis settings are not saved until the workspace is saved To save analysis settings without saving the workspace select Workspace Save Plate or right click on the plate name above the plate diagram on the left side of the window and choose Save Plate Changes to the analysis settings are saved at the end of the plate data file without overwriting previous setti
100. click the X button on the column header or right click on the well in the Plate View or Plate List and select Remove Well P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 59 Viewing Zero Baselines All electropherograms produced with the instrument show some amount of background fluorescence By default the LabChip Dx software enables the zero baseline function To remove the zeroing select Analysis gt Analysis Settings to open the Assay Analysis Window click the Peak Find Tab and select the None check box under Baseline Algorithm Demo UMA 5k 2009 09 14 09 40H09fA 7 PRATA ESUR 50 nul EP11367 EP178 E J Fluorescence Demo DNA 5k 2009 08 14 09 90 0947 Phix174 BeuRl 50 agul EP136 EP1078 IT mpa E EFE Fluorescence Figure 16 Zero Baseline Off P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 60 Adjust Pane Widths The LabChip Dx Main Window displays several different views of the data files open in the workspace You can change the height and width of the views to make the views smaller or larger To adjust panes 1 3 Place the cursor over the edge of the pane that you want to adjust The cursor changes to a line with arrows on each end Click and drag up down left or right The pane is resized after you release the mouse button The layout setting is saved as part of the collection To save the setting sav
101. clicking on the well and selecting Remove Well Save the workspace to save the wells selected in the collection LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 43 Using Sample Name Files Sample name files are used to import sample names into a data file A sample name file can be selected in the Advanced Tab on the Start Run Window to assign the sample names and expected peaks as the assay is running The Sample Name file can also contain expected peaks After the run is complete you can use the Sample Name Editor Window to rename the samples or to import an existing sample name file Sample name files are saved as csv files and can be edited with a spreadsheet program such as Microsoft Excel The Color Name and Display Property for an Expected Peak cannot be set in the Sample Name Editor window When new Expected Peaks are created in the Sample Name Editor window default values are assigned for these properties To create a Sample Name file 1 Select Tools gt Sample Name Editor on the LabChip Dx Main Window The Sample Name Editor Window opens 2 Modify the sample names as desired in the Sample Name Editor window 3 Enter any desired comments for the samples in the Sample Comment column 4 If desired click the Edit Expected Peaks check box and enter the desired Expected Peaks and Window in the columns Separate each peak size or window value with a semi colon If only one Window value is
102. ct Tools gt Plate Editor to open the Plate Information Window 2 Click the Custom Plates tab 3 Click the Add Plate button The Add Plate Window opens 4 Type the settings for the new plate The diagram on the Add Plate window shows the location for each measurement Acceptable plate parameters are e PlateHeight O to 16 mm e WellDepth O to 36 mm e SipHeight gt 2 5 mm e WellDepth SipHeight lt PlateHeight 5 Click the OK button 6 Perform a Punch Test from the Plate Information window to verify the new plate settings are acceptable e Tape a piece of ParaFilm to cover the corner wells on the plate e Use an old dead chip with a good sipper e Inthe Plate Editor select the new plate name and click the Verify Plate button e Follow the onscreen instructions P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Operation 33 Adding a New Plate Continued e The instrument will move to five wells in each corner of the plate punching holes in the ParaFilm e The Punch test is acceptable if the punched hole is 50 5mm from the edge of the well Holes will probably not be perfectly centered 0 5mm from edge OC oor AIr Possible sources of errors P N 128682 Rev 00 Sipper splay Plate tolerances Robot alignment error e Ifthe holes are too close to the edge lt 0 5mm adjust the X Margin or Y Margin values in the Add Plate window Select the new plate name in the Star
103. ction 1 Select the collection where the wells will be displayed 2 Using the plate diagram in the Plate View select the wells to P N 128682 Rev 00 display as described below 123245 6 7 8 934011124 720000000000 PARA PP PAA n PLA PLA PLA 12 345 6 7 8 54011124 Figure 8 Selecting Wells tl A CC Bi E G L Select individual wells by clicking on the well Select a block of wells by clicking and dragging around the desired wells Select entire rows by clicking the row letter at the left of the microplate Select an entire row and the corresponding ladder by clicking the row letter at the right of the microplate only if the plate sip order is row wise Select entire columns by clicking the column number at the top of the microplate Select an entire column and any corresponding ladder by clicking the column number at the bottom of the microplate only if the plate sip order is column wise Select all the wells in the microplate by rows by clicking the double arrow button in the top left corner of the microplate Select all the wells in the microplate by columns by clicking the double arrow button in the top right corner of the microplate Select all ladder wells and microplate wells by clicking the arrow button at the bottom right corner of the microplate Select all ladder wells by clicking the L icon at the bottom left corner of the microplate Clear individual wells by right
104. ctions Chip Status Assay The name of the assay file that is being run or that generated the data P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 91 Chip Status and Run Status Continued Chip Reagent Status Displays the time and number of samples whichever comes first until the chip reagents expire Reagent expiration depends on the type of chip inserted in the instrument The LabChip Dx automatically detects the chip type from an embedded RF ID tag in each chip The expiration time and number of samples reset whenever the chip holder is ejected Chip Expiration Displays the date when the chip expires Chip expiration depends on the type of chip inserted in the instrument The LabChip Dx automatically detects the chip type from an embedded RF ID tag in each chip Chip Life Status Displays the number of samples or number of primes until the chip expires Chip Life depends on the type of chip inserted in the instrument The LabChip Dx reads the chip type and Chip Life Status from an embedded RF ID tag in each chip Run Status Run Time Left Displays the time remaining until the assay is complete Plate Name The name of the plate being used in the assay Auto Export Displays Yes if Auto Export was selected in the Output Tab on the Start Run Window Barcode If Use Barcode was selected in the Run Tab or Output Tab on the Start Run Window displays the barcode that was r
105. ctropherograms for each sample see Figure 2 Figure 2 Electropherogram The data can also be viewed in a gel like format on the Gel Tab to achieve the appearance of a slab gel The colors of the gel can be changed Figure 3 Gel View P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Introduction 19 Principles of Operation Continued Quantitating the concentration and accurately sizing each fragment are achieved by comparing against a sizing ladder and running internal standards or markers with each sample Internal standards of known concentration are mixed with the sample to aid in quantitation The amount of sample sipped into the chip depends on pH salt concentration and buffer additives The internal standards normalize these factors so that the software can use the ratio of the area of the curve of the standard to the unknown peak to determine concentration directly The internal standards lie slightly outside the assay range so they do not interfere with analysis P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Operation 20 Operation This section includes general instructions for using the LabChip Dx hardware and software to run an assay For assay specific information see the LabChip Dx Assay User Guide for the specific assay that you are running To run an assay in the LabChip Dx Open the LabChip Dx software See Opening the LabChip Dx Software
106. d to display at the bottom of the pane Right If selected the view displays on the left side of the Collection pane The view displays at the top if any view is selected to display at the bottom of the pane Bottom If selected the view displays at the bottom of the Collection pane The view displays at the top if there are no views displayed at the top left or right in the pane Apply button Applies the selections to the active collection and closes the Layout Options window Restore to Factory Defaults button Restores the active collection to the default Layout options table views table columns and viewer properties Cancel button Closes the Layout Properties window without changing the collection layout P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 143 Layout Options Window Continued NOTES e A view can only be displayed in one location Selecting a location automatically clears any other selected location e To hide a view click on the selected location to clear the selection e A location is hidden if it contains no views e The Gel View Peak Table View and Well Table View are always displayed and cannot be hidden P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 144 New Collection Window The New Collection window is used to create a new collection using either a Blank Collection default or settings f
107. d as the expected peak even if it is not the exact size specified To change the peak identified as an expected peak see Forcing Expected Peaks on page 47 A default color is automatically assigned To change the color click on the color block in the Color column and select the desired color in the Color window If desired change the name shown in the Name column If desired change the Property Displayed in the Well Table This setting specifies the property that will be displayed in the Expected Peak column for each expected peak listed in the Well Table View To apply the expected peak only to specific wells click in the Apply to Wells column The Select Wells window opens Click or click and drag to select the wells that you want to apply the expected peaks to and then click the OK button To apply the EFs to the active plate click the Apply button To apply the EFs to all plates in the workspace click the Apply Global button LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 47 Exporting EFs 1 After the EFs are entered in the Expected Fragments Tab click the Export button at the bottom of the window The Export Expected Fragments Window opens 2 Navigate to the desired location for the file type the desired name for the file in the File Name text box and then click the Save button A GEP file is created to save the expected peak settings Importing EFs After an Expected Peak file
108. d wells to view in each collection in the workspace see page 42 See Modifying Analysis Parameters on page 51 for information about changing analysis parameters LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 41 Adding a Collection to a Workspace Collections are used to specify the wells selected for view in each plate data file the layout of the views in the Collection tab and the display properties for each view in each collection To add a new collection to an open workspace 1 On the menu bar select Collection gt New Collection The New Collection Window opens 2 Select the desired option for creating the new collection e Blank Collection Opens a new collection using the default collection settings e Current Collection Opens a new collection based on the settings in the currently open collection Only displays if a collection is open 3 If no plates are open in the collection choose the desired Assay Type for the collection DNA Only data files from the selected assay type can be imported into the workspace 4 If desired type a new name for the collection in the Name text box 5 Click the OK button to open the new collection P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 42 Selecting the Wells in a Collection Each collection can display different wells or the same wells in different orders To select the wells to display in a colle
109. de check box The plate barcode can be used to name the data file if selected On the Plate diagram select the wells to be sampled e To select all wells and ladders on the plate click the double arrow button in the lower right corner of the plate e To select all rows on the plate click the double arrow button at the top left corner of the plate e To select all columns on the plate click the double down arrow button at the top right corner of the plate e To select a single column click the column number at the top or bottom of the plate e To select a single row click the row letter on the left or right side of the plate e Clear specific wells by clicking on the selected well again Select the desired order to sample the selected wells Row wise or Column wise Click the Output Tab in the Start Run window To change the Data Path either type the desired path or click the Browse button and select the desired location for the data files Clicking the Default button restores the default data path LabChip Dx User Manual Caliper Life Sciences Inc Operation 23 Running an Assay Continued NOTE Data files should be saved to a local folder on the computer s hard drive Saving data files to a network drive may cause loss of data if the network connection is slow or interrupted 11 If desired select the Create Daily Sub Directory check box to create a new sub directory for data files each day 12 To sav
110. ded 2 Select Exclude Peak from the shortcut menu The Type for the peak changes to X excluded and the value is not used in the analysis 3 Right click on an Excluded Peak in the Graph view and select Include Peak to include the peak in the data analysis P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 54 Merging Two Peaks If the analysis has defined two separate peaks the two distinct adjacent peaks can now be merged into one peak This will include the area of both peaks in the total concentration and purity calculations To merge two adjacent peaks 1 Exclude one of the peaks from the analysis following the procedure Excluding a Peak on page 53 Verify that Show Peak Baselines is selected in the Graph View Properties Click and drag the baseline of the remaining peak to include the area under the excluded peak Changing the Time Window for Analysis The Start Time and End Time parameters in the Peak Find tab define the time window within which peaks are found To change the Start Time and End Time parameters for all wells in the open assay 1 P N 128682 Rev 00 Select Analysis gt Analysis Settings to open the Assay Analysis Window and then click the Peak Find Tab Change the parameters as necessary Click the OK button to save the setting reanalyze the data and close the window Click the Apply button to apply the changes and reanalyze the data but
111. e Agreement except that you may permanently transfer all of your rights under this License Agreement provided that you retain no copies you transfer all of the Program and the transferee agrees to the terms of this License Agreement You agree that you may not reverse assemble reverse compile or otherwise translate the Software Upon loading the Software into your computer you may retain the Software media for backup purposes In addition you may make one copy of the Software on a second medium for the purpose of backup in the event the Software media is damaged or destroyed Any such copies of the Software shall include Licensor s copyright and other proprietary notices Except as authorized under this paragraph no copies of the Program or any portions thereof may be made by you or any person under your authority or control Licensor s Rights Licensor has invested significant time and money in developing the products purchased with the Program The Program contains Licensor s trade secrets which must be used in confidence You acknowledge and agree that the program is proprietary to Licensor and protected under U S copyright law You further acknowledge and agree that all right title and interest in and to the Program including associated intellectual property rights are and shall remain with Licensor This License Agreement does not convey to you an interest in or to the Program but only a limited right to use it revocable in accordance
112. e Any alteration of hardware or software on products covered under this Warranty that are not performed by Caliper or an approved Caliper vendor will void this Warranty e A product that has been subject to misuse accident negligence or improper transportation handling installation storage use or maintenance is not covered under this Warranty e Many Caliper products require the use of Caliper Automation Certified Disposables for proper operation These may include but are not limited to pipet tips seals labels and filters Use of a Caliper product with any disposables other than the specified Caliper Automation Certified Disposables will void this Warranty e This Warranty covers equipment manufactured by Caliper Equipment purchased from other vendors is not covered by this Warranty e Damage to Limited Life Parts caused by insufficient maintenance or cleaning practices or unauthorized applications are not covered under this Warranty e This Warranty applies only to the original buyer and delivery location It is not transferable to other buyers or locations without Caliper s prior written approval e The Sciclone 384 channel low volume head is warranted for one 1 year or 750 000 aspirate or dispense movements whichever comes first e The Sciclone 100nL head is warranted for one 1 year or 600 000 aspirate or dispense movements whichever comes first e The laser component of the LabChip 3000 is warranted for the earlier of one 1 ye
113. e Positions Correct check box is selected the Next button changes to a Finish button If the Positions Correct check box is not selected displays the Verification Failed Window Click the Next button to display the Teach Robot Window to adjust the taught positions Finish button Closes the Robot Teach Wizard Cancel button Closes the Robot Teach Wizard without saving changes to any positions P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 159 Run File Editor Window Use the Run File Editor window to create run files xml for use with Caliper s automation control software When the LabChip Dx is running in automation mode and is being controlled by software such as iLink Pro you must create a run file to specify the settings for the assay that will be run The run file contains all of the run settings that would be specified in the Start Run Window Run files can also be imported into the Start Run window to start a run To open the Run File Editor window choose Tools gt Run File Editor on the LabChip Dx Main Window Bum File Eden HK OH H ates H aii a Figure 77 Run File Editor Window The tabs on the Run File Editor contain the same options as the tabs on the Start Run window See Start Run Window for definitions of specific options or settings The following buttons are located at the bottom of the Run File Editor window
114. e a second copy of the data files see Automatically Exporting Copies of Data Files on page 26 13 In the File Prefix text box type the desired prefix for all data files The File Name Format text box displays the selected format for the data files 14 To add the Computer Name Project Name Barcode Date and or Time to the data file name select or clear the desired check boxes or type the desired project name 15 To automatically export graphs or gels click the Auto Export Settings button and then select the desired Auto Export settings see page 25 16 Click the Advanced Tab in the Start Run window 17 To perform the assay multiple times on the same plate select the desired number of times to run the assay in the Plate Cycles text box 18 To randomly sample a specific percent of the selected wells select the Random Selection check box and specify the percent of wells to sample during the run 19 To repeatedly run the selected wells and combine the data into one data file select the Sample Saver check box and select the number of times to repeatedly run the selected wells in the Repeats text box P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Running an Operation 24 Assay Continued 20 To use a file to supply the sample names click the Browse 21 22 23 button next to Sample Names File select the name of the csv file that contains the sample names and click the Open butt
115. e fits but can be changed to Polynomial Markers The size and concentration in ng uL for the upper and lower markers for the DNA assay Data Range e Baseline Specifies the time in seconds after the start of the run when the first peak can appear any peaks appearing before this time are ignored e Well End Specifies the time when peak detection stops The graph ends at this time P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Peak Find Tab Software Reference 125 Use the Peak Find tab on the Assay Analysis Window to adjust parameters to detect peaks for individual wells rows columns a single plate or the entire plate specified in the Plate field Merete Parak With pe Gen Test pap Hion Taree L une Sit Tite lus End Tres Ha Filler fh bad Basgia Plat Ipa Perse rv A High Sam Feng Fiber Wish ina Tranakon Time ipec PF Seige _ __ _ _ Vel hame 1 a Pise T POP co ii BF WH Leije Te Tires cUe Fiais waia pok Column poby Plate Rss Plate Cancel Figure 54 Assay Analysis Window Peak Find Tab Initial individual plate and well selections are made by right clicking on a well in the Gel View or the graph in the Graph View and selecting the Analysis Settings option The corresponding well settings are displayed in the Well Peak Find Settings fields Subsequent well selections in a plate can be made using
116. e page 185 Run the Current Leak Diagnostic Test see page 186 If the problem is not resolved contact Caliper Technical Support see page 2 Chip Temperature Warning Warning Message Average chip temperature is out of range Possible Causes Recommended Actions Chip heater failed Restart the instrument If problem persists contact Caliper Technical Support see page 2 P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 198 Troubleshooting Assay Problems For problems with assays see the Assay User Guide for the specific assay you are running The Assay Guides contain common problems that may occur for each type of assay and suggested solutions to resolve the problems If the problem is not resolved by following the suggestions in the Assay User Guide contact Caliper Technical Support see page 2 P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 199 Troubleshooting Software Problems If any of the following software problems occur follow the suggestions to correct the problem e Software Disconnects e Cannot Save a File e Computer Software Lock Ups Software Disconnects USB Device unplugged During Run The LabChip XT instrument may disconnect and the software may go offline if any USB devices are plugged into or unplugged from the computer Do not plug in or unplug any USB device from the compute
117. e run to finish the reading the plate When you select the wells for the assay you should select only the wells that were not read so that the reading starts with the well that was not completed To continue a run 1 Click Start in the upper left corner of the main window to open the Start Run Window 2 Select the wells that were not read in the previous run beginning with the well that was in progress when the run was stopped 3 Select the same options for this run as were selected for the stopped run 4 Click the Start button to begin The run starts with the well that was not completed in the previous run A separate data file is created for the current run P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Operation 30 Saving Data Files While running an assay the raw time series data received from the instrument is automatically saved to the data file dxd one well at a time as each well is completed If a run is stopped before it is complete the data for the completed wells is saved in the data file The name of the data file is specified in the Output Tab on the Start Run Window The analysis settings for a plate are saved at the end of the data file dxd If analysis settings are changed in the Assay Analysis Window and the data file is saved the new settings are added to the end of the data file but the previous settings are not overwritten This enables a plate to be restored to previous
118. e that is the same as the well label for each well in a 96 well plate Blank 384 Wells Clears the sample names in the window and creates a new sample name that is the same as the well label for each well in a 384 well plate Order by Column If selected the sample names display check box Apply Applies the sample name changes to the plate Sample names cannot be applied during a run Close Closes the Edit Sample Names window If changes have not been applied to the plate prompts you to discard the changes To save the changes click the Apply button before clicking the Close button P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 163 Save Workspace As Window The Save Workspace File As window saves the currently open workspace with the specified name in the specified location To open this window choose File gt Save Workspace As This window also opens the first time you save a new workspace Sake Werkiaace File Ai A Organise Pdea l mi Adobe i d Adobe Media Planet amp RA di Aapke So basic Wedstr Demo DINA dew A Broadcom Cosporation A Business Objects d Calpe Life Sciences d LabChip DX Ji Avis Data d Demo Data b Cecumentabon Fde mme So Sare ai NP Wet paos Hg tra Figure 80 Save Workspace As Window Tip You may want to save the workspace file in the same location as the plate data files to prevent m
119. e the baseline click the triangle at either end of the peak baseline and drag to the desired location To reset the baseline to the original position right click near the baseline end point and choose Reset to Defaults While a run is in progress the Active Data Tab displays the raw unanalyzed data as it is being read from the chip As data is acquired the selected well increments to the well that is currently being run and the data displays in real time Graph View Shortcut Menus Right Click Menu not near a peak Right click away from a peak in the graph to display a shortcut menu containing the following commands Synchronize Zoom If selected the zoom is synchronized for all graphs displayed in the Electropherograms Tab all gels in the Gel View and data in the Peak Table View If not selected each view and graph can be zoomed independently Unzoom Zooms out to the previous zoom level Unzoom All Zooms out and returns to the standard view Set Scale Opens the Set Graph Scales window to specify the X and Y ranges to show on the graph Scale to Sample Peaks Scales the view to the minimum and maximum X values of the current sample peaks Marker and or system peaks are ignored Scale to All Peaks Scales the view to the minimum and maximum X values of the all peaks including marker peaks and system peaks Copy Copies the selected graph to the clipboard in a bmp format Analysis Settings Opens the Assay
120. e the curve while increasing the RFU Diameter does not P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Glossary of Terms 215 mal ll THE Figure 101 Rolling Ball 10 Sec x 200 RFU Run Button To begin running an assay click the Run button located at the top left of the LabChip Dx Main Window The Start Run Window opens to select the assay wells data file name etc After the run has begun this button changes to Stop See Stopping a Run on page 28 NOTE The Run button does not display if the software was installed in Reviewer mode P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Glossary of Terms 216 Slope Threshold The Slope Threshold setting represents the amount of change in response over time required to differentiate between a peak and baseline noise Changing this setting may cause certain peaks that were previously detected to be ignored or to interpret noise as peaks For details see Understanding Peak Finding on page 76 The Slope Threshold setting can be changed in the Peak Find Tab Standard Curve Window The Standard curve window shows the Standard curve used for the selected plate data Each window displays the following menus View menu Select or clear the ladders to display in the window Copy menu Copies the current view to the clipboard Print menu Displays the Print Preview or prints the Standard Curve DNA Assays
121. e the workspace Show or Hide Views The views displayed in the LabChip Dx Main Window can be hidden to maximize other views in the main window To hide a view 1 Select Collection gt Layout on the LabChip Dx Main window The Layout Options Window opens Click on the location that is selected for the view to clear the selection The view is hidden If a location Left Right or Bottom does not contain any views the pane closes and the remaining panes enlarge to fill the space Note The Gel View Peak Table View and Well Table View are always displayed and cannot be hidden To display a hidden view 1 Select Collection gt Layout on the LabChip Dx Main window The Layout Options Window opens Click on the desired location for the hidden view Left Right or Bottom If multiple views are displayed in the same location use the tabs at the top of the location to switch between views Zoom In and Zoom Out You can zoom in and out on data displayed in the Gel View and the Graph View The Graph View and the Gel view both zoom to the same levels when either view is zoomed in P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 61 To zoom in e Click and drag to enclose the region of interest When you release the mouse button the selected area enlarges to fill the view In the Gel view all lanes in the collection zoom to the same level e You can continue zooming in un
122. e which the last peak or fragment will be located any peaks appearing after this time are ignored Filter Width This setting on the Peak Find Tab determines the width of the polynomial in seconds to be applied to the data for filtering noise reduction The default depends on the assay selected DXD Files The file extension for data files created in the LabChip Dx software The data file contains the data from the read assay information analysis settings and Run Information for the run Data is saved to the file as each well is read If a run is stopped before the run is complete the data for any completed wells is saved in the data file The file name is specified in the Start Run Window Hardware Diagnostics Whenever a run begins the instrument checks for errors e g defective high voltage supplies missing conductivity between wells etc If an error is detected a message box displays and the run stops The message box describes the problem and either contains information on how to resolve the problem or directs you to call Caliper Technical Support see page 2 P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Glossary of Terms 207 Inflection Threshold Peaks that are very close together are identified as a single peak if the peaks do not have a clear valley between them The Inflection Threshold property splits peaks based on the slope The inflection threshold defines the value that t
123. ead from the plate If Use Barcode was not selected displays N A Cycles Displays lt CurrentPlateCycleNumber gt lt TotalPlateCycleNumber gt where CurrentPlateCycleNumber is the number of the plate cycle currently executing and TotalPlateCycleNumber is the total number of plate cycles specified in the Advanced Tab on the Start Run Window CurrentPlateCycleNumber displays 0 during the priming and Warming steps before reading the first well Status Displays the action the system is performing and the time remaining in the step Run Time Left above displays the time remaining in the entire assay Errors If an error occurs during an assay a line of red text displays a description of the error below the Run Status area in the Error Message Area Click the red text to view details about the error P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 92 Error Message Area Wash Run Status Fun Time Left Plate Mans 96 PCR Skirted Sap Middle Alo Boot Yes Barcode M A Cycles 1 1 Status lum aborted due lo enor C Cartridge is ected Please ceci plate befor Error messages are displayed below the Chip Status and Run Status on the LabChip Dx Main Window Error messages can result from hardware or software problems Most are the result of peaks not being located by the analysis algorithms of the software This can be due to a sample or ladder peak not appearing a
124. eak Defines the selected peak as the specified Expected Fragment A list of all of the defined Expected Peaks displays beside the shortcut menu Select the desired Expected Peak from the list Clear Forced EP Clears the forced peak and allows the analysis to determine the expected peak P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 100 Active Data Tab The Active Data tab on the Graph View displays the raw unanalyzed data as it is being read from the chip The Active Data tab only displays while a run is in progress After a well is read view the data in the Overlay Electropherograms Tab or the Electropherograms Tab Figure 35 Active Data Tab The Active Data tab does not show any peak labels or marker indicators The labels and markers are identified during analysis which occurs after all data from the well is collected P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 101 Overlay Electropherograms Tab Use the Overlay Electropherograms tab on the Graph View to view a single graph or multiple graphs overlaid on top of each other Demo DNA Sk 200906 14 06 8049 AT PR UR 50 ol P13 af PR01746s3uRI 25 mou Fe LAS PR LE 12 T sil _ JEP a Last LE La um o la O E Li paa OO Ki CA ill il Aligned Time sec Figure 36 Overlay Electropherograms Tab The sample li
125. ectTCal S Ale cene Sd eu cee 10 NAGO GO Ko KE AI AA teh nn dise enn 10 FUSOS paaa AA AA AA AA Nada 11 Mechanical SATEN aa ANAN nn AKA a NLA de son degree 11 NUE O GUC WON ANA NA a a a 16 PHACIDIeS OO D TOUR ade diese sat cetacean shea Va de teen 17 Operation AA ANA AA 20 Opening the LabChip Dx Software aaa 20 Creaung a New ASSAY aa AANGAL een ds ce Nada 21 RUNAM AN ASSAY aaa AA AA AA AA eue 22 Selecting the Auto Export Settings VV 25 Automatically Exporting Copies of Data Files 0 00000 20 00 asaaaaaaa 26 MONO RUN Se AS A ie ne ble one a do 27 SOPONNA AT 28 GContinuing Si0pped BUN aaa aah GAIN maan apia 29 Savino Data AA 30 Saving WORKSDdACe F IES aiarar a neo dec e un 31 Adding a New Pilale maa AA Aa 32 Placing the Barcode on the Plate VV 34 Data ANAIVSIS AA AA AA ces 35 How the Software Analyzes DNA Data VV 36 Organizing Retrieving and Backing Up Data Files ccccccecceceeeeeeeeeeeeneeees 39 Opening a New Workspace cccccceccece a 39 Opening a Data laka ententes 40 Adding a Collection to a Workspace VV 41 Selecting the Wells in a Collection VV 42 Using Sample Name Files ae E T 43 USNO Expected Fragments LU RS te 46 Entering EFs in the Assay Analysis Window 46 XDONMINA EPS NE entente ane eee 47 Mp MING ES RTE ER aa AH tested tit ha habal 47 Forcing Expected PRARS LE aaa a Aka Unan 47 Viewing the EFs in the Graph View Vs 4
126. ected image format Click the Browse button to specify the desired path for the image file The file names are lt plate names Gel well numbers The entire collection is exported when automatically exporting gels e Single File If selected the gels are all included in the same image file e Separate Files If selected the gels are each exported to a separate image file e Contrast Lane Specifies the gel lane to use to set the minimum and maximum RFU values for all lanes in the collection before exporting the gels All exported gels are set to the minimum and maximum RFU values in the selected well The contrast lane option only displays in the Auto Export window after the dwell pattern has been selected e Height Specifies the desired height in pixels of the gel graphic Image Format for Gel and Electropherogram Select the desired format for the exported image files P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 136 Data File Version Window Use the Data File Version Window to view the saved versions of the data file To open the Data File Version Window select View gt Version Change Details on the main menu ARE tall E LE u Asaan Pa mara es FE CE eke aao Naa haie se ssh M3 DNA IE me la res Figure 59 Data File Version Window The Data File Version Window lists each version of the plate data file and describes the changes that were performed
127. ection Pane see Selecting the Wells in a Collection on page 42 Plate View Right Click Menu Right clicking on the plate name in the Plate view displays the following options in the shortcut menu Keep Gel in Sip Order If selected keeps the gel in sip order when selecting wells in the plate view If not selected the gel displays the wells in the order in which the wells were selected Save Plate Saves the current data file Copy Plate Saves a copy of the plate data file dxd to the selected folder Export Assay Saves a copy of the assay settings for the plate to an assay file asy in the selected folder Rename Plate Renames the plate in the workspace If desired the original data file can be renamed by selecting the Rename File to Match check box P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 94 Remove Plate Removes the plate data file from the workspace The data file is not deleted only the workspace view changes Analysis Settings Displays the Assay Analysis Window to change the analysis settings for the data file Version Change Details Displays the Data File Version Window to change the version of the data file displayed in the workspace Run Info Displays the Run Info Window to view the run information and Event Log Plate Well Color Code z AG BIO Ci o E Fi Gi fe White Wells are not included in the open collection
128. ed Poaks 118210 R Expected Peaks 722101 Tipa Expected Ponts ic P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 117 Filter View Continued When using multiple filters that include peak properties if AND Peak is selected a single peak in the well must meet all selected filter properties See the examples below which each use two filters e Height gt 100 AND Peak Conc gt 50 selects any well that contains a single peak that meets both criteria e Height 5100 OR Conc gt 50 selects any well that contains a peak that meets either or both criteria e Height 5100 AND Well Height lt 50 selects any wells that contain peaks that are greater than 100 and also contains peaks that are less than 50 e Height 5100 AND Peak Height lt 50 does not select any wells because no single peak can have a height that is both less than 50 and greater than 100 Use OR to select wells that have peaks that match either criteria Use AND Well to select wells that contain peaks that match both criteria Expected Peak Filters can contain multiple size peaks in the same filter as shown above Expected Peak filters with multiple peak sizes in the same filter always select only wells that contain all the peaks listed The plate diagram in Figure 46 shows two filters Expected Peaks 72 10 OR Expected Peaks 118 10 The EP 72 filter color is yellow the EP
129. ed Wells Figure 90 Top of Chip RF ID Tag Chip Locators Figure 91 Bottom of Chip P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc LabChip Dx Instrument Description 179 Chip Cartridge The Chip Cartridge holds the chip provides the voltage to the chip channels to load inject and separate the sample provides pressure to prime the chip with separation gel and provides vacuum to the chip wells to pull samples from the microplate into the chip The Chip Cartridge also contains a heating element to maintain a constant temperature in the chip s microfluidic channels and provides an optically black beam dump to increase sensitivity and aid fluorescence detection Lid Optical Window Optical Beam Dump Pressure Plate Sipper Slot Electrodes O Rings Pressure Ports Figure 93 Chip Cartridge Lid P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc LabChip Dx Instrument Description 180 Chip Cartridge Continued Lid Latch Figure 94 Lid Latch Lid Holds the electrodes and o rings to supply voltage and pressure to the chip Bottom of Cartridge Holds the chip The sipper on the chip extends through the sipper slot Optical Window Window for laser to illuminate chip Optical Beam Provides an optically dark background under the chip Dump Pressure Plate with Maintains a constant temperature in the chip s microfluidic Heating Element channels E
130. ed fragments 129 Expected Peaks button 129 Export window 138 Manually 72 75 Sample names 43 Select the Auto Export Settings 25 Export As Assay button 121 Exporting an assay 57 F File menu 89 Filter View 115 Filter Width 36 125 206 Filtered Peaks only 114 Filtering parameters 51 Finding peaks 212 First Peak Time 217 Focus Failed Error 194 195 FOCU Dewa wa KARA Veet rra 177 KC PT 4 eeees 103 Forcing expected peaks 47 Front PANG sis seen 175 Front view 174 FUSOS pa kaaa mn ede se Oe ee si 11 182 P N 128682 Rev 00 LabChip Dx User Manual Index 225 G e ETETETT EEEE T ETE 65 105 COPDYINOS EE EE EE 65 exporting 74 Gel color 58 Gel View 105 Gel View Properties 108 PINUNO 44 4 sas 68 Gel Color 108 Gel Contrast Range 108 Gel View Properties 108 Global Analysis settings 121 Global Peak Find 36 Cie APAN 36 58 65 216 Active Data tab 100 CODVING 4 a KA BA o 654 ic 65 Electropherograms tab 102 Graph View Properties 103 max per page 103 overlay od ov NG esters 62 Overlay Electropherog
131. ents Version Forrest Figure 51 Assay Analysis Window Assay Info Tab The following read only information is displayed Assay Class DNA Name The name of the assay Title The title of the assay Comments Any comments that were added in the Start Run Window Version The version of the assay that was run Format The format of the data file P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 123 Alignment Tab The Alignment tab on the Assay Analysis Window is used to assign alternate ladders to a specified group of wells in the event of a faulty ladder result The default assignment for full rows uses the ladder adjacent to the row where the sample is located If this ladder cannot be analyzed the software automatically looks for another nearby ladder to perform the analysis The actual ladder used for the analysis is shown in the Well Peak Find Settings panel of the Peak Find Tab It can be changed by selecting the Align Well Groups to Specified Ladder option and then selecting a different ladder in the To Ladder column corresponding to the row to be changed Assay info Akgnn Align Wed Groups to Previous Ladder U Agn Vitel Groups to Specified Ladders Markers if W Figure 52 Assay Analysis Window Alignment Tab The Alignment tab contains the following settings e Align Well Groups to Previous Ladder If selected each row is aligned to the
132. er Life Sciences Inc Maintenance and Service 185 Cleaning the Chip Cartridge Daily Cleaning 1 2 Inspect the inside of the chip cartridge and O rings for debris Use the provided lint free swab dampened with DI water or 70 isopropanol solution in DI water to clean the O rings using a circular motion If the O rings stick to the chip or a pressure leak is detected perform the more extensive monthly cleaning procedure below Monthly Cleaning 1 P N 128682 Rev 00 To reduce pressure leaks at the chip interface clean the O rings frequently Remove the O rings from the top plate of the chip interface on the LabChip Dx instrument Soak O rings in DI water for a few minutes Clean the O ring faces by rubbing between two fingers To reduce the occurrence of current leaks clean the chip interface frequently Clean the top plate of the chip interface using the provided lint free swab dampened with DI water Allow the O rings and chip interface to air dry Reinsert the O rings into the chip cartridge LabChip Dx User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 186 Troubleshooting and Diagnostics This section contains the following topics to help troubleshoot problems with the LabChip Dx software e Diagnostics e Searching for Events in the Events Tab on page 191 e Viewing Current Events in the Events Tab on page 192 e Error Messages on page 193 e Troubleshooting Assay Pr
133. er Technical 2 Laser or detector failure Support see page 2 3 Laser interlock switch failure 4 Bad or jammed focus motor P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 196 Chip has Expired Warning Message Chip has expired Please install new chip Possible Causes Recommended Actions Chip has already been Replace the chip with a new chip Prepare and reprime used to process the the new chip as necessary maximum number of samples primes Chip Expiration Date has Replace the chip with a new chip Prepare and reprime been reached the new chip as necessary HV Check Failed Warning Message HV check failed Possible Causes Recommended Actions 1 Dirty electrode block 1 Run the Current Leak Diagnostics test see 2 CI hip page 186 If test fails clean o rings and electrode SE block see page 185 2 Re priming can sometimes clear chip clogs Eject the chip drawer push the drawer back in and restart the run See the LabChip Dx Assay User Guide for troubleshooting 3 If the problem is not resolved contact Caliper Technical Support see page 2 P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 197 Current Leakage Check Failed Warning Message Current leakage check failed Possible Causes Recommended Actions Dirty electrode block Clean the O rings se
134. es Inc Instrument Safety 9 Laser Safety WARNING AA BRIGHT LIGHT HAZARD Caliper LabChip Dx Instruments contain Class 3B laser diodes The LabChip Dx is classified as a Class 1 device because the lasers are appropriately enclosed embedded and indicated with Warning labels Complies with IEC 60825 1 1993 A1 1997 A2 2001 Class 1 Laser Product 635 nm visible red laser source 10 mW maximum continuous CW WARNING e Use of controls or adjustments or performance of procedures other than those specified herein may result in hazardous radiation exposure e NEVER remove back side or front panels of the instrument while the laser is powered Panels which if removed could lead to laser exposure are marked with the labels shown below e These panels are intended to be removed for service only by qualified personnel they are not intended to be removed during operation or for maintenance by users The only removable maintenance panel is the lower panel at the back of the instrument which can be removed to access the back of the robot if cleaning is necessary P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Instrument Safety 10 Electrical Safety The LabChip Dx is powered by a UL CSA VDE approved 100 240 VAC 50 60 Hz input 5 15 24 VDC output power supply Additionally the LabChip Dx High Voltage circuitry is current limited to non hazardous levels Users should observe the
135. etailed description of the event or error that occurred Viewing Past Events in the Events Tab All events and errors that have occurred during the screening of previous jobs or batches display in fields on the Past Events tab in the Event Viewer Window e On the Event Viewer window click the Past Events tab The Past Events fields display These fields are read only The Past Events tab contains the following fields Time The time the event or error occurred Source The source of the event or error Event Code The event error ID number used by Caliper to troubleshoot problems Description A detailed description of the event or error that occurred P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 193 Error Messages Before a run is started and while an assay is running the instrument firmware and software checks for errors e g disconnected devices bad parameters bad data etc If an error is detected an error or warning message displays in the Run Status Depending on the error the run may continue or be aborted The error or warning message describes the problem and either contains information on how to resolve the problem or directs you to call Caliper Technical Support see page 2 For specific information about an error or warning message click one of the links below General Errors e Device Names is Disconnected e Plate Carrier Motion Blocked
136. ew Well Table View Peak Table View Filter View The views in the Collection pane are synchronized with each other P N 128682 Rev 00 Selecting a graph on the Graph tab automatically selects the same well on the Gel tab Selecting a peak in the Peak Table automatically selects the same peak in the Graph tab and the Gel tab Closing a gel on the Gel tab closes the graph for the well and removes the well data from the Peak Table and Well Table tabs LabChip Dx User Manual Caliper Life Sciences Inc Graph View LI E z LE Ka Le 2 ra Software Reference 97 The Graph view in the Collection Pane is a visual representation of the data from each well as an electropherogram The Graph view contains the Active Data Tab while a run is in progress Use the Overlay Electropherograms Tab and the Electropherograms Tab to view data from completed wells To change the view in the Overlay Electropherograms tab see Viewing Graphs in the Overlay Electropherograms Tab on page 62 To change the view in the Electropherograms tab see Viewing Graphs in the Electropherograms Tab on page 63 Demo DAA Sk 2006 08 14 06 40 09 AT PROT Aur S0 nul AS Phak url 35 nglul LE at a LAS PR Tour 12 5 ngu 16 Aligned Time sec Figure 34 Graph View If Type is selected as an annotation the lower and upper markers are displayed in the graph view with large green arrows labeled LM and UM respecti
137. f the plate that will be used to test the plate settings ne Pichon Teaching Wizard AA andy Las Pete iri HE i y PN UN Cao p plais ian aa Por BAN aa iy re HiH Ci Hef ce Figure 72 Verify a Plate Window The Verify a Plate Window contains the following options and buttons k n Plate Name list Displays the names of the plates that have been created for use in the instrument View Plate Info Opens the Plate Information Window to view add edit or button delete plates from the LabChip Dx software Back button Displays the Teach the X Y and Z Reference Positions Window Next button Displays the Verify Positions Window Cancel button Closes the Robot Teach Wizard without saving changes to any positions P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 155 Verify Positions Window Use the Verify Positions Window to verify the taught reference position and the settings for the plate selected in the Verify a Plate Window hr Pob T Peri Pid bias E ary The ag Kan ay a er ed pote Leeder ao beter ein IT ak muse Be ad plate oc p nal n ho famhokia T Bokt mhi gia CT sl biais Cale Co CU A D pla bi meme care Ba ka errant of es Slee ih Pl o a poli delire Listes aka qij the me poesie Geer Mer eh cale GA a Line T Ck ai Ta lation E then iaie on oe pareari iiem es bec a Pa paa deters Hess heed f cee T oO thw lebi jaie oe ot pakana coy go bak ej ey he
138. following WARNING AA Do not open the instrument enclosure There are no user serviceable parts inside The wall outlet or the power cable connector on the back of the instrument should be accessible after the system s installation to enable trained service personnel to safely disconnect power from the system during servicing The computer supplied with the LabChip Dx instrument has internal lithium batteries Batteries should not be incinerated WARNING Danger of explosion if battery is incorrectly replaced Replace only with the same or equivalent type recommended by the manufacturer s instructions Power Cord Selection United States and Canada The LabChip Dx instrument is shipped with a NEMA 5 15 IEC 320 power cord If the power cord needs to be replaced substitute power cords must be UL Listed Type SJT or equivalent minimum No 18 AWG 3 conductor with ground conductor that for safety considerations should never be disconnected or defeated The cord s plug to the wall must be a three pin grounding type connector with a NEMA 5 15P 15A 125V plug configuration The cord s connector at the unit must conform to requirements for an EN 60 320 IEC 320 Standard Sheet C13 connector The equipment is intended to be plugged into a standard NEMA 5 15R receptacle in the wall P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Fuses Instrument Safety 11 International All power cord sets mu
139. g 197 Cleaning the Chip Cartridge 185 198 Current Leakage Check Failed 197 Device Name is Disconnected 194 Excluding apeak 36 Focus Failed 195 Home Timeout 194 HV Check Failed 196 Move Timeout 195 Plate Carrier Motion Blocked 194 Pressure Leak Detected 195 Software 199 Troubleshooting Assay Problems 198 U Upper marker 217 USB cable 176 USB device unplugged 199 User Standard 133 V Validation menu 88 Valley to Valley 133 Ventilation 182 Verify Plate 32 Version assay 122 View MENU 88 Viewing Current Events in the Events Tab 192 Viewing Graphs in the Electropherograms Tab 63 Viewing Past Events in the Events Tab 192 VICWS oa 6484 64 at crise 97 Filter View 115 Gel VIeW 105 Graph View 97 hiding views 60 Peak Table View 110 showing and hiding 60 Well Table View 109 Voltage Calibration Test 189 Voltage safety 10 P N 128682 Rev 00 LabChip Dx User Manual Index 229 W Warnings 196 197 Chip has Expired 196 Chip Temperature Warning 197 Current Leakage Chec
140. gle Peak Setting the inflection threshold above the value of the valleys in the slope splits the peak shoulders into separate peaks The higher the inflection threshold the more peak splitting occurs In this example a value of 150 sec splits off both shoulders value of 110 sec only splits off the left shoulder See Figure 31 on page 81 P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Understanding Peak Finding 81 Figure 31 Inflection Threshold Peak Identification Peak identification involves generation of a peak baseline using the Slope Threshold and Baseline Plateau detection of each peak using Slope and Inflection Thresholds and then discarding peaks using the Minimum Height and Minimum Width thresholds This process only occurs between the Start Time and End Time peak find properties The Minimum Height threshold sets the minimum peak baseline to peak apex value needed for a peak to be identified by the analysis The Minimum Width is the minimum left edge to right edge value needed for a peak to be identified P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 82 Software Reference This section describes the windows in the LabChip Dx software Each window description describes the options and buttons on the window and how to open the window This section describes the following windows e LabChip Dx Main Window on page 83 e About LabChip Dx Wi
141. h e Well Table Prints the well table for either all wells in the collection or all selected wells The columns selected for view in the well table are printed Changing the columns selected to view in the Well Table View changes the columns that are printed e Peak Table Prints the peak table for all wells in the collection or all selected wells The columns selected for view in the peak table are printed Changing the columns selected to view in the Peak Table View changes the columns that are printed e Exclude Marker If selected markers are not printed Page Option Select the page orientation either Portrait or Landscape P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 147 Print Window Continued Well Option Select the wells to be included in the printout either Entire Collection or Selected Wells Preview button Displays a preview of the selected options Add Border Option If selected the Well Table and Peak Table will print with a border between each column and a border below the column header Add Well Name as Header If selected a well header containing the plate well and sample name for the well is printed before each set of peaks in a well This option is only available if Peak Table is selected Column Header Specifies where to print the column headers which identify each column in the Peak Table This option is only available if Peak Table is
142. half as far apart as the ladder markers they are assumed to be the wrong peaks and analysis of the well stops producing the error Marker peaks not detected P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 56 Aligning or Unaligning the Marker Peaks Continued In DNA assays the height of marker peaks is assay dependant Ladder peaks are analyzed to calculate a marker peak threshold that is used to locate the marker peaks in the sample wells If the marker peaks found using this calculated method fail to align with those of a sample the LabChip Dx software will use the minimum peak height threshold setting instead if this value is lower than the value for the marker peak For example the calculated threshold might be too high to find the sample s markers if they happen to be very small for some reason Either no markers will be found or the wrong peaks will be assumed to be markers and these may not align with the ladder markers Consequently the software attempts to use the minimum peak height threshold that if it is set low enough will identify the real markers allowing the sample to align If you get unexpected peaks in the ladder analysis or the markers have been set incorrectly you can manually exclude peaks or set a peak to be used as a marker NOTES e Excluding a peak or manually setting a peak to be an upper or lower marker for a DNA assay can cause errors with analysis e You can
143. he properties that can be set for the Electropherograms tab P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 103 Graph View Properties To view the Properties for the Electropherograms Tab or the Overlay Electropherograms Tab click the Properties tab on the right side of the Graph View Properties roperies GP Annotation A Set Font Annotation Set Font Type IH Arnotation2 i Type IH Nona iH AnncstionZ TE lca i E FA Peak Annotation Legend TT Peak Annotation Legend paaa LE Wel Annotation Mons iH 44 Show Data Points la Data Points Show Peak Baselines L Show Paak Basatnes L Or Annotate Expected Peaks Orly Annotate Expected Peaks Sample Name Color Graph Selected Gale Cnty i DHA Marker 77 E Sample Name Coy Po Ladder 12 Ladder 1 4 Ladder Plank Phix174 EsuRl Pi X Ade Scale E BE Cline CSi AX bois Sole Grid Sye E Time See Data Legend Sa ir Grd Sle ES ki of Se Figure 38 Electropherograms Properties and Overlay Electropherograms Properties This window contains the following options Maximum Graphs Specifies the maximum number of graphs displayed on the per Page Electropherograms Tab If more than the maximum are selected use the scroll bar on the right side of the tab to scroll through the graphs Only displayed when the Electropherograms tab is selected Annotation
144. he slope minimum must be below to trigger a splitting of the peak As the threshold is increased more peak splitting occurs For details see Understanding Peak Finding on page 76 Lab on a Chip Ladder FPluorescance The generic term for a microfluidic product signifying a chemical process or material movement taking place on a microchip In contrast to analysis in a standard laboratory that relies on human intervention at several stages to manipulate or observe samples and record results the self contained lab on a chip represents an almost hands free technology A ladder well is located at the bottom right of the chip after the ladder has been loaded this well also functions as a waste well The ladder is analyzed first before sample analysis starts The peak sizes and markers defined for the ladder in the assay are assigned consecutively starting with the first peak detected in the ladder If too few peaks are detected in the ladder well analysis stops and an error is generated Peaks appearing above the upper marker do not have to be detected The Peak Table View for the ladder well shows the peak size and concentration set in the Assay Analysis Window Demo DNA Sk 2009 06 14 09 40 09 A 1 Ladder Aligned Time 56c Figure 97 Ladder Graph P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Glossary of Terms 208 Ladder Analysis A ladder is a mix of compounds of known sizes that is
145. icroplate during the assay Some of the channels in the chip are larger than others The larger channels contain buffer During the chip preparation the smaller channels and some of the wells are filled with sieving gel and buffer Bl Figure 1 DNA Chip Schematic After the channels are filled the chip functions as an integrated electrical circuit The circuit is driven by the 7 electrodes in the electrode cartridge that contact solutions in the chip s wells when the chip holder is closed Each electrode is connected to an independent power supply that provides maximum control and flexibility The polymer filling the smaller channels in the chip is designed to sieve DNA fragments by size as they are driven through it by means of electrophoresis similar to using agarose or polyacrylamide gels The sample and sieving buffers also contain a fluorescent dye that gets brighter upon binding to double stranded DNA complex P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Introduction 18 Principles of Operation Continued In the chip each sample is sipped by negative pressure until a sufficient quantity is loaded in the chip The sample is then moved electrophoretically into the central channel As the fragments move down the central channel they separate by size finally passing the laser that excites the fluorescent dye bound to the molecule The software plots fluorescence intensity versus time and produces ele
146. iewer Window to view events and errors that occur during the current run or during a previous run Run Info Opens the Run Info Window to view information about the run Version Change Details Displays the Data File Version Change Details window to view changed versions of the selected open data file Validation Menu The Validation menu contains the following commands Software IQ Opens the Installation Qualification Window to perform the IQ Diagnostics Opens the System Diagnostics Window to run diagnostic tests to verify system operation and performance Reports Opens the Print Validation Reports Window to view or print IQ OQ results P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Window Menu Help Menu Software Reference 89 The Window menu contains the following commands Cascade Displays each Collection in a separate cascading window in the Collection Pane Tile Vertical Displays each Collection in separate side by side windows in the Collection Pane Tile Horizontal Displays each Collection in separate top to bottom windows in the Collection Pane Tabbed Displays each Collection in a separate tab in the Collection Pane The Help menu contains the following commands LabChip Dx Help Opens the Contents Index page for the LabChip Dx Help file About LabChip Dx Opens the About LabChip Dx Window showing the software version number and firmware version number P
147. iginal order The analysis normally labels the upper marker UM and lower marker LM in each sample and in the ladder The labels display in the Type column of the table If the analysis has misidentified the markers the correct marker can be selected manually by right clicking on the peak row to open a shortcut menu of possible peak types for the peak This can also be used to label a peak as Excluded X The concentration of an excluded peak is forced to zero so that it does not affect the total well concentration and the Purity calculation P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 111 Peak Table View Continued Expected Peaks are indicated by the Expected Peak Name in the Type column The output of an exported Peak Table includes only the columns displayed in the Peak Table in the order at export time A Peak Table is exported to a CSV format which can be imported into a program such as Microsoft Excel If the workspace contains multiple collections the data is exported from the active selected collection To show only filtered peaks sort within each well or hide excluded peaks see Peak Table Properties The Peak Table can display the following columns Well Number The number of the well in the same order as the wells were selected in the collection See Selecting the Wells in a Collection Plate Number The number of the plate in the same order as the plates are disp
148. isplay the data To open a new workspace 1 On the menu bar select File gt New Workspace If changes have been made to an open workspace you are prompted to save any unsaved changes A blank workspace opens in the LabChip Dx Main Window To view data see e Opening a Data File e Adding a Collection to a Workspace e Selecting the Wells in a Collection e Modifying Analysis Parameters e Saving and Exporting Assays P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 40 Opening a Data File Open a data file to view the data to compare the data to other data files in the same workspace or to change analysis setting and view the reanalyzed data Data files generated by the LabChip Dx software have a dxd file extension To open a data file 1 P N 128682 Rev 00 Open a new workspace see page 39 or a workspace that already contains compatible data files On the menu bar select File gt Import Data File The Select a Data File Window opens Select the name of the data file to open and click the Open button The selected data file is imported into the open workspace Use Ctrl click or Shift click to select multiple files If desired right click on the data file name in the Plate View or Plate List and select Rename Plate to change the name of the plate in the display If desired select the Rename File to Match check box to change the name of the data file Select the desire
149. issing plate data files when moving workspace files P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 164 Select a Data File Window When you choose Import Data File from the File Menu the Select a Data File window opens as shown in Figure 81 Data files generated by the LabChip Dx software have a dxd file extension Select a Daga File A i LabChip DX Demo Data n Dema DRIA SK S elles cho b ADA A Apple Softeute Update L Broadcom Coeperateon D Business Objects Calpe Le ce E LabChip OK b Arr Sy Data so Dero Data k Det arr Fila nine a Laban Ce Da San oa H Figure 81 Select A Data File Window Select a data file name in the list box and click the Open button or double click a file name to open the data file To select multiple files press and hold CTRL then click each file name To select a continuous block of files click the first file press and hold SHIFT and then click the last file To select all files press CTRL A P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 165 Start Run Window The Start Run window specifies the assay to run the plate type the wells to read the options for the data file auto export settings plate cycles and import options for sample names and expected peaks E i I a L L om du mr x fw oy a di Pur N br miie A N
150. k Failed 197 HV Check Failed Warning 196 Wash button 90 Waste disposal 8 Waste wells 178 Wavelength 182 NEON paha sas des spin 182 Well Depth 32 120 Well Groups aligning 123 Well Peak Find Settings 125 Well Table View 109 adding columns 64 HULA amp 54 oo kee edd eS OS 70 Wells selecting 42 Window menu 89 Workspace 41 85 217 adding collection 41 opening a new workspace 39 printing 68 Saving Workspace Files 31 Workspace Menu 85 X X Margin paa 4b KR Dae wo 32 120 Y Y MANGIN 4 ss roue 32 120 Z Zero baseline 36 58 218 ZOOM a saa 4 4 Oe koe rai ri 60 ZOOM OW cic eo amp oe wpe bee Gaew ee 60 Caliper Life Sciences Inc D y Caliper Caliper Life Sciences Inc 68 Elm Street Hopkinton Massachusetts 01748 TEL 508 435 9500 FAX 508 435 3439 http www caliperLS com
151. keep the Assay Analysis window open LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 55 Aligning or Unaligning the Marker Peaks To perform data analysis for DNA assays the LabChip Dx software aligns marker peaks included in the sample wells with markers from the ladder e To view the raw data without analysis choose Analysis Turn Off Analysis e To re enable analysis choose Analysis Turn On Analysis The default setting for this function is enabled Turning off the analysis displays the data without aligning the markers in the wells and the ladders and without analyzing any of the data al m CC Figure 13 Data with Analysis Off and Analysis On Upper and Lower Marker Peaks for DNA Assays For each DNA sample the upper and lower marker peaks are assigned first and then the data is aligned so that the well markers match the ladder markers in time allowing the size and concentration of the sample peaks to be determined For DNA assays the first peak is assigned to be the lower marker and is then offset to match the lower marker in the ladder The upper marker is then assigned to the last peak in the sample well or to the peak nearest the ladder s upper marker The Upper Marker and Lower Marker are aligned to the ladder markers by resampling the well data in a linear stretch or compression using a point to point fit If the sample marker peaks are either more than twice as far apart or less than
152. ker e Force Upper Marker e Force Expected Peak NOTE Excluding a peak or manually setting a peak to be an upper or lower marker can cause errors with analysis P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 114 Peak Table Properties To view the Peak Table Properties click the Properties tab on the right side of the Peak Table View Properties ve Hide excluded peaks Peaks Displayed _ Expected Peaks Only i Filtered Peaks Only Show All Peaks Weds Desplaryed _ Selected in Gel ta Entire collection Figure 44 Peak Table Properties This window contains the following options Sort within If selected default sorting occurs only within each well rather each well than across the entire table Click a column header to sort the table rows by the column value If cleared uses conventional sorting which mixes together peaks from all wells Clicking the column header sorts in ascending descending original order Hide excluded If selected excluded peaks and unknown peaks are hidden in the peaks Peak Table view Expected If selected only peaks identified as Expected Peaks display in the Peaks only Peak Table Filtered peaks If selected the Peak Table displays only peaks that match the filter only criteria Useful when generating a collection based on a filter whose selection criteria are peak specific such as Area Concentration Purity Expected Peaks and Size
153. l filter that is applied to the raw data The figure below approximates the shape of the filter and shows what peaks may resemble if the filter application is too strong Polynomial Order This setting on the Peak Find Tab determines the order of the polynomial filter used to convolve with the data A polynomial filter is used to filter the data to increase the signal to noise ratio and calculate filter slope information for peak detection The default setting is 6 for 6th order A setting of 4 produces a straighter baseline preventing quick changes in the signal P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Glossary of Terms 214 Rolling Ball Baseline Curve Example The figures below show the effect of changing the size of the ball when using the Rolling Ball Baseline Curve Figure 100 shows a baseline the light blue line generated by a ball with settings of Time Diameter 5 sec and Signal Diameter 100 RFU Figure 100 Rolling Ball 5 Sec x 200 RFU Figure 101 on page 215 shows a baseline the light blue line generated by a ball with settings of Time Diameter 10 sec and Signal Diameter 200 RFU The baseline curve does not follow the signal as closely because the ball is larger Increasing the ball size generates a smoother baseline Either ball dimension can be used to increase the smoothness of the curve but increasing the Time Diameter increases the computation time required to comput
154. layed in the Plate View or Plate List Plate Name The name of the plate defined in the workspace Plate File The name of the original plate data file This name cannot be changed Instrument Name The name of the instrument that was used to run the plate and create the data file Date Time The date and time that the plate data files was created Well Label The row letter and column number of the well A1 H12 for 96 well plates or A1 P24 for 384 well plates Sample Name The sample name defined in the Sample Name File selected in the Advanced Tab on the Start Run Window The Sample name can also be changed in the Well Table View or the Gel View Chip ID The ID number of the Chip used to run the plate P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 112 Peak Table View Continued Barcode The barcode on the plate used in the run Peak Index The index number of the peaks in the sample Marker peaks peaks before the lower marker and peaks after the upper marker are not numbered Peak Number The order in which the peaks were detected for each well All peaks in each well are numbered starting at 1 Migration Time Center The time from injection to the peak apex in seconds Height The value at the apex of the peak minus the local baseline start value Area The peak area is calculated as the sum of the parallelograms of a point to point fit down to absolute zero
155. lected the data for all wells in the plate is exported to one CSV file If not selected the data from each well is exported to a separate CSV file Electropherogram If selected the graph displayed in the Graph View is exported to the specified folder in the selected image format Click the Browse button to specify the desired path for the image file The file names are lt plate name gt _Gel_ lt well number gt The following options are available on the Export window e Entire Collection If selected a separate graph is exported for each well in the collection e Selected Wells If selected a separate graph is exported for each of the wells selected in the Gel View or Plate View or Plate List P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 140 Export Window Continued Gel If selected the gels selected in the Gel View are exported to the specified folder in the selected image format Click the Browse button to specify the desired path for the image file The file names are lt plate names Gel_ lt well numbers The following options are available on the Export window Entire Collection If selected a gel is exported for each well in the collection Selected Wells If selected a gel is exported for each of the wells selected in the Gel View or Plate View or Plate List Single File If selected the selected gels are all included in the same image file Separate
156. lected wells overlaid onto a single graph Figure 21 Printed Overlay Electropherogram P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 8 70 Well Table Choosing this option prints the columns displayed in the Well Table View To change the columns that are printed or the order of the columns change the columns in the Well Table View e Selecting the Add Border check box prints the table with a border around each cell in the table e Selecting the Add Well Name as Header check box prints the well name well label and sample name at the top of the page e Selecting both the Well Table and the Peak Table prints each well on a separate page with the Well Table row at the top of the page and the Peak Table for the well below it ama Pa cum mon Faga fe Pag es 1a a Haba mn j ns mens Mb tn laslas FFE Lies ee im Fiii nn fm pe LL De n prk a assy si pi DT Seea Fi Na EERE si a Da eee See te os LERSE a LT Le a a Tama rab hehe aki Uti La i a a wa LG om ab he hi hpu hyt a i ha EE Hi CAN di OF CHU BEA ra al si kik a a DT aba KALA TG CU GI as LE a ya WG bp Dm i Dal Ga JEN TL m LE ayu NG Tae pii Na Paa is buwa u hi a aya kd Sum pi Ta Tib LEKE aaa Ka bg is hi TET DT ae Dea la BELA ua TED o LE LY a wa LT Sao KA Na a al it r LA 2 we LT Tama Te la CL aid ihm sa si a os wa Tawi ZA Ta LCE iam PA si ii DN ET si Tama D PU anan
157. lection Pane on page 96 e Graph View on page 97 e Graph View Properties on page 103 e Gel View on page 105 e Gel View Properties on page 108 e Well Table View on page 109 e Peak Table View on page 110 e Peak Table Properties on page 114 e Filter View on page 115 Clicking and dragging the borders between the views changes the size of the views in the collection To change the location of the views see Changing the View of the Results on page 58 P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 84 Menu Bar The menu bar is directly below the title bar on the LabChip Dx Main Window Clicking a menu name displays a list of commands to access software functions The LabChip Dx software contains the following menus e File Menu on page 85 e Workspace Menu on page 85 e Collection Menu on page 86 e Analysis Menu on page 86 e Instrument Menu on page 87 e Tools Menu on page 87 e View Menu on page 88 e Validation Menu on page 88 e Window Menu on page 89 e Help Menu on page 89 P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc File Menu Software Reference 85 The File menu contains the following commands New Workspace Creates a new blank workspace Open Workspace Opens a saved workspace Import Data File Opens a saved DNA data file for
158. lectrodes Apply voltage to the chip to move fluid through the chip and drive electrophoretic separations in the chip channels O Rings Create a seal between the chip cartridge and the chip to apply pressure or vacuum to the wells Pressure Port Supplies pressure positive or negative to prime the chip or move samples through the chip Lid Latch Locks the chip cartridge closed High Voltage Interface Supplies DC voltage to the separation channels in the chip via inert electrodes that are immersed in specific wells on the chip There are 6 voltage channels for the LabChip Dx chips HV channels can be run in either constant voltage or constant current mode P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc LabChip Dx Instrument Description 181 Microplate Carrier The LabChip Dx instruments contain a stepper motor driven robot that moves the microplate to be accessed by the LabChip Microplate Microplate Carrier Ladder Vial Bufer Vial Microplate Locator Spring Figure 95 Microplate Carrier Parts Microplate Holds the microplate Carrier Microplate Positions the microplate correctly for access by the sipper on the Locator Spring chip Buffer Vial Contains buffer to be accessed by the sipper on the chip Ladder Vial Contains ladder standards to be accessed by the sipper on the chip P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc LabChip Dx Instrument Description 182
159. les per liter nmol l Concentration is measured in nanograms per microliter ng ul Size is measured in base pairs bp 660 g mol bp is the molecular weight of a single base pair P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Glossary of Terms 211 Molecular Separation Techniques Processes such as gel electrophoresis liquid chromatography and capillary electrophoresis which can separate biomolecular organic substances from other compounds Peak Baseline A local peak baseline is calculated for each peak For isolated peaks the local peak baseline is a straight line connecting the start point with the end point For peaks that are very close together an average baseline is used when the value between the peaks does not drop to the actual baseline The peak baseline for each peak in Figure 99 is shown in a different color Lamo DMA Sk AT AH DNA Marker 25 nga Figure 99 Peak Baselines The peak baseline algorithm starts at the earliest peak and checks whether the end point is within a certain distance from the start of the next peak When a cluster of peaks is detected the peak baseline is the line joining the first peak s start to the last peak s end The start and end points of adjacent peaks in the cluster are averaged to the same point so that no gaps exist between peaks The peak baseline Start Point and End Point can be moved in the Overlay Electropherograms Tab if Show Peak Baseline
160. ll other Expected Peaks of the same size use the same window as the first Expected Peak To overcome this restriction use Expected Peaks of slightly different sizes e g 200 200 1 200 2 etc to apply different windows to the same Expected Peak in different wells Sample Name File Import Errors Any row in the CSV file that does not match the expected format and cannot be interpreted is ignored If none of the rows can be interpreted usually because the first column does not contain the well label the following error message displays No rows found matching format label name comment EP window P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 46 Using Expected Fragments You can track expected DNA fragments EFs You enter the EFs in the Assay Analysis Window Entering EFs in the Assay Analysis Window 1 10 11 P N 128682 Rev 00 Select Analysis gt Analysis Settings on the Menu Bar The Assay Analysis Window opens Click on the Expected Fragments Tab Click in the bottom empty row in the table In the column labeled Size enter the size of the expected fragment in bp In the Window column if desired change the tolerance value to allow for variations in the expected fragment size This value is specified as a percent of the expected size for that fragment The default is 10 Note If there are multiple peaks in the tolerance range the largest peak is labele
161. lls NOTE The software allows you to define upper and lower markers Changing the markers causes quantitative changes in the calibration procedure however and therefore in the entire data evaluation P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 39 Organizing Retrieving and Backing Up Data Files As you work in the LabChip Dx software it s a good practice to organize the LabChip Dx files e Create a folder in which to save the data files If desired each person can save data files to their own subfolder to organize the data files e Save Workspace files in the same directory as the data files to prevent missing data files in the workspaces e Review the files periodically even if only one person uses the LabChip Dx software Archive files you are no longer using but want to save to a backup disk and discard unneeded files Verify there is enough free space on the hard drive to save new plate data files e Each user in the laboratory can specify a particular data file name prefix to easily differentiate data files e A new folder can be created each day to store the data from all runs To automatically create the folders select the Create Daily Sub Directory check box on the Output Tab in the Start Run Window Opening a New Workspace A workspace displays data from one or more plate data files from the same type of assay Each workspace can contain one or more Collections to d
162. mage format This section shows export examples for the following e Peak Table e Raw Data Gel Peak Table ASCII text file that contains the data in all columns in the Peak Table Figure 24 is an example of part of a Peak Table file exported from a DNA assay data truncated for this example B D E F G H 1 Plate Name Sample Name Size BP Conc ing Punty Expected Type Malanty nmol 2 DMATK LP5 F1XLad 7 3 DATE LP5 F1MLad 15 5 15 LM b5 05 4 DNA1K_LPS F1XLad 2514905 1 048493 9919347 25 LOUE 63 16538 5 IDNAIK LP5 F 1XLad 50 50482 0967021 9 337781 50 L0050 2961074 6 ONATK_LPS_F 1XLad 100 0837 0980348 9 274644 100 LO100 14 84132 T DHAIK_LPS_F 1lad 150 4032 0 966136 9 159115 150 LO150 9 752927 B DHATK LPS F1XLad 200 0971 0 960094 5 093032 200 LOZE 7269901 3 CHAR LP5 F1dad 300 4446 0953961 9 025009 300 LOS 4 410849 10 CHATK_LPS_F1XLad 400 3406 0940726 6 899796 400 LUIH 3 56032 11 ONATK LP5 F 1MLad 5004173 0947964 6967327 500 LOS00 2 059916 12 DNATK_LPS F ixLad 699 6755 0993113 682776 FOO LOTO 2 020805 13 ONATK_LPS F 1XLad 649 691 0929357 B 792785 660 LOBO 1 654976 14 ONATK_LPS_F 1XLad 1004273 0922079 6 723387 1000 L1000 1 391143 15 IDMNA K LPS F1XLad 1500 5 1500 UM 5 0505 Figure 24 Exported Peak Table Peaks that are excluded are not exported and are missing in the exported file For example if peaks 3 5 and 7 are excluded when the data is exported into Microsoft Excel peaks 3 5 and
163. me A Well Table is exported to a CSV format which you can import to a program such as Microsoft Excel If your workspace contains multiple collections the data is exported from the active selected collection P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 110 Peak Table View The Peak Table view in the Collection Pane is a text based representation of all the information about each peak To view or hide columns in the Well Table view right click on the column headers in the table The following columns are required by the Seegene Viewer and cannot be hidden Plate Number Well Label Sample Name Migration Time Size Height Conc ng uL and Type The Select Peak Table Columns window displays all available columns in the Selected Columns list Show or hide columns in the peak table moving the column names between the Available Columns list and the Selected Columns list in the Select Peak Table Columns window Drag and drop the column names in the Selected Columns list to change the order of the columns displayed in the Peak Table 16 j Ga ib 7 iT rok El iiti ng imitinn AG Bid aii 2 815 idi EP Li ng a ang ALD 147 So AN T E EP dt Figure 43 Peak Table View The order of columns in the table can be changed by clicking on a column header and dragging the column to the desired position in the table Click a Column header to sort the table in ascending descending or
164. me column Column as the selected well Apply All Displays only if a ladder is selected in the Well field Applies peak Ladders find settings to all ladders in the plate Apply Plate Apply well specific peak find settings to all wells on the same plate P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 129 Expected Fragments Tab Use the Expected Fragments tab on the Assay Analysis Window to enter Expected Fragments for DNA assays See Using Expected Fragments on page 46 for more information After the data is analyzed any peaks matching the expected fragments are shown in the Peak Table View Well Table View Gel View and Graph View if Type is selected as an Annotation in the Graph View Properties Figure 55 Assay Analysis Expected Fragments Tab The Expected Fragments tab contains the following options and buttons Expected Peak Table Lisis the expected peaks for the assay analysis e Size Specifies the expected size of the peak in BP P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 130 Expected Fragments Tab Continued Window Specifies the tolerance window as a percent of the expected size for the peak to allow for small variations in expected peak size Color Displays the color to use to mark the peak in the Graph View or the Gel View Name Specifies a name to display in the Type description for
165. move the boundary between the Peak Table and the Graph view up or down to increase or decrease the size of the Peak Table making it possible to see all of the results at once Right clicking in the Peak Table View of a well of a DNA assay opens a shortcut menu with the following commands e Include Peak only for peak type e Exclude Peak e Force Lower Marker e Force Upper Marker e Add Expected Peak NOTE You can also right click on a peak in the Graph View to view the same menu P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 57 Saving and Exporting Assays Assays are created by Caliper and are included with the LabChip Dx software The instrument and software settings used to run each plate and to analyze the plate are contained in an assay asy file which is selected at the start of the run in the Start Run Window After each well is complete the data is analyzed using the analysis settings in the assay file If the default analysis settings often need to be modified for more optimal analysis a new assay file can be created with the modified settings to be used on subsequent runs To save a modified assay 1 Run a plate with the original assay file 2 Modify the analysis settings for the plate as needed 3 Right click on the plate title in the Plate View or Plate List select Export Assay specify a name and location for the assay file and click the Save button OR
166. mparing two or more gel wells To drag and drop a gel lane click in the header of the lane to be moved and drag the gel lane to the desired location Double click in the Gel view to zoom out to the previous zoom level Gel data can be exported to a graphic file by choosing Export on the File Menu see Exporting Data on page 72 for details If the workspace contains multiple collections data is exported from the active selected collection To change the Lane Width or Gel Contrast Range see Gel View Properties Right Click Menu Right click anywhere in a gel to display a shortcut menu containing the following commands Unzoom Zooms out to the previous zoom level Unzoom All Zooms out completely and returns to the standard view Scale Gel Contrast to this Lane If selected for a lane the minimum and maximum RFU values for all lanes in the collection are set to the minimum and maximum RFU values in the selected lane Scale Gel Contrast to Collection Restores the minimum and maximum RFU values for all lanes in the collection to the default values Only available when Scale Gel Contrast to This Lane has been selected for a lane P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 107 Gel View Continued Remove Removes the sample from the collection Copy Gel Copies all of the open lanes wells to the clipboard in a bmp format Copy Lane Copies the selected la
167. n Window Plate Type Specifies the number of wells in the plate either 96 or 384 X Margin The distance from the outer edge of the plate to the center of well A1 in the X direction Y Margin The distance from the outer edge of the plate to the center of well A1 in the Y direction Plate Height The distance from the bottom of the plate to the top of the plate Well Depth The distance from the top of the plate to the bottom of the well Sip Height The distance from the bottom of the well to the bottom of the sipper when the sipper is positioned to sip sample from the well P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 121 Assay Analysis Window The Assay Analysis window specifies the analysis parameters These settings are used to display assay settings and change the analysis and peak finding parameters to help resolve hard to decipher data To open the Assay Analysis window select Analysis 3 Analysis Settings on the main menu The Assay Analysis window contains the following tabs e Assay Information Tab e Alignment Tab e Analysis Tab e Peak Find Tab e Expected Fragments Tab e Excluded Peaks Tab e Advanced Tab Plate The name of the plate in the workspace Usually the same as the name of the data file that was created when the plate was run unless the plate name is changed after the plate is added to the workspace The following buttons at the bottom of the
168. n Window Run Tab Assay Type Select the type of assay to run The LabChip Dx only supports DNA assays Operator Specifies the name of the operator running the assay The Operator Name is saved in the data file Plate Name Choose the type of plate that will be used in the run Use Barcode check box If selected the LabChip Dx will read the customer applied barcode on the short portrait end of the plate The barcode will be saved in the data file and can be used as part of the name of the data file P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 167 Run Tab Continued Samples Select the wells to be read during the assay Selected wells are blue cleared not read wells are white To select all wells on the plate click the double arrow button in the lower right corner of the plate To select all rows on the plate click the double arrow button at the top left corner of the plate To select all columns on the plate click the double down arrow button at the top right corner of the plate To select a column click the column number at the top or bottom of the plate To select a row click the row letter on the left or right side of the plate Clear specific wells by clicking on the selected well again Sipping Order Select the order in which the wells will be sampled during the assay P N 128682 Rev 00 Select Row wise to sample all wells in each row before proceedi
169. n object blocking the robot motion and the robot motion remove the blockage 2 Robot Motor has failed Restart the instrument If the problem is not resolved contact Caliper Technical Support see page 2 P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 195 Move Timeout Error Message Robot Failure Possible Causes Recommended Actions 1 Robot failure Check for an object blocking the robot motion and remove the blockage Restart the instrument If the problem is not resolved contact Caliper Technical Support see page 2 Pressure Leak Detected Error Message Pressure leak detected Check and clean the O rings at the chip interface Possible Causes Recommended Actions 1 O Ring missing or Clean the O rings see page 185 dirty a Run the Pressure Diagnostic Tests see page 186 If the problem is not resolved contact Caliper Technical Support see page 2 Focus Failed Error Messages e Focus failed due to less than 2 peaks found during horizontal scan e Focus failed due to more than 3 peaks found during horizontal scan e Focus failed due to dry focus marks not found e Focus failed due to error in horizontal scan Possible Causes Recommended Actions 1 Focus nominal starting Run the Optics Diagnostics tests see page 186 osition is incorrect i If the problem is not resolved contact Calip
170. n the Events Tab Events and errors that occurred during the screening of previous jobs are displayed in the Past Events tab in the Event Viewer Window To search for a specific event 1 On the Event Viewer window click the Search Result tab 2 Inthe Events list select Current Past or All 3 In the Search Text box type a search query and click the Search button The Source Event Code and Description fields are searched The search results appear in the Search Result fields The Search Result tab contains the following fields Time The time the event or error occurred Source The source of the event or error Event Code The event error ID number used by Caliper to troubleshoot problems Description A detailed description of the event or error that occurred P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 192 Viewing Current Events in the Events Tab While a job or batch is running the events and errors that occur during the screening display in the Current Events tab in the Event Viewer Window e Onthe Event Viewer window click the Current Events tab The Current Events fields display These fields are read only The Current Events tab contains the following fields Time the time the event or error occurred Source The source of the event or error Event Code The event error ID number used by Caliper to troubleshoot problems Description A d
171. nd the integrity of each file specified for the software application To run the IQ 1 On the LabChip Dx Main Window select Validation gt Software IQ The Installation Qualification Window opens 2 To view the results of the previous IQ before running a new IQ click the Previous Result button The View Installation Qualification Results Window displays the results of the last 1Q that was run 3 To start the IQ click the Start IQ button The Installation Qualification window displays the tests that are run for the IQ the progress of each test and the Pass Fail status of each test as it is completed 4 To save the results of the IQ click the Save As button specify the desired location and name of the file and click the Save button IQ results are saved as xml files Running Operational Qualification OQ The System Diagnostics window performs an automated Operational Qualification whenever required by your laboratory procedures The System Diagnostics Window displays the tests that are performed on the left side of the window The test results are displayed on the right side of the window After all tests are complete the test report is generated and saved to a file for review printing and documentation purposes See Diagnostics on page 186 for details on running the Diagnostics P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 191 Searching for Events i
172. ndow on page 118 e Add New Expected Peak Window on page 119 e Add Plate Window on page 120 e Assay Analysis Window on page 121 e Auto Export Window on page 134 e Data File Version Window on page 136 e Event Viewer Window on page 137 e Export Window on page 138 e Installation Qualification Window on page 141 e Layout Options Window on page 142 e New Collection Window on page 144 e Plate Information Window on page 145 e Print Window on page 146 e Print Validation Reports Window on page 148 e Rename Collection Window on page 149 e Robot Teaching Wizard on page 150 e Run File Editor Window on page 159 e Run Info Window on page 160 e Sample Name Editor Window on page 161 e Save Workspace As Window on page 163 e Select a Data File Window on page 164 Start Run Window on page 165 System Diagnostics Window on page 172 P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 83 LabChip Dx Main Window Graph View 7 Chip and Run Status Tita dae Wel Table View Peak Table View Filter View and Gel View Figure 32 LabChip Dx Main Window The main window of the LabChip Dx software includes e Menu Bar on page 84 e Chip Status and Run Status on page 90 e Plate View or Plate List on page 93 e Col
173. ne well to the clipboard in a bmp format Analysis Settings Opens the Assay Analysis Window to change the analysis settings Edit Sample Name Opens the Sample Name Editor Window to change the well name or add a comment to the well The comment displays in the Well Table View and in printed reports Rename Plate Opens the Rename Plate window to specify a new name for the plate P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 108 Gel View Properties To view the Gel View Properties click the Properties tab on the right side of the Gel View Pa Auto fa Ce Cortrast Hange i Se 65 1333 Gal Color s Foreground Background Set Lane Label Fort W Show Expected Peaks Show Expected Peaks Legend Figure 41 Gel View Properties The following properties can be set for the Gel view Option Button Function CC Lane Width Sets the width of the Collection column Select Auto Fit to have the software automatically fit all the data or use the slider to manually set the width Gel Contrast Sets the minimum and maximum Gel Band Contrast for the bands Range in each well Use the sliders to change the min and max values Gel Color Click on the Foreground color or the Background color to open the Color window to choose the desired colors for the gel Set Lane Label Opens the Font window to change the font or size of the labels in Font button the gel headers
174. nformation Start Time Specifies the time after the start of a run when the first peak will be detected any peaks appearing before this time are ignored The Gel and Graph views will not plot data earlier than this time End Time Specifies the time after which peak detection stops The Gel and Graph views will not plot data beyond this time Filter Width Specifies the width in seconds of the low pass filter to be convolved with the data The width of this filter should be about 6 samples wide i e 0 1 sec for 60 Hz sampling If this setting is too large peaks will develop spurious side lodes ringing due to over filtering Baseline Specifies a baseline selection parameter for peak finding The signal Plateau is at baseline whenever the slope of the data is less than the slope threshold setting positive or negative for longer than the Baseline Plateau This rejects brief low slope areas such as in between non baseline resolved peaks Polynomial A filter algorithm is used to filter the data increasing the signal to Order noise ratio The data is convolved with a polynomial of this order to produce filter data and a filter slope and decrease the background or baseline noise and or spikes in the signal This value is read only P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 127 Table 1 Plate Peak Find Settings Plate Settings Baseline e None No correction Algorithm
175. ng to the next row A1 A2 A3 Select Column wise to sample all wells in each column before proceeding to the next column A1 B1 C1 Ladders are sipped every 12 wells so some columns will include a ladder in the middle of the column LabChip Dx User Manual Caliper Life Sciences Inc Output Tab Software Reference 168 The Output tab on the Start Run Window specifies the location name and export settings for plate data files dxd created during the run The data file name can include a specific prefix the date the time and the plate barcode For example including the prefix LabChip Dx the barcode the date and the time would create file names such as LabChip Dx_ lt Barcode gt _ 2008 04 24 10 23 48 NOTE If you choose not to use the time of the run as part of the data file name the LabChip Dx software automatically appends 1 72 etc for each subsequent run on the same day a Start Euh A Dura Paes CProgres Fier Caper Lie Scese abg 00 Dont Wi paan day mud dhreci oy _ Copy To Fis img Mc i Hans Pa Haa Dale Wi Time ubo Expo Setinga Sari mp Ca Figure 84 Start Run Window Output Tab Data Path Specifies the location where the data files will be saved The default location is C Program Files Caliper Life Sciences LabChip DX Data Click the Browse button to choose a different location Click the Default button to reset the text box to the defaul
176. ngs in the file The Restore Plate option can be used to return to previous analysis settings Data Points Data points are determined by the data collection rate set in the assay properties Show Data Points is an option in the Graph View Properties that displays the data points used to generate the graph P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Glossary of Terms 205 Data Filtering Before identification of peaks in the fluorescence data can proceed the raw data must be smoothed to prevent the detection of signal noise as peaks For details on the data filtering process see Data Smoothing on page 76 DNA Assay Analysis DNA samples contain two marker peaks outside the limits of the DNA fragment sizes the assay is designed to detect The ladders contain the same two marker peaks The sample data is aligned to the ladder data by matching the peak times of the two markers in the sample data with the same two markers in the ladder data The size of each sample peak is calculated by linear interpolation between the known ladder peak migration time and size using the peak aligned migration time The analysis settings can be changed to perform the interpolation using a local third order polynomial fit to the time instead of the size relationship provided by the ladder The concentration of the sample peaks is calculated using the known area and concentration of the ladder peaks The molarity of each
177. nt plates or different runs Each workspace can contain multiple Collections for viewing the same data in different layouts A Workspace file includes e the links to the plate data files in each collection e the selected wells and arrangement of the wells in the views e the layout selected for each collection P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Glossary of Terms 218 Zero Baseline Selecting this setting in the Peak Find Tab offsets the graphs shown for the individual wells but does not affect analysis The mean of 100 points before the baseline time derived when calculating well noise is used as the zero baseline value All electropherograms produced with the instrument show some amount of background fluorescence By default the LabChip Dx software enables the Zero Baseline function To change the Baseline Algorithm select None Zero Baseline or Baseline Subtraction on the Peak Find Tab Fluorescenc Figure 103 Zero Baseline On EPedi 15X E Fluorescence Figure 104 Zero Baseline Off P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Caliper Life Sciences Inc Product Warranty 219 Caliper Life Sciences Inc Product Warranty l INSTRUMENTS Caliper Life Sciences Inc Caliper warrants your Caliper manufactured instrument s hardware and firmware against defects in material and workmanship for a period of one 1 year from the date of ins
178. ntifying peaks 212 AUS ba oes bow ee eae ey 208 turning on off 55 Analysis Tab 124 Annotation Annotate expected peaks 103 OXE ps EE Oe hee OS 103 ROCK anh bes oR SEE ED E ee as 36 202 ASSAY bbb NABA boc eee es 17 20 57 Assay Analysis window 121 Assay file 202 Assay Information Tab 122 Assay User Guides 20 Assay Voltage 182 CE ea re oe ea TE 122 Comments 122 P N 128682 Rev 00 LabChip Dx User Manual Index 223 Exporting an assay 57 AEI CA od amp eae bee ed 122 Principles 17 Saving an assay 57 StartingaRun 20 TG naa oe hates 122 Assay Analysis Window 121 AUO EXPO sss GB KAGK ee MAKA KA 25 Auto Export window 134 B Backing up data files 39 Barcode 182 Barcode Engine 182 Barcode reader 177 Barcode Test 189 Label position 34 Supported Barcode Types 182 Baseline 36 124 125 202 211 Algorithm 4 4 see dos co 125 Analysis Tab 124 Plateau 36 125 Bracketed ladder 123 2101010 AA APA AN 203 Buffer vial 181 C CaADIGS rss sde 176 Calibration Point 133 Caliper Center for Training and Development
179. o DNA 5K96 waka bro Naa RER ma a i Erore Cobecton Selected Weka Ga D Dis Loan Era DAG ese coule DA i T Eire Ceim Sed Wah Cange F e Becario Fin Hagi 376 Figure 61 Export Window Peak Table If selected the data in the Peak Table View is exported to a CSV file Click the Browse button to specify the desired path and file name for the CSV file P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 139 Export Window Continued Well Table If selected the data in the Well Table View is exported to a CSV file Click the Browse button to specify the desired path and file name for the CSV file Raw Data If selected the raw unanalyzed data from the run is exported e If the AIA Format check box is selected the raw data is exported to a file in the Chromatography Data Interchange Format formerly AIA Include Size Data and Export Single Table are not available e If the AIA Format check box is NOT selected the raw data is exported to a CSV file Click the Browse button to specify the desired path and file name for the CSV file The following options are available Include Size Data If selected the data is aligned to the well s ladder for one file per well or to the first well for a single data file and the size data is included in the exported data If not selected the data is not aligned to a ladder Export Single Table If se
180. oblems on page 198 e Troubleshooting Software Problems on page 199 Cannot Save a File on page 199 Computer Software Lock Ups on page 200 Diagnostics The LabChip Dx software contains a set of diagnostic tests to verify proper operation of the LabChip Dx instrument These tests are not dependant on assay chemistry All tests must pass to ensure the instrument is functioning properly To open the System Diagnostics Window select Validation gt Diagnostics The following procedures are included in this section e Running the Diagnostics Tests e Description of Diagnostic Tests on page 187 e Installation Qualification IQ on page 190 e Running Operational Qualification OQ on page 190 Running the Diagnostics Tests To begin running the Diagnostics tests click the Run Tests button on the System Diagnostics Window The tests run from top to bottom prompting you to load the correct chips or plates as required for each test Follow the prompts As each test is completed the results display on the right side of the window Supplies required to run diagnostics tests e Test Chip A Caliper P N 760453 e Test Chip B Caliper P N 760489 e Test Plate with barcode label To order Test Chip A or B contact Caliper Technical Support see page 2 P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 187 Description of Diagnostic Tests The
181. on Closes the Run Info window P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 161 Sample Name Editor Window Use the Sample Name Editor window to specify names for the samples in the plate and to view add edit or delete expected peaks Sample Names can be exported to a CSV file to be re used in other workspaces or for other plates To open the Sample Name Editor window choose Tools gt Sample Name Editor on the LabChip Dx Main Window or click the Edit button next to the Sample Name File text box on the Advanced Tab in the Start Run Window after selecting the desired Sample Name File Sample Name Edzor Apk to Creme DINA Sk 200940614 09 40 08 KA Edi Expected Peaks Expected Peaks Windosdgii Care Mana Laser 142 Leija 14 Ladies Hlan Phl Anal 125 nad Phil ef 125 ngid Phat TA 750 nga 100300500700 101010 10000500700 101010 TONO SON TOO 181010 TZR TH 110 10 THA eS 101010 PEA MIM 101010 Blain SOO ba SON 3000 ba mi F0 150 TMi 64554 PEL ES ol REF Ba 1 na Pa G S320 14 PG bp 19 bp DRA Make 25 regal Didi by Ca Tr kai F lagare Er dark Se Wiel Blank 243 Well Figure 79 Sample Name Editor Window Edit Expected Peaks check box If selected displays the Expected Peaks and Window columns The following columns display in the Sample Name Editor window Column Description Well Label Displays the
182. on The path and name of the file displays in the text box To use a file to supply the Expected Peaks click the Browse button next to Expected Peaks File select the name of the csv file that contains the expected peaks and click the Open button The path and name of the file displays in the text box See Using Expected Fragments on page 46 for more information To use a file to supply the Excluded Peaks click the Browse button next to Excluded Peaks File select the name of the csv file that contains the excluded peaks and click the Open button The path and name of the file displays in the text box Click the Start button to start the assay A new workspace opens to display the data See Monitoring the Run on page 27 for information about viewing data during the run P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Operation 25 Selecting the Auto Export Settings The Auto Export settings specify which views to automatically export at the end of each run and specifies the format for each view Click the Auto Export Settings button in the Output Tab on the Start Run Window to open the Auto Export Window The Peak Table Well Table and Raw data are always exported for compatibility with the Seegene Viewer To select the desired views to export 1 P N 128682 Rev 00 select the check boxes next to the views to export Selecting Export All selects all check boxes To change the loc
183. ooting and Diagnostics 200 Computer Software Lock Ups lf a computer or software lock up occurs 1 2 P N 128682 Rev 00 Try to exit and then re launch the LabChip Dx software If this is not successful exit the application using the Task Manager a d Right click in the desktop menu bar and select Task Manager Click on the Applications tab While holding down the Shift key select all running applications Hold the Ctrl key and click End Task If the Task Manager cannot be accessed try one or all of the following Press the Ctrl Alt and Delete keys on the keyboard simultaneously Perform a hard reboot by turning off the computer and then restarting it Power cycle the LabChip Dx instrument Contact Caliper Technical Support see page 2 LabChip Dx User Manual Caliper Life Sciences Inc Tips and Shortcuts 201 Tips and Shortcuts This section describes the shortcuts and actions that can be performed in the LabChip Dx software by clicking right clicking etc Single Click e In Plate View Selects or de selects a well e In Gel View Selects a well and displays the graph in the Graph View e In Well Table View Selects a well displays the graph in the Graph view and selects the well in the Gel view e In Peak Table View Selects a peak displays the graph in the Graph view and selects the well in the Gel view Ctrl Click e In Gel View Overlays second and subsequent well da
184. ort Plans Caliper offers a full range of services to ensure your success From our original factory warranty through a comprehensive line of customer support plans Caliper offers you Field Service Engineers and in house Specialists who are dedicated to supporting your hardware software and application development needs Call 508 435 9761 Fax 508 435 0950 Email techsupport caliperLS com Our programs can include such useful services as e Preventive maintenance e Diagnostic servicing performed on site by Caliper field service engineers or remotely via Technical Support e Validation performed on site by Caliper field service engineers e Extended use of the Caliper Technical Support Center e Software updates e Parts labor and travel expense coverage e Other customized services upon request Training For Your Product FCC CE Contact the Caliper Center for Training and Development for information about the availability of training courses for your product Call 508 497 2634 Fax 508 435 3439 This device complies with part 15 of the FCC United States Federal Communications Commission Rules Operation is subject to the following two conditions e This device may not cause harmful interference and e This device must accept any interference received including interference that may cause undesired operation This device complies with all CE rules and requirements P N 128682 Rev 00 LabChip Dx User Manual
185. othing the data signal applying the selected baseline algorithm identifying the peak baseline detecting peaks within the smoothed signal and discarding peaks failing to meet user specified thresholds This process is controlled by the Peak Find analysis parameters selected in the Assay Analysis Window on the Peak Find Tab Data Smoothing The raw data signal is initially smoothed using the Filter Width and Polynomial Order parameters This filter removes high frequency noise from the data by performing a local weighted averaging of the data using a Savitzky Golay convolution kernel The filter width defines the range over which the averaging takes place a 0 3 sec filter width averages over 0 3 seconds of data or more precisely the data is convolved with a weight array that is 0 3 seconds wide At the typical sampling rate of 60 HZ this kernel is 0 3 60 18 1 19 points wide forced to be odd by algorithm requirements Using a very large filter width to try and reduce signal noise will have an adverse effect on sharp peaks Typically the over filtering of sharp peaks causes side lode artifacts to appear The sample shown below has both sharp peaks and signal noise particularly near the end of the trace Removing the noise in the broad tail of the upper marker by setting the filter width to 1 0 sec causes the early sharp peaks to lose height and become distorted T z ka Filter Width 0 1 sec Filter Width 1 0 sec HAN
186. ow on page 153 e Verify a Plate Window on page 154 e Verify Positions Window on page 155 e Finished Window on page 156 e Verify All Target Positions Window on page 157 e Verify All Target Positions Correct Window on page 158 P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 151 Welcome Window The Welcome window is the first window displayed in the Robot Teaching Wizard Fab Testing Year ry AA ch aid Figure 69 Robot Teaching Welcome Window The Welcome Window contains oe raa Verify Target If selected clicking the Next button displays the Verify All Positions Only Target Positions Window check box Restore Default Displays a Restore prompt to reset the reference positions to button the factory default values Next button If Verify Target Positions Only is not selected displays the Teach Robot Window If Verify Target Positions Only is selected displays the Verify All Target Positions Window Cancel button Closes the Robot Teach Wizard without saving changes to any positions P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 152 Teach Robot Window The Teach Robot Window displays instructions on preparing the robot for teaching the reference position Tend Aoba Tis ini nep n aching iha ooh pasion ac So bei Be iamos paion Figure 70 Teach Robot Window The Teach Robot Window cont
187. ow contains the following options and buttons Option Button Left Right buttons Moves the plate holder toward the left or right side of the instrument The distance the plate holder moves is set in the Step Size option below the buttons Forward Backward Moves the plate holder toward the front or back of the buttons instrument The distance the plate holder moves is set in the Step Size option below the buttons Up Down buttons Moves the plate holder up toward the top of the instrument or down toward the bottom of the instrument Step Size options Select the desired distance to move the plate holder each time the positioning buttons are clicked Use the Step size buttons under the positioning buttons for the axis that is being moved Set button Sets the current position of the plate holder as the reference position Test button Moves the plate holder to verify that the reference position is set properly If set properly the sipper moves into the hole on the plate holder without hitting the sides of the hole P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 154 Back button Displays the Teach Robot Window Next button Displays the Verify a Plate Window Follow the instructions in the window before clicking the Next button Cancel button Closes the Robot Teach Wizard without saving changes to any positions Verify a Plate Window Use the Verify a Plate Window to select the name o
188. per Life Sciences Inc Glossary of Terms 203 constrained to never cross into the signal therefore the baseline curve is never greater than the signal and will not produce negative signal values when subtracted from the signal See Rolling Ball Baseline Curve Example on page 214 for more information For isolated peaks the local peak baseline is a straight line connecting the start point of the peak with the end point For peaks that are very close together an average baseline is used when the value between the peaks does not drop to the actual baseline Figure 96 shows baselines established for DNA assay peaks based on the settings in the Peak Find Tab DNA peaks are determined on a peak by peak basis Demo DNA Sk 2009 08 14 9 40 09 B DNA Marker 25 nglu Figure 96 Baselines Bubble If the tip of a pipette is not positioned below the liquid level in the well bubbles can result If a large bubble forms at the bottom of a well remove the sample from the well pipette the sample back into the well and continue with the loading procedure Clipboard A temporary storage area that contains information you have cut or copied You can paste the contents of the clipboard into other programs provided that program supports that type of information Information remains on the clipboard until you replace it with the information from another cut or copy command P N 128682 Rev 00 LabChip Dx User Manual Caliper Life S
189. r while the LabChip XT software is running If a run is in progress the run may be aborted and data may be lost Computer Hibernates or Sleeps During Run The LabChip XT instrument will disconnect and the data for the current run will be lost if the computer enters Hibernation mode or Sleep mode during a long run The computer Power Options are properly configured to Never sleep or hibernate when it is configured by Caliper Do not change the computer Power Options Cannot Save a File File has been saved as a Read Only file If you editing an existing file verify the file is not Read Only If it is the title bar shows Read Only after the file name Read only files can be edited and saved with a new name or in a new location with the same name but cannot be saved over the original file Hard drive is full Verify there is sufficient free space on the drive to save the file If not clear some space on the hard drive You can archive files that you are not using to another location If you do have sufficient space try closing all open applications and then turning off the power to the computer After a few seconds restart the computer open another file and try resaving it to verify the Save function is working properly LabChip Dx software is corrupted Reinstall the software If the problem persists contact Caliper Technical Support see page 2 P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Troublesh
190. rams Tab 101 PUNU AA PAA 69 selected gels only 103 Standard curve 36 216 Graph selected gels only 103 Graph View 97 Grounding 182 H Hard Drive full 199 Hardware Diagnostics 206 Heat Emission 182 Help menu 89 Hibernate 199 Hide excluded peaks 114 Hiding views 60 High Voltage safety 10 Home Timeout 194 How the Software Analyzes DNA Data36 HV Check Failed Warning 196 Identifying peaks 212 IPON kaawa kami ha KA 40 43 129 131 data file 40 Excluded Peaks button 131 Expected Peaks button 129 Caliper Life Sciences Inc sample names 43 Inflection Threshold 80 125 207 Installation Qualification Window 141 Instrument description 174 Instrument menu 87 Instrument safety 7 IQ running 190 L LabChip Dx main window 83 LabChip Kit assay description 17 Label position 34 Lab on a Chip 207 Ladder 36 124 207 208 Alignment tab 123 concentration 124 Ladder Analysis 208 ratio 124 Ladder vial 181 Lane Width
191. re Range 182 HAO a eee ea 68 Print Validation Reports Window 148 Print Window 146 mani AA AA 68 electropherogram 69 e AAO PAPA PT 68 peak table 71 well table 4 4880 70 Workspace information 68 Properties Gel View 108 Graph view 103 Peak Table 114 PUNCH TeSt sawa sawa css 189 Punch test 32 Puncture test 32 Q Quantitation 17 36 133 R Raw Data exporting 73 Read Only files 199 Reagent Expiration 90 Reanalyzing data 66 Red Laser sama aa RAANG 177 Rename Collection Window 149 Reports printing 68 Restore Plate button 121 Revision data file 67 RFID TAGs 466845 6856 woes an 178 RF lag Test naana naaa 187 BUN ss 20 22 28 29 208 ADOrUNG sl siens cit 28 assay principles 17 CON NUNG aaa ss 29 Caliper Life Sciences Inc Og au AE AA kos 208 monitoring the run 27 running an assay 22 Starting a run 20 Run button 90 215 Run File Editor Window 159 Run Info Window 160 RUN SIAIUS 3254242 2 NG AGA 90 Run Tab Start Run Window 166 S SO eq dane gees es 7 8 9 10 11 chemical 8 electrical
192. rom the currently open collection To open the New Collection window select Collection gt New Collection on the LabChip Dx Main Window New Collection a Create a new colection using SE Nene ae Lance Figure 64 New Collection Window The following options are available Blank Collection Opens a blank collection that does not contain any data The new collection will use the same settings as the last saved collection of the same assay type The current collection settings are automatically saved in a blank collection template in the current user s Documents and Settings folder on the local computer These preferences are applied when a blank collection is created User preferences are saved by assay type Current Collection Opens a blank collection and applies the settings from the currently open collection as a template Assay Type DNA Specifies the type of data files that can be imported into the collection Only enabled if this is the first collection and no plates have been imported into the workspace If a workspace already contains a collection all new collections are the same type as the existing collections Name Specifies the name of the new collection P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 145 Plate Information Window Use the Plate Information window to view add change or delete plate names and measurements To open the
193. row letter and column number of each well Wells are ordered by column if the Order by Column check box is selected If the window is opened from the Start Run Window the wells display by column or well depending on the selection on the Run tab If a plate is running when the window is opened the wells display by column or well based on the sip order of the currently running plate Sample Name The sample name for the sample in the specified well Type a new name to change the sample name P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 162 Sample Any comment to be associated with each well of the plate Comment Displays in the Well Table View Expected Peaks Displays the Expected Peaks The Expected Peaks are also displayed in the Expected Fragments Tab on the Assay Analysis Window Only displays if the Edit Expected Peaks check box is selected Window Specifies the tolerance window as a percent of the expected size for the peak to allow for small variations in expected peak size Only displays if the Edit Expected Peaks check box is selected The following buttons are located at the bottom of the Sample Name Editor window Banon Bomseoooe o Import Imports a sample name file csv into the Edit Sample Names window Exports the current sample names and comments into a csv file See Blank 96 Wells Clears the sample names in the window and creates a new sample nam
194. s specified in the Expected Fragments Tab To display the expected peak indicators in the Graph view 1 Click the Properties tab on the right side of the Graph view to open the Graph View Properties 2 To view the size of all expected peaks select Size in one of the Annotation list boxes Demo DNA 5k 2009 08 14 09 40 09 A5 PhiX1 4 BsuRl 125 ng ul LM 1500 1000 Ti O Ti an a O 3 LL 500 EPP 34P271B10 EP72 EP118 14 n Time wa Figure 10 Expected Fragments P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 49 Viewing the EFs in the Gel View Expected Fragments are indicated in the Gel View by colored lines The color of the line matches the color specified in the Expected Fragments Tab To display the expected peaks in the Gel View 1 Click the Properties tab on the right side of the Gel View to open the Gel View Properties 2 Select the Show Expected Peaks check box To display the legend that identifies the colors and sizes of the expected peaks 1 Click the Properties tab on the right side of the Gel View to open the Gel View Properties 2 Select the Show Expected Peaks Legend check box CE PERLAS PP pry Le Figure 11 Expected Peaks Legend Viewing the EFs in the Well Table A column is added to the Well Table for each Expected Peak entered in the Expected Fragments Tab The column displays the property selected in
195. s Window and then click the Peak Find Tab In the Well drop down list select the well number that you want to change the settings for Change the settings at the bottom of the window under Well Peak Find Settings to change the settings for the selected well Click the OK button to save the setting reanalyze the data and close the window Click the Apply button to apply the changes and reanalyze the data but keep the Assay Analysis window open LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 53 Adding a Peak You can manually add a peak in a region where a peak has not been identified 1 Inthe Graph View right click at the top of the area where the peak is to be added The area must be outside any previously identified peak and the cursor must be an up arrow 2 Select Add Manual Peak from the shortcut menu A new peak centered at the selected location is created 3 If necessary adjust the Peak Baseline Excluding a Peak You can exclude any peak or fragment from being used in the analysis To exclude a peak 1 Inthe Peak Table View right click on the peak to be excluded 2 Select Exclude Peak from the shortcut menu The Type for the peak changes to X excluded and the value is not used in the analysis 3 Right click on an Excluded Peak in the peak table and select Include Peak to include the peak in the data analysis OR 1 Inthe Graph View right click near the top of the peak to be exclu
196. s expected The software settings in the Peak Find Tab can also cause peaks to be undetected which can cause errors Additionally manually excluding a peak see page 53 from analysis in the Peak Table View or changing the start or end times for a run can cause errors with the peak find algorithm See Error Messages on page 193 for a list of errors and tips on preventing or resolving errors P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 93 Plate View or Plate List Plate View The Plate View or Plate List View displays on the lower left side of the LabChip Dx Main Window The Plate View or List View displays the data files in the open collection and enables you to select specific wells of microplate data Click the tabs at the bottom of the view to switch between Plate View and List View The Plate View displays a graphical representation of the microplates in the collection see below and indicates selected wells filtered wells and wells with errors Wells included in the collection are colored blue The wells selected to view in the Gel View and Well Table View are outlined in black Select the Plates tab at the bottom of the Workspace pane to see the Plates view 1 Demo DNA 5k 2003 05 14 5 40 05 sli 2 3 4 5 6 7 8 9 10 11 12 H PR 1000000000 000000008800 1000000000 BU 7 35456 7 5 Se A B Cc D E F G H To select the wells to view in the Coll
197. s is selected in the Graph View Properties Peak Height The value at the apex of the peak minus the local baseline start value P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Glossary of Terms 212 Peak Identification From the smoothed data peaks are identified using a hill climbing algorithm running along the smoothed data and its first derivative The peak baseline is drawn across the peak bottom by taking local averages Just outside the peak start and end points and connecting the two points The peak height measured from the apex down to the peak baseline must exceed the minimum peak height specified in the Assay Analysis Window for the bump to be identified as a peak For details see Understanding Peak Finding on page 76 The peak start end and baseline can be viewed in the Graph View by selecting the Show Peak Baselines option in the Graph View Properties The area of each peak is determined by trapezoidal integration of the peak signal between peak boundaries and above the peak baseline Point to Point Fit This curve fit is composed of line segments between each pair of data points that are used to interpolate data between the points P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Glossary of Terms 213 Polynomial Filter The first step the software takes in analyzing the raw data is to apply Data Filtering Data filtering is performed by means of a polynomia
198. s the New Collection Window where you choose whether to create a new Collection from a Blank Collection or the Current Collection Rename Collection Opens the Rename Collection Window to rename the currently selected Collection Delete Collection Deletes the current Collection Layout Opens the Layout Options Window to change where tabs are displayed by default on the main window Analysis Menu The Analysis menu contains the following commands Turn On Off Analysis Toggles analysis on and off When analysis is on the data displayed in the main window uses the analysis settings in the Assay Analysis Window When analysis is off the raw unanalyzed data displays Scale to Sample Peaks Scales the view to the minimum and maximum X values of the current sample peaks Marker and or system peaks are ignored Scale to All Peaks Scales the view to the minimum and maximum X values of the all peaks including marker peaks and system peaks Analysis Settings Opens the Assay Analysis Window to choose analysis parameters for the selected plate These settings are applied to all wells in the microplate Use these settings to change the analysis and peak finding parameters to help resolve hard to decipher data Standard Curve Opens the Standard Curve Window to view the ladder as a curve with a point to point fit P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 87 Instrument Menu
199. sample peak is calculated using the sample concentration the DNA fragment size in base pairs attributed to the peak and the known molecular weight of the DNA base pair Electrokinetic Forces Electrokinetic forces are used to move switch mix and separate the nucleic acid samples Active control over voltage gradients directs the movement of materials using the phenomenon of electroosmotic flow or electromigration Electroosmotic Flow A phenomenon that results from an electrical double layer formed by ions in the fluid and surface electrical charges immobilized on the capillary walls When an electric field is applied the bulk solution moves towards one of the electrodes This phenomenon can be used to move fluids through microfabricated channels P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Glossary of Terms 206 Electrophoresis A technique of separating molecules on the basis of their mobility An electrical potential is applied across a capillary containing a sample in a fluid medium Positive molecules migrate towards the cathode and negative molecules migrate towards the anode at different speeds depending on their electrophoretic mobility End Point The peak find algorithm looks for a leveling off when the value of the slope is less than the value set for the slope threshold This is marked as the end point of the peak End Time This setting determines the time after the start of a run befor
200. settings can be changed after the run is complete or when reanalyzing a previously saved data file P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 52 Changing the Peak Find Parameters After data filtering the peak find algorithm locates the peaks and calculates the local peak baselines The algorithm begins by finding all the peaks above the noise threshold to determine the baseline after which any peaks below the noise threshold are rejected A local baseline is calculated for each peak to allow for baseline drift The following Peak Find parameters can be changed Min Peak Height Min Peak Width Slope Threshold Inflection Threshold Start Time End Time Filter Width Baseline Plateau To change the Peak Find parameters for all wells 1 Select Analysis gt Analysis Settings to open the Assay Analysis Window and then click the Peak Find Tab Change the parameters as necessary at the top of the window Click the OK button to save the setting reanalyze the data and close the window Click the Apply button to apply the changes and reanalyze the data but keep the Assay Analysis window open Click the Apply Global button the apply the settings to all plates in the workspace and reanalyze the data but keep the Assay Analysis window open To change peak find settings for individual wells 1 P N 128682 Rev 00 Select Analysis gt Analysis Settings to open the Assay Analysi
201. sis on page 3b To stop the run before it is complete see Stopping a Run When the assay is complete Run Successfully Completed displays in the Status line If desired remove the plate and or remove the chip To save the analyzed data 1 Select File y Save Workspace The Save Workspace As Window opens with the default workspace name as the name of the data file If desired change the location and or the name of the workspace file and click the Save button Workspace files have a dxw file extension To view or re analyze the data see Data Analysis P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Operation 28 Stopping a Run If you need to stop the run before it is complete click the Stop button Stop A message box confirms that you want to stop the run in progress Stop Run Do you want to stop the run currently in progress Click Yes to stop the run The Status line displays Run Aborted by User Run 5tatus Run Time Left Plate Name 96 PCR Skirted Sip Middle Auto Export Mo Barcode N A Cycles 0 1 Status Run aborted by user Data for any completed wells displays in the LabChip Dx Main Window To continue to read wells from an aborted run see Continuing a Stopped Run P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Operation 29 Continuing a Stopped Run If a run is stopped before it is complete you can restart th
202. ssachusetts 9 Severability Should any term of this License Agreement be declared void or unenforceable by any court of competent jurisdiction such declaration shall have no effect on the remaining terms hereof 10 No Waiver The failure of either party to enforce any rights granted hereunder or to take action against the other party in the event of any breach hereunder shall not be deemed a waiver by that party as to subsequent enforcement of rights or subsequent actions in the event of future breaches P N 104954 Rev 3 Caliper Life Sciences Inc Index A Aborting arun 28 About LabChip Dx Window 118 AC power cable 176 Active Data Tab 100 Add New Expected Peak Window 119 Add Plate Window 120 Adding a New Plate 32 Adding a peak 33 Advanced Tab 133 170 Assay Analysis Window 133 Start Run Window 170 AIA format 75 73 Algorithm Baseline 125 Align marker peaks 55 Alignment OpticS 177 turning on off 55 Alignment Tab 123 AItUde sn es si 182 Analysis 51 86 205 208 212 Analysis menu 86 Analysis On Off 86 Analysis parameters 51 Assay Analysis window 121 DNA assays 205 How the Software Analyzes DNA DAA ght PPT TA PA 36 ide
203. st at the upper right displays the name of each sample and the color assigned to the graph for each sample If only one graph is displayed the Gel View Well Table View and Plate View or Plate List all show the same selected well The gel lanes selected in the Gel View are synchronized with the graphs displayed in the Overlay Electropherograms tab For information on changing the view in the Overlay Electropherograms tab see Viewing Graphs in the Overlay Electropherograms Tab on page 62 See Graph View Properties on page 103 for descriptions of the properties that can be set for the Overlay Electropherograms tab P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 102 Electropherograms Tab Use the Electropherograms tab on the Graph View to view a single graph or multiple graphs in the same tab The Electropherograms tab is not displayed by default To display the tab see Viewing Graphs in the Electropherograms Tab on page 63 Electropherograms Overlay Electropherogram art Des a DORE LUC CE EC Ma z PAPS al l LC i ji ep7 P118 Epas 2346 1110 Figure 37 Electropherograms Tab Each graph displays the data file name and well name at the top of the graph For information on changing the view properties in the Electropherograms tab see Viewing Graphs in the Electropherograms Tab on page 63 See Graph View Properties on page 103 for descriptions of t
204. st be approved by an acceptable accredited agency responsible for evaluation in the country where the power cord set and system will be used The flexible cord must be lt HAR gt Type HO5VV F 3 conductor minimum 0 75 1 mm conductor size 230 volt input Power cord set fittings that is the appliance coupler and wall plug must bear the certification mark of the agency responsible for evaluation in the country where it will be used The appliance coupler must meet the mechanical configuration of an EN 60 320 IEC 320 Standard Sheet C13 connector for mating with appliance inlet on the system The LabChip Dx instruments do not contain any user replaceable fuses Contact Caliper Technical Support see Contact Us on page 2 if blown fuses are suspected Mechanical Safety The LabChip Dx instruments have a three axis robot that moves quickly and can be a pinch hazard Keep the front door of the instrument closed when the robot is moving Keep hands away from the robot when not actually placing microplates in the instrument or changing the ladder and buffer vials Robot access areas are marked with the following warning label Keep hands clear Finch points P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Table of Contents 12 Table of Contents PROTACC Nan GANAN NANANG a 2 INSTFUMENLC Salely 2na ANA AA a E 7 REQUIS MAA AA APP na 7 Chemical ANN paha RAANG SA Adana 8 LAS ST ALENA AA AA TA LA Daan 9 El
205. t Run Window when starting the run LabChip Dx User Manual Caliper Life Sciences Inc Operation 34 Placing the Barcode on the Plate Figure 4 shows the size limits for the barcode label and the location on the microplate where the label should be placed The barcode must be located on the short portrait end of the microplate closest to well A1 If the barcode is not positioned properly the barcode reader will not be able to read the barcode 6 3 mm 6 3 mm white space white space Quiet zone Quiet zone NU H CC a E E a L a A oo ee ee 6G 3 m m Well A1 Chamfer Barcode center and Plate Skint center aligned 3 mm Figure 4 Barcode Label Position P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 35 Data Analysis After a run is complete use the LabChip Dx software to view and analyze the plate data The LabChip Dx software can open multiple data files in the same workspace to compare the data from different plates Analysis settings can be changed for single wells entire plates or all plates in the workspace This section contains the following information P N 128682 Rev 00 How the Software Analyzes DNA Data Organizing Retrieving and Backing Up Data Files Opening a New Workspace Opening a Data File Adding a Collection to a Workspace Selecting the Wells in a Collection Using Sample Name Files Using Expected Fragments Modifying Analysis Parame
206. t connected to power 1000V Ensure all supply Contact Caliper current goes to sink Technical Support see page 2 Plate Sensor TestChipA Check the plate sensor Faulty sensor Contact correctly detects Caliper Technical Support presence and absence see page 2 of a plate Punch Test TestChipA Check that plate robot Misaligned punches has been trained indicate poor robot training properly Teach plate position Contact Caliper Technical Support see page 2 Barcode Any Chip Read barcode on test Plate missing barcode Requires plate Place barcode on plate in Test Plate correct position see page 34 Barcode is not read correctly Barcode reader disconnected or misaligned Contact Caliper Technical Support see page 2 P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 190 Installation Qualification IQ The Installation Qualification IQ verifies proper installation of the LabChip Dx software and verifies no unauthorized changes have been made to the software The IQ can be run whenever required by your laboratory procedures The Installation Qualification can be used to check software installation qualification after routine computer maintenance such as disk cleanup after installing antivirus software or after installing Microsoft service packs The Installation Qualification checks LabChip Dx software registry settings the directory structure a
207. t directory P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 169 Output Tab Continued NOTE Data files should be saved to a local folder on the computer s hard drive Saving data files to a network drive may cause loss of data if the network connection is slow or interrupted Create Daily Sub Directory check box If selected a new directory is created each day in the specified Data Path and all of the data files from that day are saved in the directory The directory name is the current date and the format is YYYY MM DD where YYYY is the year MM is the month and DD is the day Copy To If selected the data file is copied to the specified folder after the run is complete File Prefix Specifies the text for the first characters of the data file name Computer Name If selected adds the name of the LabChip Dx computer to the data file names Project Name The text is added to the data file names Barcode check box If selected the instrument reads the customer supplied barcode on the short portrait edge of the microplate and includes the barcode in the data file name Date check box If selected the current date is included in the data file name The date format is YYYY M DD where YYYY is the year M is the month and DD is the day Time check box If selected the time that the run was started is included in the data file name The time format is H M S where H is the ho
208. ta over original well data in the Graph view for each Ctrl click on a lane in the gel Each well in the graph is shown in a different color e In Well Table view Overlays second and subsequent well data over original well data in the Graph view for each Ctrl click on a row in the Well Table Each well in the graph is shown in a different color Ctrl Shift Click e In Gel View Highlights corresponding well data trace in Overlay Electropherogram view adds trace to overlay if not already included This trace becomes the foreground trace for peak selection Repeat click to undo highlighting Right Click e Right click in any view to display a shortcut menu with available options In the Graph View different shortcut menus display depending on whether the cursor is near a peak or not near a peak P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Apex Glossary of Terms 202 Glossary of Terms After locating a start point the peak find algorithm looks for the first negative slope value and saves the previous point as the apex If the value of the apex is less than the minimum peak height limit the algorithm starts looking for a new peak Assay File Baseline File created by the LabChip Dx software to specify assay and analysis settings such as Ladder and marker sizes and concentrations peak find settings expected peaks and excluded peaks A baseline is established just after the start
209. table below lists the test names descriptions potential failures and the chip required to run the test Chip Compute Memory Check Available memory below 500 MB System may function with lower memory but there is risk of failure if analyzing many plates Resources Disk Space Check Available disk space below 4 GB Risk of losing data as disk space is used Free space on local hard drive System Verify Fan operation Damaged fan Contact Components Caliper Technical Support see page 2 Check chip cartridge Chip Drawer is open Close interlock chip drawer Interlock Switch is defective Contact Caliper Technical Support see page 2 Chip Interface Remove Checks Marker Clog in pressure line Chip Priming and Sipping Contact Caliper Technical pressure lines for Support see page 2 clogs RF Tag TestChipA Reads tag on test chip Bad tag on chip Try another chip with known good RF Tag Problem with RF Tag reader Contact Caliper Technical Support see page 2 P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Troubleshooting and Diagnostics 188 Chip Pressure Leak TestChipA Verifies Marker Pressure leak at O rings Priming and Sipping Clean or replace the O pressures reach set rings see page 185 and points within time clean the chip cartridge limits Measures leak rate from set point Problem with pressure lines Contact Caliper Technical Support
210. tallation but not later than 14 months from shipment subject to the exclusions set forth below and i the warranty for Limited Life Parts as defined below shall be thirty 30 days from the date of installation and ii the warranty for cosmetic surfaces shall be thirty 30 days from the date of installation each a Warranty Period Ongoing service support after the Warranty Period may be available at an additional expense A What is Included during the Warranty Period unlimited emergency on site repair services parts and software updates that affect original functional design specifications their associated labor and travel expenses e unlimited access to Caliper s Technical Support Center which provides troubleshooting repair instruction service dispatching other than for LabChip XT and Twister I replacement part information and shipment e A completed Caliper Field Service Report provides thorough documentation of all maintenance and service work performed by the Caliper Field Service Engineer during an on site visit Documentation is not provided when Caliper provides service via telephone fax or email Any failure of a product to conform to this Warranty shall be corrected by replacing or repairing the affected product or refunding the purchase price as described below in each case at Caliper s option Parts replaced during the Warranty Period will be covered for the remaining term of the original Warranty Period
211. ters Saving and Exporting Assays Changing the View of the Results Copying Information Reanalyzing a Data File Reverting to a Specific Data File Revision Printing Workspace Information Exporting Data LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 36 How the Software Analyzes DNA Data The LabChip Dx DNA Assay Analysis calculates the size and concentration of nucleic acid fragments Results for each well are calculated after all data for that well has been read The data analysis process for DNA assays consists of the following steps 1 Raw data is read and stored by the system for each individual well 2 The data is filtered see Data Filtering on page 205 and the resulting electropherograms of all wells are plotted 3 Peaks are identified see Understanding Peak Finding on page 76 for all wells and are tabulated by migration time The settings of the peak find algorithm can be changed and the data can be reanalyzed after the run has finished See Reanalyzing a Data File on page 66 The peak find settings can be changed for all or only certain wells 4 A sizing ladder see Figure 5 which is a mixture of DNA fragments of different known sizes is run first from the ladder vial The concentrations and sizes of the individual base pairs are preset in the assay and cannot be changed Demo DNA 5k 2009 06 14 09 40 09 A1 Ladder 1600 LM 1600 T 1400 m 1200 a 1000 LA a
212. the Events Tab 192 Viewing Past Events in the Events Tab aa 192 Error MESSAYET AG aaa ANAN a cn en te Mau 193 Device lt Name gt is Disconnected a 194 Plate Carrier Motion Blocked a 194 AA sde at Sd ds Mes pe ec 194 Move MIM QOUT ne an ana res needed EEE ee nn anne 195 Pressure Leak Detected sn La a AA 195 FOCUS KAEO a AA AA AA AA NAA 195 Chip Nas EX DIRS G Le near deniers oue 196 HV Check Failed aaa eee ee er eee 196 Current Leakage Check Failed VV 197 Chip Temperature WarniNO kaaa uns An MA ie Mere 197 Troubleshooting Assay Problems 4 198 Troubleshooting Software Problems 199 Software DISCONNEOI yros EEEE einen dns 199 Cannot sae a Pile sc tart en erin eaten ieee ae ceed bee 199 Computer Software Lock Ups R 200 TIPS ANG SMOMGUUS NAALAGAAN ANAN 201 Glossary OF TEMS NA ANAN AA 202 Caliper Life Sciences Inc Product Warranty cccccceeeeeeeeeeeeeeeeeeeeeeeeeeeeesenes 219 Caliper Life Sciences Inc Software License Agreement 221 Jakol AA KNA AO AA AA AA AA AA 223 P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Introduction 16 Introduction This manual includes general instructions for using the LabChip Dx hardware and software It includes general procedures for operating the system analyzing the data instrument maintenance and hardware and software troubleshooting DNA and Reagent Kits are available to
213. the Property Displayed in Well Table list in the Assay Analysis Window P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Viewing the EFs in the Peak Table Data Analysis 50 Expected Fragments are identified in the Peak Table with the peak name displayed in the Type column PHA TIA EaR 25 ng Ad Ph0C174 BsuRil 725 ngAd PROC174 BsuRil 25 ng Ad Phi6174 BsuR 25 ng ul PX 74 BauRil 25 ng id PHDC174 BsuRl 25 ngAd PROCI 74 BeuFi 725 ngu m Da m pas mrs po PHETT Tal Pe P N 128682 Rev 00 PhiX174 BeuRl 25 ngh TAARAAAAAE 13 11 1383 14 s 15 48 16 02 15 18 15 46 18 15 TA AA 102 48 war 24141 234 47 32076 335 94 337 24 588 13 T 75 Ng 202 FA 278 289 318 629 RIR 036 EP77 044 EP118 065 EP154 087 EP24 1 00 EP271 106 EP281 1 17 EP310 237 EP603 141l EPR7 Figure 12 DNA Assay Peak Table LabChip Dx User Manual 11 87 11 40 1747 21 30 25 01 28 1 2324 Sra TA 4i Caliper Life Sciences Inc Data Analysis 51 Modifying Analysis Parameters Some analysis parameters can be changed in the software to modify the data evaluation for sample analysis The following procedures are included in this section Changing the Peak Find Parameters Adding a Peak Excluding a Peak Merging Two Peaks Changing the Time Window for Analysis Aligning or Unaligning the Marker Peaks These
214. the test report was created the name of the test report log and the location where the test report was saved Test report files can be opened with a text editor such as Windows Notepad Abort button Stops the tests in progress Only enabled when tests are running Limits Report button Generates a report of test limits After the report is generated the Limits Report Generation section at the bottom of the right side of the window displays the date and time when the limit report was generated the name of the limits report and the location where the limits report was saved Print button Prints the last generated report to the default Windows printer Close button Closes the System Diagnostics window The bottom of the window displays a progress bar for the entire set of selected tests and a separate progress bar for the test that is currently running P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc LabChip Dx Instrument Description 174 LabChip Dx Instrument Description This section identifies and describes the hardware components of the LabChip Dx instrument All of the components described in this section are the same for the Dx instrument The LabChip Dx runs DNA assays This section includes the following topics e Front View e Front Panel e Rear Connectors e Optics e Chip Pressure System e Barcode Reader e DNA Chips e Chip Cartridge e Microplate Carrier e Specifications
215. til you reach the maximum magnification the graph will not zoom in any closer To zoom out e Right click in the Graph view or Gel view and select Unzoom to go to the previous zoom setting or select Unzoom All to zoom out to the default view For more information see Viewing Graphs in the Overlay Electropherograms Tab P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Data Analysis 62 Viewing Graphs in the Overlay Electropherograms Tab a LI E a EK Le LL If the Overlay Electropherograms Tab is not open select Collection gt Layout on the LabChip Dx Main Window select the location where you want to display the Overlay Electropherograms tab and click the Apply button The Overlay Electropherograms tab opens Demo DNA Sk 2009 00 14 06 8049 Figure 17 Overlay Electropherograms Tab with Multiple Graphs Data from multiple wells can be overlaid in the same graph for visual comparison Click on one well then hold down the CTRL key and click on the additional wells to view in the graph Each peak graph is shown in a different color and line style with a legend at the top of the window You can remove wells from the overlay by CRTL clicking the corresponding wells the bounding box disappears To add samples to the Overlay Electropherograms Tab Ctrl click on the sample that you want to add in the Plate View or Plate List Gel View Well Table View or Peak Table View Selected
216. tings Well Settings Well Displays the well being edited Select any well or ladder on the plate belonging to the current collection Ladder Read only Displays the ladder used for aligning this well Use Alignment tab to edit New value displays here after clicking Apply Minimum Specifies an override to the Peak Find Settings for Minimum Peak Peak Height Height for the entire plate Specify a valid numeric value to override or clear the field to reset to the Global setting P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 128 Table 2 Well Peak Find Settings Well Settings Minimum Specifies an override to the Peak Find Setting for Minimum Peak Peak Width Width for the entire plate Specify a valid numeric value to override or clear the field to reset to the Global setting Slope Specifies an override to the Peak Find Setting for Slope threshold for Threshold the entire plate Specify a valid numeric value to override or clear the field to reset to the Global setting Use Plate Sets Min Peak Height Min Peak Width and Slope Threshold text Value button boxes to lt Uses plate value gt settings Apply Apply well specific peak find settings only to the well or ladder Well Ladder showing in the Well field Apply Row Apply well specific peak find settings to all wells in the same row as the selected well Apply Apply well specific peak find settings to all wells in the sa
217. umns displayed in the Well Table Fi Plate Home iratramart Hare Lane Sample hame aidara Basi 1 Demo DACA Ske 2000 08 14 084008 CAILABCHIPOXE ADE sa Jar 1258 Damo DECA G_2009 06 1 OHIO CAMABCHIPGKS AB be 1280 1 Chemo DINA Se 2009081 054005 CANLABCHIPGKE A 000k 26 3 1 Demo DHA H ATSR CSSS CAT LA Hie Al EU bes 1255 a 1 Demo DAWA Ek 20080814 O80 CAI LABCHIPGKE An 150 bp 1267 2 1 Dermo DHA Sk 2009 06 14 OMG CAHLABCHIPGS B01 DHA Marker 25 1267 1 Demo DACA Sk 200908 14 054009 CATLADCHIPGKS 60 DNA Make 2 27 13 1 Do DUHA 29 05 18 8 20 05 KATLABTHIPGKE BOI Lila Baha T2 1230 lz 1 Demo DALA Sk 2009 08 14 080508 CALLABCHIPGKE pii lak 127 1 Demo DA Ske 20090814 OMG CANLARCHIPGXS BOE Samin A 27 1 Demo DAA Se 2008 08 054005 CAHLADCHPGXS 806 Sel 1271 F GEG WA NPA N R Figure 42 Well Table View Change the order of columns in the table by clicking on a column header and dragging the column to the desired position in the table Click a column header to sort the table in ascending descending original order Right click in the Plate Name column to open the Rename Plate window to rename the plate Right click in the Sample Name column to edit the well name or copy the well name to the clipboard Right click in the User Comment column to add or edit the User Comment or copy the comment to the clipboard The output of an exported Well Table includes the columns in the order displayed in the Collection Pane at export ti
218. ur 0 to 24 M is the minutes and S is the seconds P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 170 Output Tab Continued File Name Example text box Read Only text box that displays the selected format for the data file name Automatic Export If selected data is automatically exported at the end of each run Select the type of data to export by clicking the Settings button and choosing the desired settings in the Export Window The Peak Table Well Table and Raw Data export options are always selected in the Automatic Export window and cannot be deselected For more information see Exporting Data Advanced Tab Use the Advanced tab on the Start Run Window to select the number of plate cycles the sample saver options the Sample Names file the Expected Peaks file and the Excluded Peaks file a Start Aun A Sa mpa oe Figure 85 Start Run Window Advanced Tab The Advanced tab contains the following options Plate Cycles Specifies how many times to repeat the same assay on the plate Random Selection If selected the instrument will randomly sample the specified percent of wells from the selected wells For example if 10 wells are selected and the Random Selection percent is set to 50 five wells selected at random will be sampled during the run P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 171 Advanced Tab
219. ury Tension dangereuse risque de blessure par lectrocution Crush hazard Risk of body parts hair jewelry or clothing getting caught in a moving part Danger d crasement Faire attention que les parties corporelles les cheveux les bijoux ou les v tements ne soient pas pris dans une pi ce mobile Risk of punciure injury Risque de blessure par piqure Risk of eye injury wear safety glasses Risque de l sion oculaire porter des lunettes de s curit Samoa e a a P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Preface 5 Table 1 Important Symbols Continued Symbol Description Symbole Description Risk of fire Risque dincendie Risk of poison Risque d empoisonnement Risk of explosion Risque d explosion Hazardous fumes manations dangereuses Laser light avoid exposure Risk of eye injury Rayonnement laser viter toute exposition Risque de l sion oculaire Lifting hazard May result in injury Levage dangereux Peut entra ner des blessures Protective ground symbol Symbole de terre de protection L Ground symbol i Symbole de terre Fuse Fusible FT Alternating current Courant alternatif On supply Marche alimentation Off supply Arr t alimentation CE compliance mark Marque de conformit CE Signifies that the unit has passed safety tests for grounding power line transience and current leakage Signifie que l appareil a r
220. used to create a size ruler for the samples Ladder data is used to convert the migration time of each sample peak into a size for the compound responsible for that peak The known sizes of the ladder compounds are supplied in the assay file and can be viewed in the Analysis Tab on the Assay Analysis Window The initial step in ladder analysis is to identify the most prominent peaks in the ladder well and associate each peak with the known ladder sizes The analyzed ladders provide a table of values relating size to migration time Typically the migration time uses the center of the peak in the ladder and the sample Failure to find the correct number of ladder peaks prevents further analysis of the sample wells using the faulty ladder The analysis automatically attempts to use another successfully analyzed nearby ladder on the plate before generating an analysis error The analysis settings can specify which ladder is used to size any particular sample row If more accurate sizing can be obtained by measuring migration times at the start of each peak this option can be selected in the Assay Analysis Window Lower Marker Log Files An internal standard that is added to a sample in a well to assist in determining size and concentration of the sample For DNA assays the marker is the same as the first peak in the DNA ladder DNA ladders and samples also contain an Upper Marker The LabChip Dx software log file displays in the Event Viewer
221. vely and any defined Expected Peaks are labeled with the corresponding colored arrows The currently selected peak in the Gel view or Peak Table displays a blue outline around the arrow above the peak You can zoom in and zoom out the Graph View of the wells Zoom in by clicking and dragging over a region of an electropherogram Zoom out by right clicking on a graph and selecting either Unzoom or Unzoom All from the shortcut menu Double clicking in the graph will zoom out to the previous zoom level Graph data can be exported to a graphic file by choosing Export on the File menu See Exporting Data on page 72 for details If the workspace contains multiple collections the data exported is from the active selected collection P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Software Reference 98 Graph View Continued To show or change the labels on the peaks in the graph show the data points on the graph show peak baselines or change the graph colors see Graph View Properties on page 103 To select a peak on the graph move the cursor near the peak and click A blue arrow above the peak shows that the peak is selected and the cursor changes to an up arrow The Gel View and Peak Table View also select the corresponding entry You can adjust the peak baselines from the graph view if desired Select Show Peak Baselines in the Graph View Properties to display the baseline for each peak To chang
222. y Period A defect for purposes of this Warranty is defined as any failure that occurs during analysis of the first one hundred 100 samples being run on a Chip During the Warranty Period if the Chip fails to comply with this Warranty Caliper will repair or replace the Chip at its option and expense If a Chip becomes damaged or its performance otherwise deteriorates due to solvents and or reagents other than those supplied or expressly recommended by Caliper Caliper will replace the Chip at Customer s request and expense No such replacement will extend the original Warranty Period This Warranty does not extend to any Chip which has been a the subject of an accident misuse or neglect b modified by a party other than Caliper c used in a manner not in accordance with the instructions contained in the product User s Manual or d used for an assay or application which has not been approved by Caliper All claims under this Warranty must be made within thirty 80 days of the discovery of the defect Caliper s obligations under this Warranty are limited to replacement as Caliper deems necessary to correct those failures of the Chip to comply with this Warranty of which Caliper is notified prior to expiration of the Warranty Period Ill GENERAL CALIPER SPECIFICALLY DISCLAIMS ANY AND ALL OTHER PROMISES REPRESENTATIONS AND WARRANTIES EXPRESSED OR IMPLIED THIS INCLUDES BUT IS NOT LIMITED TO THE PRODUCT S CONDITION ITS CONFOR
223. y View are displayed in the Electropherograms tab If not selected all wells in the collection are displayed Only displayed when the Electropherograms tab is selected Sample Displays the names of the samples well names on the graph Name Color and the color associated with each sample well Click on the Table color to choose a different color for a sample X Axis Scale Changes the X Axis from Time to Size Grid Style Displays grid lines on the graph vertical horizontal both or none Click the button to cycle through the grid options Data Legend If multiple wells are displayed in the Overlay Electropherograms Location tab specifies the location where the legend displays on the graph The legend shows the color used for each well Only for the Overlay Electropherograms Tab Pin icon In the top right corner this is used to lock in place or unlock the Properties tab If locked in place the Graph is resized to accommodate the tab P N 128682 Rev 00 LabChip Dx User Manual Caliper Life Sciences Inc Gel View Software Reference 105 The Gel view in the Collection Pane is a visual representation of the data formatted to look like the Gel slabs that were originally used to provide DNA data The data is shown in Time vs Fluorescence or digital form Click on a gel lane well to select the well Ctrl click to select multiple wells Selected wells are outlined with a dotted gray line Wells selected in the

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