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SmartArrayer user manual

1. Figure 7 7 The spotting parameters setting interface Step 1 Cleaning The Cleaning Section describes the cleaning function of the system The cleaning protocol has four steps Rinse Sonicate Rinse Dry The number of cycles of this CapitalBio Corporation 54 SmartArrayer M Chapter 7 Spotting or Dispensing iteration is dependent on the sample characteristics Samples with high viscosity require more cycles and an elongated time span It is recommended to optimize the cleaning protocol to save time by conducting a test for remnant fluorescence test prior to full state usage e Specify Rinse Time Sonicate Time and Dry Time respectively and confirm that the check box in front of the desired operation is selected e Click the Add button to insert the selected operations into the protocol Adjust the protocol with the tools provided in the list box such as Delete Delete all Copy Paste Move up and Move down e You can save and load protocols for different sample types with the aid of the Save and Open Buttons Step 2 Sample Uptake The parameters of sample uptake are corresponding to different sample preparations In case the sample phase boundary in the plate well deviates from the record of the Z axis position calibration it is necessary to compensate for the sample uptake descending stroke of the pin The positive values represent deeper deviations while negative values indicate the opposite Delay time refers to time spen
2. Home LJ Humidity Figure 7 1 Preparation before spotting CapitalBio Corporation 47 SmartArrayer M Chapter 7 Spotting or Dispensing 7 3 1 Cleaning Section In the cleaning section you can carry out operations including Circulate the water held in the rinsing basin Rinse the pin or dispenser Vacuum by vacuum pump Dry the pins or dispensers by inserting them into the inhalant holes on the wash dry station Excite water held in the basin by turning on the sonicator and Sonicate the pins by inserting them into the basin For the NDM Excite and Sonicate will be replaced with Drain the channel inside the dispenser 7 3 1 1 Circulate Click on the Rinse button to start the rinsing program The pump starts working prior to spotting with the microarray workstation in order to drive a water flow through the basin and make sure that there is enough distilled water in the basin during the subsequent rinse operations Operation Guide e Click on the Rinse button and push it down to a depressed appearance for Rinse to start circulating Meanwhile the rinse indicator light will light up e Click on the Rinse button again to pop it up to a released appearance and stop the water circulating Meanwhile the rinse indicator light will turn off 7 3 1 2 Pin Rinse Move the pins or dispensers to the location indicated by the rinsing position calibration record and rinse them in the basin prior to commencing spo
3. Step 1 Check the protocol and save it Step 2 Check that the microplate and pre spotting slides are placed in the proper positions Click the Start button on the run page to perform spotting Once the spotting procedure is initiated the slide information plate information and progress bar will notice users of the status of the operation in time The Pause button will be enabled in need operation halt see Section 7 6 3 for details Warning If the Start button remains in a disabled state while the microarray workstation is fully functional it is possible that you have not performed the configuration settings especially the position calibration after an installation or hardware change 7 6 2 Running Status Prompt Status Notification consists of Slide information Plate information and Progress section as shown in Figure 7 11 CapitalBio Corporation 60 SmartArrayer M Chapter 7 Spotting or Dispensing or CapitalBio 4 Spotted geai omartArrayer 136 m samp Md papa papa pa a a EEEE F HER ee Teee ae D pianeneeebesrerseeceen E mala ole le le fe le a a le lee we a Eel MOC 22 ul EEE IERIE ICE spotted Shania ome 34 l se 70 ILI pco io ma ma mm a EA E Aaa pa iaa ES a fo T o Ls E MEA 73 A AL a m l a 14 102 oof ez 74 Hal Sample to be spotted EEE EEES CAKARA Slides for spotting ma i 2 129 117 105 es e 77 iei E a 430 112 Mb toc
4. coonnininnoninincnnonininnononininncnoninons 79 Table XIX SmartArrayer 48 Number of Sample Dispensing Time cooninicnonininicnonininnononinininucncnons 79 Table XX SmartArrayer 136 Number of Sample Spotting Time ooonicicccnonononinononnonononononincnnananononos 80 Table XXI SmartArrayer 136 Number of Sample Dispensing Time ooooninicnoninininnoninincnnonininicucninons 80 Table XXII Aspiration volume of 10 glycerol under different conditions coooooooccnncccnnnnonnnonocnnnnnnss 81 Table XXIII Aspiration volume of 30 glycerol under different conditions ooooooooccncccnnnonooonnncnnnnnnss 81 Table XXIV Aspiration volume of 50 DMSO under different conditions ccconooooocnnnnccnnnnonannnonon ns 82 CapitalBio Corporation V SmartArrayer Chapter 0 Preface Chapter 0 Preface 0 1 Overview In this chapter the function principles and series of CapitalBio SmartArrayer microarray workstations will be introduced Also the contents of this manual abbreviations and alternative names will be listed 0 2 Contents of This Manual Chapter Description Chapter 1 Provides crucial information to use the system safely All Important Safety SmartArrayer users should read this chapter before installing and Information using the system Chapter 2 TM Fiardware Provides SmartArrayer hardware specifications and the Installation step by step instructions for installation of the system Chapter 3 Pro
5. hereinafter referred to as System This Agreement is an indispensable part of the System documents You have the right to require the whole documents from the seller of this System in order to protect your rights and interests This System consists of computer software including relevant media printed materials and electronic documents This System may also include any updated or upgraded software and supplemental materials which are provided by CapitalBio for the use of the original System This System and relevant documents shall be granted to you in accordance with this Agreement By installing copying downloading or using this System in any way you agree to be bound by the terms of this Agreement If you do not agree to be bound by the terms of this Agreement Do not install or use this System and return it to the place where you bought it and request a refund of your payment License Grant Subject to the terms of this Agreement CapitalBio hereby grants you a limited right to use this System As a condition of your use of this System you must guarantee that you will not use copy modify rent or assign this System or any portion of it outside the scope of this Agreement Reserved Rights All rights that have not been explicitly authorized to you are reserved by CapitalBio GRANT OF LICENSE CapitalBio grants you the following rights 1 Install and use only one copy of this System on a single computer 2 Make only one cop
6. the microplate will default to the type specified in the protocol and is beyond the user s modifications Assign Tags Click the Tag button to assign the tag inputs in the left grid cells to the listed sample sequence items on the right and then the Save button is enabled which allows files to be stored by describing sample tags namely the sample flag files sas Clear Click the Clear button to remove all the input and settings and bring the page to the status just after initialization Save and Load Click Save or Open buttons to save or load the sample flag file in Excel format The format specifications of the sample flag file are depicted in Figure 8 4 CapitalBio Corporation 65 SmartArrayer M Chapter 8 CapitalBio Corporation Additional Software Features Index Y Index ID xX 3 Y 3 Namel umber 3 direction direction ID Name 120 number number Sample Sample ID name Feature size um Figure 8 4 The sample marker information file format 66 SmartArrayer M Chapter 9 Operation amp Maintenance Chapter 9 Operation amp Maintenance 9 1 Overview This chapter will introduce operations and safety items including daily operation and routine maintenance Daily operation mainly includes open and close the upper enclosure of the arrayer load and unload slides load and unload pins Routine maintenance mainly includes periodically cleaning and replenishing distilled water for the humidifyin
7. user can click System configuration button on the right top toolbar of main window and input the password to access the configuration Position Rinsing Position Calibration see Section 6 3 1 Calibration Drying Position Calibration see Section 6 3 2 1365 4858 Sonicator Position Calibration see Section 6 3 3 System Liquid Position Calibration see Section 6 3 3 136S 136D 136 slides see Section 6 3 4 136D 48D CapitalBio Corporation 27 SmartArrayer Chapter 4 Tutorial Position 48S 48D A48 slides see Section 6 3 4 Calibration Microplate Position Calibration see Section 6 3 5 136D 48D pe Position Calibration see Section Motion setting see Section 6 4 Pressure parameters setting see Section 6 5 DA Dispensing parameters setting see Section 6 6 Slide Parameters setting see Section 6 7 Sample Selection Priority setting see Section 6 7 4 4 Preparation You can access the preparation panel by clicking on the Prepare button on the left Circulate see Section 7 3 1 1 Rinse see Section 7 3 1 2 Vacuum see Section 7 3 1 3 Cleaning Dry see Section 7 3 1 4 Excite see Section 7 3 1 5 Sonicate see Section 7 3 1 6 Step 2 Load slide see Section 7 3 2 Step 3 Home see Section 7 3 3 Step 4 Humidify see Section 7 3 4 4 5 Protocol Click the Protocol button on the left to gain access to the microarray setting sample sequence Virtual plate and the spotting dispensing page process Su
8. 5MPa 2 3 Receiving Inspection 2 3 1 Initial Inspection upon receipt of equipment Please check if the number of packages is correct and whether they are in good condition or not Please refer to the following table Table VII Packed box listing Wood packing box Cardboard packing box 2 3 2 Unpacking It is important to avoid shaking and dropping the equipment while transporting it or while opening their packing boxes Please check if the components are all present after opening the packing boxes Please contact CapitalBio if you have any questions or concerns 2 3 3 Components List Please refer to packing list in the package 2 4 Hardware Installation 2 4 1 Hardware Installation The hardware installation should be carried out by specialized technicians End users must have a thorough knowledge of the microarray workstation components in order to operate the workstation correctly and efficiently It is essential that end users fully understand the operations required to switch between the 136D and 1365 functions or to switch between the 48S and the 48D functions CapitalBio Corporation 10 SmartArrayer Chapter 2 Hardware Installation 2 4 2 Description and Components Upper o enclosure gt Workbench Safety protection Switch pannel Frame Figure 2 1 The 1365 instrument components The 1365 microarray workstation instrument components include the frame the body the enclosure the control panel and a
9. CapitalBio Corporation 19 SmartArrayer Chapter 2 Hardware Installation The 136th slide Vacuum position 8 drying hole Rinse tank The 1st slide position an Za ae an 7 se ss m la lo de Q gt aE ep W axis Upper Plate gt A Barcode manne a Em En a2 PlateA24 m oS as ss a an f i Me d take am m an am 44 The73rd A TA The 72nd __ l slide positip _ slide position Sonicator gt 4 gt Po Slide O p e rato f Pin frame Z axis nel Figure 2 9 The 736S position information Top view CapitalBio Corporation 20 SmartArrayer Chapter 2 Hardware Installation Slide Barcode whe 1st slide position Platen n 1 a rrerercererere a Plat A24 RECAE ate ROO KOC ORL EOELOCOEEOOORE i t F epcecoerecercecocen encore 33 CO PRSORADO 1 Template COCOCOCOCOCOCOCOCOCCOCCCCC COCODOPOCOCCOODOPOPOODODE bracket COKCOCCOCCOKOOOC Ee Y re esceercccoce rrecrroert reece f Per OOCOCOCOCOCCOOCOCOCOr COCOCOCODODODCOOCOCOCI The 48th reeaernrorecrencnrere The 1st pinhole eo no 1 Pin frame Sonicator Rinse tank Lf t X axis Inspiration pinhole Ope rator Figure 2 10 The 48S position information Top view In the front view of the 48S the slide at the top right corner of the platen is referred to as the Ist slide while the slide at the bottom left of the platen is the 48th slide The microplate
10. Number of Slides CapitalBio Corporation 77 SmartArrayer M Appendix I Dispensing Time Hours CapitalBio Corporation 100 00 90 00 80 00 70 00 60 00 50 00 40 00 Spotting Time Hours 30 00 20 00 10 00 0 00 Throughput and Time Table XVI SmartArrayer 136 Number of Slides Spotting Time SmartArrayer 136 Number of Slides Time 960 samples 5 Replications Sample 3 Replications Sample 1 Replications Sample Ean 40 52 64 76 88 100 112 124 136 Number of Slides Table XVII SmartArrayer 136 Number of Slides Dispensing Time 100 00 90 00 80 00 70 00 60 00 50 00 40 00 30 00 20 00 10 00 0 00 SmartArrayer 136 Number of Slides Dispensing Time 960 Samples 5Replications Sample Replications Sample 1Replications Sample 40 52 64 76 78 88 100 112 124 136 Number of Slides SmartArrayer M Appendix I Throughput and Time Table X VIII SmartArrayer 48 Number of Sample Spotting Time SmartArrayer 48 Number of Sample Spotting Time 3 Replications Sample 27 00 24 00 21 00 18 00 e T 15 00 oO F 12 00 O 6 9 00 a ze 4 pins 47 slides 6 00 3 00 8 pins 47 lides 32 pins 47 slides 0 00 0 200 400 600 800 1000 Number of Sample Table XIX SmartArrayer 48 Number of Sample Dispensing Time
11. TA ODER IE Wa A A SE 47 Wed SNS TEMES TAR TR AA A aise aclu AA 47 Gc Die PREPARE sascha hatte a A a 47 Vidi EC EUNE SE N ON A anager ead 48 as OEI a IIT ACT E EERE EPO Ie ACs Pe Oe RPT mY OnE PRET ES ee PS PRE PET eA 49 EE Doo Mam 1 jf RTE ANe RRC A OE EC ER PET T OI ROE OEE ee 49 TiS ATO A A EN T O Jenene uahon AE SG 49 Vee PROTOCOL EA E E E A NE A E TE E A A tated E EETA T AA E E ET 50 Pad AITONEN E NAER AE E N N E N TE O AA 50 TAD POMPES CUENCA Rias 52 LARS OPONE TITOLO S AAA Ai 54 LAE DISPERSIA ETTO S E AAA AS A 56 TAD BACKUP amp Load SUME T lerraire AA a 57 du SPOTTING PREVIEW orate aT E E EAN EE O E E EAO 58 7 5 1 SAUC PAV I CW A A II II a tealvadusdcnseastabes 38 TZ DAME PIN a data 59 o STAR Nd E E S A AT A E A OO Oe A A 60 7 6 1 OI re A A A 60 702 Ruan AUS ATOM DE cia 60 7 03 Pause CNG RESUME did 6l POIT NOE E ENA NETET 62 CHAPTERS ADDITIONAL SOFTWARE FEATURES ccccsscsccsssccssccccsccccscccccssccssccccsccccsccccsscccees 63 Sl OVERVIEW ri A E E A 63 S STEPS OF REPRINTING tad E AA SAA 63 S3 TAGGING SAMPLE AA A E AS 64 CHAPTER 9 OPERATION amp MAINTENANCE 22 ccccccsssccssccccccccccsccccsscccsscccssccccsccccsccccccccccscccseccces 67 Da OVERVIEW AN AA AA AA AAA A A 67 92 DATIEY OPERATIONS aia 67 Yo MAINTENANCE 0d Adi 69 CHAPTER TO TROUBEESHOO TIN Gio aaa eaa eaaa aaa oa aiaia desae 73 10 1 COVE RVI We AA A A AAA a 73 10 2 EROUL FO TIN AA A AS 73 APPENDIX I THR
12. Z axis and the drying stops Meanwhile the dry indicator turns off 7 3 1 5 Excite Excite refers to the operation to power up the sonicator Operation Guide e Click the Sonicate button and push it down to a depressed appearance for Sonicate and the sonicator starts working Meanwhile the sonicator indicator light is on e Click on the Sonicate button again to pop it up to a released appearance and the sonicator stops working Meanwhile the sonicator indicator light 1s off 7 3 1 6 Sonicate Move the pins or dispensers to locations indicated by the sonicating position calibration record and sonicate them in the basin prior to spotting Operation Guide e Click the Pin Sonicate button and push it down to a depressed appearance for Pin Sonicate The Y axis and Z axis are moved to the drying position and sonicating starts Meanwhile the sonicate indicator light continues to be on e Click on the Pin Sonicate button again to pop it up to a released appearance The pins or dispensers are lifted along the Z axis and sonicating stops Meanwhile the sonicate indicator light is turned off 7 3 2 Load Slide Click on Load Slide button and the platen moves out automatically to facilitate slide loading for the user The platen of the 48S D moves closer to the user The platens of the 136S D move laterally to the left and the right sides 7 3 3 Home Click the Home button to send the X axis W axis also if 136S D Y axis and Z axis to
13. Z axis in slow incremental moves step by step and carefully watching until the desired location is achieved Warning It is strongly recommended that you carry out this pre dispensing position calibration just after you complete the microplate position calibration with out moving the X axis or W axis and Y axis and keep the microplate in position for reference When moving the axes always be aware of the position of the print head and pins dispensers Make sure that the planned routines of all the moving components are clear of any obstacle before you apply actual movement in case of potential disastrous collisions Step 4 Calibration In the Current Position Parameters section confirm that the checked box in front of the Z axis coordinate is ticked Click on the Calibrate button and confirm it when notified to save the calibration position to the hard disk The corresponding coordinates in the Calibrated Position Parameters section will be updated by the time the Z axis has moved to the home position 6 4 Motion Setting The velocity and acceleration parameters control long distance movement of each axis These parameters influence the time and the cost of the spotting procedure as well as the performance It 1s recommended to set the acceleration to 5 10 times of velocity The acceleration to velocity ratio should be smaller with higher velocity settings and greater with lower velocity settings Operation Guide e Acce
14. a corresponding text box If it is the initial calibration the initial values are all set to 0 Step 2 Initialization of the Z axis Confirm that the Z axis is in the home position If not send it to the home position by clicking on the Z Home button Step 3 Adjustments of the X and Y position Move the X axis and Y axis by gradually moving step by step and carefully watch until the pin head or dispenser is located just over the upper left corner of the slide CapitalBio Corporation 39 SmartArrayer M Chapter 6 System Configuration Warning When moving the axes always be aware of the position of the print head and pins dispensers Make sure that the planned routines of all the moving components are clear of any obstacle before you apply actual movement to avoid potentially disastrous outcomes Step 4 Calibration of the X and Y position In the Current Position Parameters section confirm that the checked boxes in front of the X and Y axis coordinates are selected but the one in front of the Z axis coordinate is not ticked Click on the Calibrate button and confirm calibration when notified to save the position to the hard disk The corresponding coordinates in the Calibrated Position Parameters section will be updated by the time the Z axis has moved to the home position Step 5 Adjustment of the Z position Firstly move the X and Y axes to the center of the pin dispenser over the first slide Move the Z axis dow
15. be eventually enabled on successful retrieval of sample information from the file mentioned above Save Tagging Info Click the Save Tagging Info button to save the combination of spot distribution and sample tag information as a GAL file which can be recognized by GeneP1x software for data analysis A dialog will pop up for users to customize the file name and path Separation of arrays al Sample Preview Save into Tag sample xa xs xe x7 xe xs xio ffxi x i2 x 13 x 14 x 15 x16 x ria ass 303 aFd 3713 3L5 aC3 SEQ 3115 355 Iga 303 3F9 5 3E9 SFT 3J15 33W21 3W19 3L3 BM 7 ih smzi 3M19 SKS SFT 3J 3E21 39 3F15 30T 3019 3r2zi MMMM ss9 3E1f cit 3c19 SEZ1 3H3 FE Y 3G4 304 3F10 3J14 3L6 3H4 B i 3100 3114 SES 3D4 3F1C Y 3K10 3F8 3J16 322 3820 3LiO MM Iis 3mez 3M20 3K10 3F8S 3J1 Y 3E22 3H10 3Fi6 3D 3120 sr22 QM cio see scis 3020 3E22 3H10 SF LE y E y A y E y E y Y 363 3D3 3F9 3713 fs 3H3 MM acs SES 3113 SKS 363 303 3F9 y Ea H7 2T1E a Wid aTa Ey H m7 23T1E cod be A 1 oO SEA ah T1E ae x Show the D18 well on plate whose number is 3 Figure 7 10 The sample preview interface TM CapitalBio Corporation 59 SmartArrayer Chapter 7 Spotting or Dispensing 7 6 Start Spotting Click the Run button on the left to access the run page which implements two functions Status notification and spotting process control 7 6 1 Start
16. be inserted into the PCIeslot in the main board of the computer The card is connected to the workstation via a 100 pin cable CapitalBio Corporation 1 SmartArrayer Chapter 2 Hardware Installation Z axis Humiditying fan Drying hole Upper Sonicator platen Y axis X axis Lower platen Temperature and humidity Sensor Control pannel W axis Figure 2 3 Top view of the Workbench Other cleaning unit attachments such as the rinsing unit and the vacuum drying unit the wash dry stations and the sonicator are fixed on different sides of the X W axes For the 136D the basin of the sonicator is used as a reservoir for system liquid such as distilled water Emergency stop EMS Device startup button Status indicator lights Figure 2 4 The control panel There are two buttons on the control panel of the 1365 The red elevated button on the left is the Emergency Stop EMS The green button on the right is the unit Startup button and it 1s used to start up the microarray workstation only after the power switch on the back of the workstation is turned ON but it is unable to shut down the workstation Located between the two buttons are five status lights that indicate the operation of the vacuum drying unit the rinser and washing unit the sonicator unit the humidifying unit and a Function Error notice respectively The power switch and the coupling connectors of the 136S are at the back of the instrument and a
17. be refreshed at this time The Z axis will move to the home position 6 3 2 Drying Position Calibration Drying Calibration Position applies to the Y axis and Z axis coordinates but not the X axis coordinate It ensures that all 32 pins for the 1365 or 48S or 8 dispensers for the 136D or 48D are inserted into the very center of the inhalant holes held by the rinse dry station at a consistent and sufficient depth to enable efficient simultaneous vacuum drying of all pins The location of the inhalant holes is depicted in Section 2 9 Step 1 Choosing Drying Location Select the Dry Location in the location section then calibrate the current position parameters for the Y axis and Z axis but not the X W axis coordinates The coordinates will be displayed in the corresponding text box If the drying location selection is being preformed for the first time the initial values are all set to 0 Step 2 Initialization of the Axes Confirm that the X axis W axis also if using the 136S D and the Z axis are in their home positions If not send the axes to the home position by clicking on the X Home W Home or Z Home buttons Step 3 Adjustments Move the Y axis and the Z axis by slowly and carefully watching until the pins or dispensers can be dried properly It is necessary to immerse the pins or dispensers in the inhalant holes a bit deeper than in the rinsing solution to make sure they are thoroughly dried CapitalBio Corporation 3
18. com globalsales capitalbio com Please be prepared with the following information for the optimum technical support OSERIAL NUMBER of your CapitalBio SmartArrayer at the back of the microarray workstation Version number of the application software Nature of the problem Please refer to the Troubleshooting Chapter Steps you have taken to solve the problem Your phone number fax number and email address In addition convenient access to your CapitalBio SmartArrayer during the duration of a technical support call would facilitate the process Additional information can be found in the following e Documentation provided with the computer workstation and its software CapitalBio Corporation 3 SmartArrayer Chapter 1 Important Safety Information Chapter 1 Important Safety Information A A Use of controls or adjustments or performance of procedures other than those specified in installation guide and user manual may result in damage to the instrument loss of data invalid data hazardous radiation exposure laser light hazardous voltage moving parts or even cause fire Exposure to the hazards may cause severe or fatal injury Warning 1 1 Certification Identification and Power Supply Label SmartArrayer 48 Ea RET Microarray Spotter Corporation INPUT RATING 730V 50Hz 3A i CAPITALBIO CORPORATION CATALOG NUMBER 1100XX 18 Life Science Parkway SERIAL NUMBER 110 8XXX Changping District
19. disinfectant 111 6 Seasonal Maintenance You can choose to perform seasonally maintenance by yourself or call for technical support 111 6 1 Check if there is any damage on the pin head under microscope which might affect spotting More attention should be paid in case of frequent use of the instrument 111 7 Semiannual Maintenance Semiannually maintenance should be carried out by professional personnel assigned or authorized by CapitalBio Corporation CapitalBio Corporation 84 SmartArrayer a e y pr Tt oe AA TA AAA AAA a A eT z E JEN a SS e gar eng Selves Corporation CapitalBio Corporation Add 18 Life Science Parkway Changping District Beijing 102206 P R China Tel 86 10 80725793 Fax 86 10 80726782 Email techsupport capitalbio com globalsales capitalbio com http www capitalbio com
20. is too Decrease the air uptake time fe Improve surrounding conditions and is too Increase the uptake time wash nozzle tip thoroughly Dispensing air Increase dispensing air pressure pressure too low Too uptake channel Nozzle damage Contact CapitalBio Waste water tank 1s full Empty the waste water tank Lower the height of the waste tubing Make sure the sample volume in source plate is adequate little sample in dispenser Tubing connected to to to remove air bubble and restore flo Lack of water W i Refill the wash water tank wash Low humidity Increase the humidity setting Dust on the nozzle tip Wash nozzle thoroughly Large gap between Adjust the distance between nozzle nozzle and slide and slide Static charge Clear static charge Low dispensing Increase the dispensing pressure pressure 75 the wash station clogs SmartArrayer M Chapter 10 Troubleshooting Small air bubbles in Increase the dispense time and channel increase the number of cycles Air bubbles in A to remove the bubbles Increase number of pre innata spots a dispensing Decrease the dispensing pressure or Low dispensing Increase dispensing pressure Inconsistent spot size P 8 p amp P pressure after several spots gt T a Dispensing time is too Make sure the dispensing time is no brief less than 0 25ms High motion speed and some moving Contact CapitalBio Irregular arr
21. it until it is clean from clogging or other contamination 11 4 2 Check repeatability of dispenser following the instructions below a Prepare 300uL 600uL for 96 well microplate aqueous solution of 10 CapitalBio Corporation 83 SmartArrayer Appendix II Routine Maintenance glycerol 0 2ug ml BSA labeled with Cy3 dye b Pipette the solution into 8 consecutive wells on a microplate 30uL per well for 384 well plate and 7OuL per well for 96 well plate c Set aspiration time to 0 5s aspiration time for system fluid to 4s and dispense pressure to 6KPa d Set up an protocol set the combination of dispenser to 1 1 sum of slides to 2 sum of spots to 18 8 X Y sample replicate s to 18 sample uptake mode to Partial Sample utilizing system liquid Then run the protocol to dispense 144 spots per slide e Scan the result calculate cv coefficient of variance value on diameter and intensity of the 144 spots per slide f If cv gt 10 please call CapitalBio or the authorized distributors for technical support 111 4 3 Check if the pressure of compressed gas source is lower than 1Mpa If it is replace the gas source 111 4 4 When you are replacing the gas source make sure the new one is clean especially in the proximity of the outlet and wipe away the dust accumulated during transportation if there is any 111 5 Monthly Maintenance 11 5 1 Wash the distilled water tank waste water tank and sonicator basin with
22. list defined in the protocol to the list on the right hand side of this page label the listed sample group items tagged untagged or blank with different marks and paint the cells on the plate profile with different colors according to corresponding sample group items These actions will highlight the locations where the tags are to be inserted as shown in Figure 8 3 CapitalBio Corporation 64 SmartArrayer M Chapter 8 Additional Software Features Tag current protocol Cueva plate gawel plate Tag Oper Save Clear Plate No E Feature sizefurny 1200 384 wel Tagged sample list 3 C31D1 Namel gt 3 E9 3 E10 379 Tagged 3 F10 Sample 3 113 Unused well A E L ii E F i H I J E L M H o P E j ca Figure 8 3 Examples of sample attention marks Input Tags Here the added Tags must comply with a defined format first comes sample ID description For instance the tag of a certain sample with ID such as ID1 and description such as Namel should be ID1 Namel Double click on the corresponding cell on the grid to activate editable status then input the desired tag and repeat the operation until all required samples are tagged Set Microplate There are two types of microplate supported by the system the microplate specified here should match to the type used for spotting When tagging the sample sequence list confined within the current protocol
23. more Display system 17 inch colored with resolution of 1024768 pixels or more CD ROM 40x speed or faster PCI slot Serial port Windows 2000 with Service Pack 4 or Windows XP with Service Pack 2 Operating system Warning Please open the computer shell and plug the control card firmly into the PCI slot of the computer In order to prevent computer errors please avoid sharing slots with other PCI cards on the same computer 2 2 6 Pressure Supply requirements In the 136D 48D models a gas bottle filled with high purity compressed nitrogen gas 1s required as a gas pressure supply The compression resistance pressure of gas bottle should be no less than 14MPa and inner volume of the bottle should be no less than 30L Between the gas tank and the Pressure Inlet of NDM there should be a pressure regulator which can be operated manually The output pressure range of the regulator must be 0 2 0 4 MPa The regulator should be equipped with suitable connectors linked to the NDM and the gas bottle while the outer diameter of the tubing connecting NDM regulator and gas tank must be 8 mm and some adaptors may be needed to interconnect different gas bottles gas regulators and the tubing CapitalBio Corporation 9 SmartArrayer Chapter 2 Hardware Installation Warning The output pressure range of the regulator Must be 0 2 0 4 MPa Make sure the output pressure of the outer pressure source is lower than 0
24. o s 78 Pre spotting 7 431 119 Nor 95 er 79 O 132 120 Ne 06 a Time elapsed 0 Day 00 Hour 22 Minute 17 Second Y ia 110 os Time left 0 Day 08 Hour 44 Minute 22 Second E 135 123 414 NN oa 436 424 Unused slides or null Reminder Processing Sample Yd Slide 4 y Y Array K Array 2 Slides for pre spotting Figure 7 11 The running state interface 7 6 3 Pause and Resume The Pause and Resume functions are supported to handle unexpected emergency events particularly during spotting applications Step 1 Click the Pause button to pop up a dialog for users to select the next action to take The microarray workstation will pause temporarily AFTER the current action is completed An action is a unit of operation or a series of operation which cannot be broken into individually controllable ones For example a sample taking procedure is composed of successively but inseparable operations of moving the X and Y axis and moving the Z axis downward delaying moving the Z axis upward Step 2 Select Next Action Five options are provided to handle different circumstances Users can select one solution to resume normal status as shown in Figure 7 12 e Select the Continue option to resume spotting dispensing at the current position If the Wash checkbox is selected the wash operation will be executed first and then the sample will be taken up If the Re uptake Sample checkbox is selected the
25. rectangle have been already selected previously they will not be re ordered by the new selection Select All Select as many sample groups as possible on the plate and REARRANGE THEM ALL according to the sample selection priority setting Clear Click to remove a single sample group or drag and draw a rectangle to remove multiple sample groups from the selection Clear all Remove all the selected sample groups from the plate Step 2 Select Plates In the section just beneath the virtual plate you can e Input or select the sequence number of the current plate If several successive plates share the same sequence pattern as the current editing virtual plate you can specify a number greater than 1 in the plates per batch combo to insert them into a list with one click The sequence number of the successive plates is automatically increased from the current one e You can determine whether to insert the current selection before or after the selected item if there 1s one in the sequence list on the right hand side or to insert the current selection at the tail default or head of the sequence list Step 3 Add to list Click the Add button to insert the current selection into the existing sequence list Step 4 Adjust sequence list optional The Delete Delete all Copy Paste Move up and Move down tool buttons are provided in the sequence list box for your convenience to adjust the content of the existing sequence list Step 5
26. should be fixed into its bracket on the platen with the number P24 well at the bottom right corner of the bracket and the number A24 well is assumed to be underneath the Ist pin Accordingly the top right hole of the vacuum drying unit is assumed to be underneath the Ist pin Sonicator A ee ee ee ee ee a ee A m m E A ee n ms e e es m ee ee ee ee Figure 2 11 Calibration of the coordinate positions of 136S CapitalBio Corporation 21 SmartArrayer Chapter 3 Software Installation Chapter 3 Software Installation 3 1 Overview The SmartArrayer CD provided contains the setup program of the application software of the SmartArrayer series which supports four different models 48S 48D 136S 136D Please confirm that the software configuration is compatible with the instrument model when you setup the application software 3 2 Preparation Power on the computer workstation linked to the microarray workstation login in the operating system insert the compact disc labeled with the SmartArrayer V4 0 into the CD DVD ROM browse the catalog of the CD and find the setup executive file named Setup exe Double click this file to launch the installation wizard 3 3 Installation Wizard Step1 Greeting page click the Next button to proceed j Smart rrayer 4 0 Ama Welcome to the SmartArrayer 4 0 Setup Wid The installer will guide you through the steps required to install Srmart rayer 4 0 on your c
27. the home position quickly The Home button is usually used after slide loading or abnormal termination during spotting operation 7 3 4 Humidify Humidify refers to operations to power up the humidifier to achieve the required humidity within the enclosure of microarray workstation Operation Guide e Click Humidify button and push it down to a depressed appearance for Humidify and start humidifying Meanwhile the humidify indicator light 1s lit up e Watch over whether the desired relative humidity is achieved by reading the display in the status bar e Click on the humidify button again to pop it up to a released appearance and stop humidifying Meanwhile the humidify indicator light is turned off CapitalBio Corporation 49 SmartArrayer M Chapter 7 Spotting or Dispensing 7 4 Protocol Click the Protocol button on the left to gain access to the microarray setting sample sequence Virtual plate and the spotting dispensing page process The microarray setting page is the default first page to display as shown in Figure 7 2 7 4 1 Array Setting Microarray Setting a Sample Sequence pr Process of Spotting Slides Starting at i Sum of slides i Pin Configuration Combination Pattern Array Settings Spot disk um Sum of spots Max sum of spots Array space mini Sum of arrays Max sum of arrays Sample replicate s i Array replication Wes kd Figure 7 2 The Pin arr
28. the Continue option to resume spotting dispensing at the current position Stop Select the Exit option to abort the current run of spotting dispensing 4 8 Shutdown the System Close main window of the microarray workstation application software Turn off the computer linked to the microarray workstation Turn off the power switch which is on the rear panel of the microarray workstation Turn off the control box power if using the NDM Turn off the vacuum pump CapitalBio Corporation 29 SmartArrayer Chapter 5 Getting Started Chapter 5 Getting Started 5 1 Overview It is essential to run the spotting system for a test immediately after the hardware and software installation Please check again whether the cables are linked correctly before you startup the system then switch on the power of the instrument and startup the application software to run the whole system 5 2 System Startup and Shutdown Procedures 5 2 1 Important Issues before Startup Warning Make sure the workbench is clean and has no obstacles for the platform movement Make sure there is enough water in the humidifier Make sure there is enough water in the tank Replace or refill water in the sonicator basin Make sure the EMS button 1s released red light is off Make sure the photoelectric stop slide does not touch the limit position sensor 5 2 2 System Startup Steps e Turn on the vacuum pump Turn on the switch which is on the rear panel of t
29. uses this computer Everyone 2 Just me Cancel Figure 3 3 Target folder interface CapitalBio Corporation 24 SmartArrayer Chapter 3 Software Installation Step 4 Confirm to install the software 7 SmartArrayer 4 0 Contirm Installation The installer ig ready to install Smart rayer 4 0 on pour computer Click Next to start the installation Figure 3 4 Confirm installation interface Step 5 An animated progress bar depicts the installation process j SmartArrayer 4 0 Installing SmartArrayer 4 0 Smart raper 4 0 12 being installed Please wait Figure 3 5 Installation interface CapitalBio Corporation 25 SmartArrayer Chapter 3 Software Installation Step6 Installation successful click the Close button to exit the installation guide j SmartArrayer 4 0 Installation Complete Smart raper 4 0 has been successtully installed Click Close to exit Figure 3 6 Installation complete interface Note Within the installation wizard you can click the Back button to return to the previous step to modify the configuration or click the Cancel button to exit the installation wizard CapitalBio Corporation 26 SmartArrayer Chapter 4 Tutorial Chapter 4 Tutorial 4 1 Overview In this chapter we will guide you to spot or dispense a microarray chip This way you can quickly grasp the basic skills to use the software and accomplish basic
30. with high viscosity requires more cycles and extended cleaning times It is recommended to optimize the cleaning protocol to compress the time required by conducting a remnant fluorescence test prior to full state usage e Specify Rinse time Drain time and Dry time respectively and confirm that the check box in front of the desired operation is selected e Click the Add button to insert the selected operations into the protocol Adjust the protocol with the tools provided in the list box such as Delete Delete All Copy Paste Move Up and Move Down You can save and load the protocols for different sample types with the aids of the Save and Open Buttons Rinse times refers to the recurrence of Rinse operations which gives the pin head a flush with circulating distilled water Each Rinse operation lasts 1 second Drain times refers to the recurrence of Drain operations which wipe out liquid droplets out from the outer side of the dispenser channel with positive pressure Each Drain operation lasts 1 second Dry times refers to the recurrence of Dry operations which dry the dispensers with a negative vacuuming pressure Each Dry operation lasts 1 second CapitalBio Corporation 56 SmartArrayer M Chapter 7 Spotting or Dispensing Step 2 Sample Uptake Select proper sampling mode for sample for different sample preparation Mode refers to sampling mode for sample and can be selected from two alternatives Full Sample mode and
31. 7 SmartArrayer M Chapter 6 System Configuration Warning When moving the axes always be aware of the position of the print head and pins dispensers Make sure that the planned routes of all the moving components are clear of any obstacles before you apply actual movement to avoid any potentially disastrous outcomes Step 4 Calibration In the current position parameters section confirm that the checked boxes in front of the Y and Z axis coordinates are selected ticked but that the ones in front of the X and W axis coordinates are not ticked Click on the Calibrate button and confirm calibration when notified to save the position to the hard disk The corresponding coordinates in the calibrated position parameters section will be refreshed by the time the Z axis moves to the home position 6 3 3 Sonicator System Liquid Position Calibration This section applies to position calibration of the sonicator basin for the pin based system and for the dispenser based system For both cases only the Y axis and Z axis coordinates are used and the X axis W axis coordinate is not used The sonicator position calibration ensures that all 32 pins for the 1365 or 48S or 8 dispensers for the 136D or 48D are immersed simultaneously into the sonicator bath For the dispenser based system the sonicator basin is used simply as a reservoir filled with system liquid for uptake into the dispenser The location of the sonicator bath is sho
32. A O Ee re ASN SEN RE Pre Rd E Oe SP PE On Ce SIRE RE AME TES RTE EER 29 a 0 T eRe A ht ah re E ea ch ie ee la ae eRe else a ene 29 Ace SHUTDOWN THE SY dia 29 CHAPTERS GETTING STARTED unicas tico 31 A A A A A am act beck uh mame ecee oe 31 CapitalBio Corporation I SmartArrayer 5 2 OYSTEMSTARTUPAND SHUTDOWN PROCEDURES e do 31 5 2 1 Important Issues before Startup cccccccccscccccccccccccccsescccccceeenesssseeeeeeeeaeesseeeeeeeeaaaeeseeeceeeeaaaaaaeseeeeeeesaages Sl IL DV SPCMEDIGIIUD SOLCD Saks docuiaus A AEEA she BNataneapacas Misa EI 31 a E 1 Id E A AEA AAR 31 Doe A O 31 5 4 SOFTWARE MAIN INTER PAGE aria A A a is 32 CHAPTER6 SYSTEM CONFIGURATION o ococccconocccnoccnonccnonccnonoccnnccnnncccnnoccnnnccnnccnnnoccnnoccnnccnonoccnnccccnnocons 33 C OT R N ea E E so 33 0 2 ACUESS OYS TEM CONFIGURATION kasis a a a a a T a A 33 03 POSTION CALIBRA NON usara 34 Ob RE TONON COMPTON oec a LEE lada 36 O52 DINE ROSA CANTAN dla 37 6 3 3 Sonicator System Liquid Position CGUDIQHON 2d dd 38 634 SMA E POSO CAN 39 63 Microplate Postion CADA id 40 63 0 lt Presdispensine POSTOR CANTAN ia 4 0 MOON SELING dd in 42 09 PRESSURE PARAMETERS SETTING dia A A 43 6 6 DISPENSING PARAMETERS SETTING ia A meteseiteras 44 0 7 COTTIER OP TON A A secede et areata a 45 0S BACK UPANDARES TORES 46 CHAPTER SPOTTING OR DISPENSING ccccssscccsssscccsscccccscscccsscccccsscccccsscccccccccesscccccscccccsecccoeees 47
33. Arrayer 136 Microarray Spotter INPUT RATING 100 120V 60Hz 5 54 CATALOG NUMBER 1100XX SERIAL NUMBER 10 8XXX MANUFACTURE DATE Month Year 1100XX SN110 8XXX This device complies with Part 15 of the FCC Rules Operation is subject to the following two conditions 1 this device may not cause harmful interference and 2 this device must accept any interference received including interference that may cause undesired operation e a Fa a Corporation CAPITALBIO CORPORATION 18 Life Science Parkway Changping District Beijing 102206 China Tel 86 10 80726868 http Mmww capitalbio com a re War i 1 C S ay US De d ma Sa mato This Class A digital apparatus complies with Canadian ICES 003 Cet appareil num rique de la classe A est conforme a la norme NMB 003 du Canada MADE IN CHINA Figure 1 2 The identification label of the 1365 SmartArrayer Chapter 1 SmartArrayer Nano Dispense Module INPUT RATING 230V 0 24 50Hz CATALOG NUMBER 110044 SERIAL NUMBER 110 6XXX MANUFACTURE DATE Month Year 1100XX SN110 6XXX Important Safety Information a m ene Ya i Corporation 5 i l CAPITALBIO CORPORATION 18 Life Science Parkway Changping District Beijing 102206 China Tel 86 10 80726868 http www capitalbio com CE MADE IN CHINA SmartArrayer Nano Dispense Module INPUT RATING 100 1720V 0 44 60 Hz CATALOG NU
34. Beijing 102206 China MANUFACTURE DATE OS 10 See Month Year http Mmww capitalbio com 1100XX SN110 8XXX MADE IN CHINA SmartArrayer 48 Microarray Spotter A E CapitalBio INPUT RATING Corporation 100 120V 5 60Hz 5A CATALOG NUMBER 1100XX CAPITALBIO CORPORATION SERIAL NUMBER 110 8XXX 18 Life Science Parkway MANUFACTURE DATE Changping District Month Year Beijing 102206 China Tel 86 10 80726868 http www capitalbio com A i 1100XX SN110 8XXX This device complies with Part 15 of the FCC Rules Operation is subject to the following two conditions 1 this device may not cause harmful This Class A digital apparatus complies with interference and 2 this device must accept any Canadian ICES 003 interference received including interference that Cet appareil num rique de la classe A est may cause undesired operation conforme a la norme NMB 003 du Canada MADE IN CHINA Figure 1 1 The identification label of the 48S CapitalBio Corporation l SmartArrayer Chapter 1 CapitalBio Corporation SmartArrayer 136 Microarray Spotter INPUT RATING 230V 50Hz 354 CATALOG NUMBER 1100XX SERIAL NUMBER 110 8XXX MANUFACTURE DATE Month Year 1100XX SN110 8XXX Important Safety Information Corporation CAPITALBIO CORPORATION 18 Life Science Parkway Changping District Beijing 102206 China Tel 86 10 80726868 http www capitalbio com CE MADE IN CHINA Smart
35. DMC settings Contact CapitalBio At least one axis NE error pops up by the ne Same as software ini one or exceeds the position software limit sensor Running a more axes exceed CapitalBio Corporation 74 SmartArrayer M Chapter 10 One or more axes moves less than it s set movement index error up on monitor non contact Invalid pops during dispensing No liquid is seen after sample uptake Air bubbles channel after uptake the sample in Large droplet on nozzle tip while dispensing Water flood at the wash station Lots of air bubbles enter the wash station Satellite drops Dispense results CapitalBio Corporation Troubleshooting Release EMS button exit software shutdown computer and system and then restart system EMS button was hit Loose connection between motor and screw Contact CapitalBio Loose signal cable linkage between the computer and the micro dispense module The power of the micro dispensing module is off Check and fasten the two cable connections between the modules Set the power to on and restart the software application Dust blocking the dispenser channel Wash the channel thoroughly and check if properties of the sample meet the sample requirements Uptake time brief Not enough sample in Increase the sample volume in the Uptake time is too Decrease the sample uptake time age eee Air uptake time
36. MBER 1100XA SERIAL NUMBER 110 6XXX MANUFACTURE DATE Month Year 1100XX SN110 6XXX This device complies with Part 15 of the FCC Rules Operation is subject to the following two CAPITALBIO CORPORATION 18 Life Science Parkway Changping District Beijing 102206 China Tel 86 10 80726868 http Nwww capitalbio com PS TE C S a q mat conditions 1 this device may not cause harmful This Class A digital apparatus complies with interference and 2 this device must accept any Canadian ICES 005 interference received including interference that Cet appareil num rique de la classe A est may cause undesired operation conforme a la norme NMB 003 du Canada MADE IN CHINA Figure 1 3 The identification label of the NDM 1 2 The protective housing Cover or Enclosure The protective housing is designed to protect users from exposure to hazardous voltage or moving parts Users are not allowed to access the interior of the CapitalBio SmartArrayer There is no component in the interior of the CapitalBio SmartArrayer that requires maintenance work to be performed by the user Users are not allowed to open or remove the cover of the CapitalBio SmartArrayer during operation otherwise warranty on the product will be voided with immediate effect CapitalBio Corporation SmartArrayer Chapter 1 Important Safety Information Warning Users are not allowed to gain access to the interior of the CapitalBi
37. OUGHPUTAND TIME iii seen socchesseeeGeesteedvaceues 77 APPENDIX IT ASPIRATION VOLUME AND ASPIRATION TIME ccccssscccssccccsccccsccccscccccscscceese 1 APPENDIX IHI ROUTINE MAINTENANCE sun tion 83 CapitalBio Corporation II SmartArrayer Figure 1 1 The identification label Of 488 orinario ne en R REE R RENEE A RERE Piour le2 The 1denttiicaton label OL LIOS nes 2 Figure 1 3 The identinceation label of NDM 3 ia ed A EE 3 Figure 2 1 The 736S instrument COMO SA AAA E A 11 Fiure 2 NC COS OM ES de OS 11 Figure 225 LOp VIEW OF LGW AD O NS 12 Figure 2 4 The control Panel See te Ne A LS 12 Figure 2 5 The connection plate back Of TAME A is 13 Figure 2 6 The 48S instrument COMPONENS cccceccescessecessccesecssseesescsssecessccssscessecssscesecssseesseesstens 14 Figure 2 7 PMC reat panel OLNDM trend nin oil iierolici s 16 Figure 2 8 1 hercarpancl Ol dOS a e a a O 17 Figure 2 9 The 136S position information Top view ooooccccncncccnnnnnnononnnnnnonononnnnnnnnnnnnnnnnnnnn non onnnnnnnnos 20 Figure 2 10 The 48S position information Top view oooooocnnnnnccccnnnnnnnnononononnnnnnnnnnnnnnnnnnnnannnnnnnnnnnnnnnos 21 Figure 2 11 Calibration of the coordinate positions Of 1368S occcccnnnnnnunuoaooononnnnnnnnnnnnnnnnnnnanananonnnnnnnnnss 21 Ficure 5 1 Installation Welt 23 Figure 3 2 Software Control System Choice Interac eiieeii cise ee ee eee weeks 24 Fiure 525 Target Tolder MET LACE a0 cis serra tenersadtsade
38. PA IIS AA O A AA 7 A2 REO OMe NIE Nl a e a S 7 Dod ENVIRONMENTAL TEGU EMENI S mdai ea dia 7 Danas SPACE VEGUINCINGIIS ioon aE TA rio 7 DDS WOWEFT COUN EMONTS ted A E A E E A S 2 2 4 Electromagnetic compatibility EMC requirements oooooonnnnnnnnnnnnnnnnnnnnnonononnnnnnnannnnnnnnnnnnnnnnnnnnnnnnnnnnns 8 Bl gt COMPUTE TC QUIT CII IIS A A Ad tas data 9 Dds BEESSUTE DUDO INTE UTE Sc A A IA AAA A AES 9 2S RAIL O a a O A e A 10 25 1 dAnitial inspection upon receipt equipa lidad 10 ZZ UPACK atari tii 10 2D COMPONETS AUST A tata tias 10 2a SSA O a a A eae 10 2 4 1 Hardware Tas tala di tada 10 242 DESCUIDO ARA Components A Ai ane 11 2 ATTENTION ITEMS OF INSTALLATION ia 14 20 DEBUGGING rooe a A ida 15 2 7 SWITCHING BETWEEN SPOTTING AND DISPENSING FUNCTION ccccccseccsscccscccusccesccessccesscesccesceeeceusceuees 16 2 8 CONTROL CARD DRIVER INSTALLATION da 19 29 HARDWARE MARK CONVENTIONS oiee E is 19 CHAPTER3 SOFTWARE INSTALLATION 2 ccccsccccscccccccccsccccscccccsccccsccccscccccsccccscccccscccccccccsseees 23 IE MCIVER TE Worle avis cisco celal skoda a ne ets to ners nes hee ade aie 23 2 NAAA E igs ascents O 23 9 INSTALACI N W IZARD id 23 CHAPTER 4 TUTORIAL e seossscssecssesosecosesosecosecoseoosesoseoosecosecosesosesososososososososssosssessesssesssesssessseossesssesssessseso 27 A DAS A O e a a a N 21 A2 LAUNCHER SYS ITEM E a N 21 a WOONPIGUR ATION A 27 Er REPARATION a a es A a DEE 28 w LOS EN 28 A0
39. Partial Sample mode In Full Sample mode only sample preparation 1s taken into the dispenser channel so the sample uptake can be put back into the sample plate In Partial Sample mode system liquid such as distilled water is first taken into the dispenser channel then some air and actual sample preparation is taken while the sample uptake cannot be put back into the sample plate Advantages and disadvantages of the two modes respectively are listed in the Table X below Table IX Sample uptaking mode Mode Full sample Partial sample Uptake sequence Sample only System liquid Air Sample Sample uptake gt 35uL gt 5uL Sample reutilization Yes No Maximum spots per uptake gt 5000 gt 200 Extraction Times refers to the recurrence of Dry operations after taking in system liquid or sample preparation Each Dry operation lasts 1 second The recurrence is related to the sample characteristics Step 3 Pre dispensing Setting Pre dispensing refers to the procedure and method to dispense a certain amount of sample preparation at a specified location immediately after taking up sample for the purpose of spots uniformity Times refers to the repeat of pre dispensing operations after taking up sample Dispense Time refers to the duration of each pre dispensing operation measured in micro seconds Step 4 Dispense time Allows one to differentiate the dispense time period for each channel when multiple channels are used in the applica
40. Set some samples as blank optional CapitalBio Corporation 53 SmartArrayer M Chapter 7 Spotting or Dispensing Note For samples whose dispensing properties are greatly different the user can divide the samples into several groups and dispense them separately using different protocols including aspiration time aspiration pressure dispensing time and dispensing pressure To do this users can insert all samples in the array and set those groups of sample which have different protocols as blank Note If certain wells on the plate actually hold no sample though corresponding sample groups are inserted into the sequence list you can select the item and click Set As Blank button to skip operations such as sample taking and spotting to these very sample groups 7 4 3 Spotting Process Spotting Process tab only applies to the 136S 48S as shown in Figure 7 7 de Microarray Setting Sample Sequence ap Process of Spotting Cleaning Sample Uptake Compensation of 2 ar E Protocol g5 position imm Rinse_1 Delay time 5 i sonicate_ Spots per uptake Dry 1 swo 4 Pre spotting Sum of slides 1 Sum of spots 40 Distance Umm S00 Z Motion settings For spotting Acceleration mms 1 200 i Velocity immis 20 Options Delay time 5 0 01 Sonicate time 5 Add W Rinse time si 1 Lifting stroke immi i Open Dropping stroke fmm W Drytime s 1 save A Min RH 5 Es
41. SmartArrayer Series Microarray Spotter User Manual Version 4 0 r pe mm TAO ap eee P ir if a role Pig eee ise eneee Gorporation Copyright Notice 2006 2008 CapitalBio Corporation All rights reserved No part of this publication may be reproduced transcribed transmitted or translated into any language in any form and by any means without the written permission of CapitalBio Corporation Important notice CapitalBio believes that the information in this document is accurate The document has been carefully reviewed for technical accuracy In the event that technical or typographical errors exist CapitalBio reserves the right to make changes to subsequent editions of this document without prior notice to holders of the edition The reader should consult CapitalBio if errors are suspected IN NO EVENT SHALL CAPITALBIO BE LIABLE FOR ANY DAMAGE ARISING OUT OF OR RELATED TO THIS DOCUMENT OR THE INFORMATION CONTAINED IN IT TRADEMARKS CapitalBio SmartArrayer is a registered trademark of CapitalBio All rights reserved CapitalBio SmartArrayer Software End User License Agreement IMPORTANT PLEASE READ CAREFULLY This End User License Agreement hereinafter referred to as Agreement is a valid and binding agreement between CapitalBio Corporation hereinafter referred to as CapitalBio and you either an individual or a single entity for the use of the SmartArrayer Software System
42. SmartArrayer 48 Number of Sample Dispensing Time 3Replications Sample 30 00 27 00 24 00 Single Despensing Head 48 Slides f 5 21 00 O 3 18 00 2 Slides 15 00 O 12 00 D Spensing Head 5 Slides S 9 00 2 oug ing Head 48 Slides 3 00 0 00 0 200 400 600 800 1000 Number of sample CapitalBio Corporation 79 SmartArrayer M Appendix I Throughput and Time Table XX SmartArrayer 136 Number of Sample Spotting Time SmartArrayer 136 Number of Sample Spotting Time Reference 3Replications Sample pin 135 Slides des S o Oo Oo oo o o o w gt o 1 pin 50 Slides N on o oS Spotting Time Hours N O O 4 pins 135 Slides en o oS o 8 pins 135 Slides a o a 32 pins 135 Slides gt o So 0 100 200 300 400 500 600 700 800 900 1000 Number of Slides Table XXI SmartArrayer 136 Number of Sample Dispensing Time SmartArrayer 136 Number of Sample Dispensing Time 3Replications Sample 72 00 66 00 1 Despensing Head 136 Slidg 60 00 54 00 1 Despensipg Head 100 Slide 48 00 42 00 36 00 30 00 24 00 Dispensing Time Hours 18 00 12 00 6 00 0 00 0 100 200 300 400 500 600 700 800 900 1000 Number of sample CapitalBio Corporation 80 SmartArrayer M Appendix II Aspiration Volume and Aspiration Time A
43. a Get as blank Set as zar SmartArrayer M Chapter 7 Spotting or Dispensing Step 1 Select sample wells on sample plate Use the tool buttons on the upper right corner to select sample wells in a certain order The tools provided are as following Select You have four ways to select the sample well into the sampling list Whatever method you apply the selection operation is based on a sample group determined by the pin dispenser pattern That means a sample group 1 1 2 2 and so on is the smallest unit that can be selected or deselected Single select Click on the corresponding well and select one sample group at one time Row Column Select When you click on a row column head as many as possible sample groups in that row column are selected when you click on the inner area as many as possible sample groups in either the row or column are selected according to Sample Selection priority setting on the configuration panel The sample groups selected by row column will also be arranged in the order indicated by the sample selection priority setting too However if some sample groups in that row column have been already selected previously they will not be re ordered by the new selection Rectangle Select Press the left mouse button and drag to draw a rectangle and sample groups within the rectangle will be selected and arranged in the order indicated by the sample selection priority setting However if some sample groups in that
44. ace System liquid For 48D 136D regular replacement of system liquid in the sonicator basin is required under partial sample mode The methods and protocol are similar to those for water in the sonicator CapitalBio Corporation 71 SmartArrayer M Chapter 10 Troubleshooting Chapter 10 Troubleshooting 10 1 Overview The user can refer to the following table for troubleshooting arrayer problems 10 2 Troubleshooting For troubleshooting check the problem analyze the cause and review the possible solutions below Some problem may have multiple causes The possible causes should be considered and eliminated one by one Table XI Troubleshooting for 136S and 48S Abnormally high speed Error light ON One or more axes exceed the sensor limits position Initialization One of more axes do not move and stay between the Home sensor and the position limit sensor Running error pops up by the software One or more axes moves less than it s set movement Restricted motion of pin s in their guide hole s Unreliable connection between the cable and motion control card Sensor Damage or the sensor light is off If head placed manually in the incorrect position beyond limits when power off Wrong DMC settings At least one axis exceeds the position limit sensor EMS button was hit connection and Loose between motor securing screw s Dirty interface of pin and hole spillage or con
45. ameters as following see Figure 6 9 Slide Parameters Section this involves dimensional information about the slide the margins preserved from spotting etc Sample Selection Priority Section applies to virtual sample plate panel see Section 7 4 2 CapitalBio Corporation 45 SmartArrayer M Chapter 6 System Configuration when editing sample list These parameters are used to control sample arrangement manner on the plate and can be customized by users to their specifications System configuration Position Calibration Motion Setting Other Slide Parameters rim Slide Size mm ea S Min margin 3 Pre spotting rea fmm A E Paii El Sample Selection Priority Row hloltv i order Pow gt Col C Col gt Row Rowl iselection l Left gt Right Right Left cane Figure 6 9 The interface for setting Other Options 6 8 Backup and Restore Confirm that all necessary modifications are put on the configuration panel and click on the OK button at the bottom of the panel to save the modifications into the system configuration file and then exit the configuration panel The settings will automatically be applied when the system starts up next time To avoid accidentally misplacing data in the system configuration file the Save and Load functions are provided You can click the Backup button to save data as a system configuration file sas and click the Open button and confirm when notified to restore se
46. and notices shown on the equipment Distinguish among the pressure inlet from the outlet and the power input from the output Connect the pneumatic tubing connectors and or adaptors in clean surroundings and make sure there is no pressure leakage in the pneumatic systems Make sure the output pressure of the outer pressure source is lower than 0 5Mpa Ensure that the work bench platen is completely level using a spirit level to align the instrument Once the dispensing module or the spotting module has been installed its position must be completely level using a spirit level to assure perfect motion between the pin dispenser tips and the glass slide surface The calibration methods can be referred to in Section 6 3 14 SmartArrayer Chapter 2 Hardware Installation Check each equipment module and unit and make sure the connectors and terminals are connected inserted and fastened correctly e Ensure that no objects obstruct the motion pathway of the printing heads Warning Make sure the equipment is correctly electrically grounded Make sure all the power switches are turned off e Do not clean the inner parts of the axis If necessary please use a cotton cloth to clean the outer parts of the axis e Avoid entry of dust into the tubing by loading the dispenser enclosure onto the dispensing unit during the installation process eo After installation Wipe off the particles and fragments from the platen and clea
47. andle it 5 4 Software Main Interface The software main interface varies with different microarray workstation models Here the main interface of the 136D is shown in Figure 5 2 Load Save System About Protocol Protocol onfisurati CapitalBio SmartArrayer 48 Microarray Spotting System Spotting R p T _ Cleaning according to the selected cleaning protocol file File Y Pin Dry Y Dy O Poy UY Sonicate UPin Sonicate ther Load Slide Home Ud Humidity Status bar Temperature umidity Figure 5 2 The Main interface 136D Warning Please check that all the axes have already moved to the home position CapitalBio Corporation 32 SmartArrayer M Chapter 6 System Configuration Chapter 6 System Configuration Note When to do this 1 Immediately after installation 2 After changing the spotting module to dispensing module or vice versa 2 Whenever the instrument is moved struck or jarred 3 Whenever pins or rings have been replaced 4 Whenever you change the type of slides used 5 Whenever you change the type of microplates used 6 When you change samples 7 When the spotting or dispensing is regularly inconsistent 8 At least once a year 6 1 Overview If you do not configure the system after installation the microarray workstation software will remind you to configure it as shown in Figure 6 1 This is separated from normal functions such as spotting or di
48. arting and ending X direction vectors from the X Direction list to specify the sub array for reprinting between the selected ranges The index selection only applies to circumstances when arrays are replicated e Select starting and ending spot replicate indexes from the Replication Replicates list to specify the sub replication list for reprinting between the selected ranges Step 3 Click on the Start button to perform the reprinting operation The following operation applies to a normal run CapitalBio Corporation 63 SmartArrayer M Chapter 8 Additional Software Features Reprinting on missing spots Start Sample 3 C D3 4 3 E F2 1 22 Slide 11 1100 hd M Y direction i E Tx direction i a 2 Replication il i TA Figure 8 1 The reprinting on missing spots setting interface 8 3 Tagging Sample Click the Tag button on the left to access the tag page as shown in Figure 8 2 Tag current protocol ai upat g MEN pla Tag Open Save Clear Plate No b 7 Feature size um 120 384 wel Tagged sample list P 3 C3 ID Name1 3 C4 3 D3 and ane i Ea 57 E and name a g cin Position ID Name F VS A E i A a T KE J K6G K ee e L Virtual 384 well plate _ i m H N HA A HET 3 E8 P 3 F7 lt gt 3 F8 Mi Figure 8 2 The interface for tagging sample Tag Current Protocol Click on the Tag Current Protocol button to load the sample sequence
49. ay parts are loose Unsuitable slide Change surface treatment protocol or surface chemistry change to a different kind of slide No preview result in saved xls files Omer emos O tnt Cat File operation Preview after saving Preview before saving CapitalBio Corporation 76 SmartArrayer M Appendix I Throughput and Time Appendix Throughput and Time Table XIII Test conditions Parameters Spotting Dispensing Velocity mm s 300 150 Z axis Acceleration mm s 3000 1500 Z axis Rinse for 3s Drain 1 times rinse 1 Cleaning protocol Rinse for 3s sonicate for 3s times drain 1 times dry 1 Rinse for 3s sonicate for 3s times Rinse for 3s sonicate for 3s Rinse for 3s dry for 1s Rinse for 3s dry for 1s dry for 2s Table XIV SmartArrayer 48 Number of Spotting Slides Spotting Time SmartArrayer 48 Number of Spotting Slides Time 960 samples 40 00 35 00 30 00 1 Replications Sample N N gl gl o o o oS O O Spotting Time Hour 10 00 5 00 0 00 0 5 10 15 20 25 30 35 40 45 50 Number of Slides piece Table XV SmartArrayer 48 Number of Slides Dispensing Time SmartArrayer 48 Number of Slides Dispensing Time 960 samples 40 00 35 00 5 Replications Sample 30 00 1 Replications Sample N N O gl o o O O 15 00 Dispensing Time Hours L e o a de o O 2 o O 0 10 20 30 40 50 60
50. ay setting interface Step 1 Specify pin dispenser pattern Select the correct pattern in the combo box which reflects the pattern of the pins dispensers actually installed on the bracket The pattern of pins can differ from 1 1 1 2 1 4 2 1 2 2 2 4 4 1 4 2 4 4 8 1 8 2 to 8 4 representing 12 different patterns Whenever you change the pin dispenser pattern parameters relevant to arrays previously set will be invalid For instance a pattern of 2 4 pin configuration is depicted in Figure 7 3 CapitalBio Corporation 50 SmartArrayer M Chapter 7 Spotting or Dispensing Pin Configuration Combination Pattern Figure 7 3 Pin configuration If the NDM is concerned the layout of the dispensers could be one of following six patterns 1 1 1 2 2 1 2 2 4 1 4 2 and should be compliant to the actual situation of the print head If a 384 well sample plate is to be used then pattern 1 1 is the only choice for you can make For instance the pattern of 2 2 dispenser configuration is depicted in Figure 7 4 Dispensing Head Configuration Combination et Pattern Figure 7 4 The 2 2 Dispensing head configuration Step 2 Slide Settings Slide parameters OX OY PX PY LX and LY are described in Figure 7 5 Parameters OX OY PX PY determine the area actually used for spotting e Confined to the scanner specifications OX and OY should be no less than the Minimum Margin specified on the configuration panel and the d
51. b step 1 Specify pin dispenser pattern Sub step 2 Slide Settings Array setting sce Section 7 4 1 Sample Sequence ce Section 742 sees bee see Section 7 4 3 santa see Section 7 4 4 Sub step 5 Minimum Relative Humidity CapitalBio Corporation 28 SmartArrayer Chapter 4 Tutorial 4 6 Preview Click on the Preview button on the left and access the spotting preview panel you can access the Save and Load buttons on the top toolbar to backup and restore the editing protocols Slide Preview the simulation of the spotting pattern on the slide will be displayed to help users confirm whether the protocol and configuration are correct Sample Preview it provides a visual aid for users to estimate the sample spot distribution on each slide according to the current microarray settings and sample sequence 4 7 Run Click the Run button on the left to access the run page which implements two functions Status notification and spotting process control Check the protocol and save it Check that the sample plate and pre spotting slides are placed in the proper Start n positions Click the Start button on the run page to perform spotting Click the Pause button to pop up a dialogue for users to select the next action to Parise take The arrayer will pause temporarily AFTER the current action is completed Select Pause after the cleaning option to halt the system after the wash operation Resume Select
52. cation Choose Rinse in the location section then calibrate the current position parameters for the Y axis and Z axis but not the X W axis coordinates If you are setting the Rinse coordinates for the first time the values will all be set at 0 Step 2 Initialization of the Axes Confirm that the X axis W axis also if using the 136S D and Z axis are in the home position If they are not in the home position place them in the home position by clicking on the X Home or W Home or Z Home buttons CapitalBio Corporation 36 SmartArrayer M Chapter 6 System Configuration Step 3 Adjustments Move the head along the Y axis and the Z axis slowly and carefully watch the head and the axes until the pins or dispensers would be rinsed thoroughly Warning When moving the axes always be aware of the position of the print head and pins dispensers Make sure that the planned routes of all the moving components are clear of any obstacles before you apply actual movement to avoid any potentially disastrous collisions Step 4 Calibration In the Current Position Parameters click box section confirm that the checked boxes in front of the Y and Z axis coordinates are ticked and that the ones in front of the X and W axis coordinates are not ticked Click on the Calibrate button and confirm calibration when notified to save the positions to the hard disk The corresponding coordinates in the calibrated position parameters section will
53. cience Parkway Changping District Beying 102206 P R China Tel 86 10 80725793 Fax 86 10 80726782 Website http www capitalbio com Email techsupport capitalbio com globalsales capitalbio com CapitalBio Corporation 111 SmartArrayer Contents CHAPTERO PREFACE comerciales ion cenas 1 O OVERVIEW a AS A ls l 02 CONTENTS OR THD MANUA e a e e E ne l 03 FUNCTIONS AND SE RUE o e a A l 0 3 1 F OSE O E T RR O 1 0 3 2 NOTO e E De lb an leidos DES 2 Y A A 2 A AR 2 CHAPTER 1 IMPORTANT SAFETY INFORMATION 2 cccccccccccscccccccccccccccccccccccccccccsccccccccccccces 1 1 1 CERTIFICATION IDENTIFICATION AND POWER SUPPLY LABEL ooocccconcccncnncccnonoccnnonocononnccononccnnnnarononnarcnoninins 1 2 THE PROTECTIVE HOUSING COVER OR ENCLOSURE cccccccccccccccceccececccceecceeeeceececeececeeeeeeeeesesseeeeseeeeeeeeeees 3 LS POWER SUPPLY CABLE CORD enron n ected a a tees 4 LA O SA A es eee II II A TON Veen OTE EE 4 Nao 4 LOS HW FON TN Gil MIS ote 4 ES E A oe aie Oe na DSTA PS EESTI tre On ERR WER aC EER UR TE RR 5 LS SAMPLER BOUIREIMIE NTS Sal 5 119 SYSTEM CLEANING ea 5 1 10 EMERGENCY STOP BUTTON a 6 1 11 PRO GE CTO OG Saree a a RA 6 112 SWITCH BETWEEN PIN PRINTING AND DISPENSING SYSTEM secccseccssccescccsccesccesccecceusccusccusceusceusceuaes 6 1 13 SER O A A II II A TAN 6 CHAPTER 2 HARDWARE INSTALLATION o oocccooccconccconoccnnccnonccnoncccnoccnonccnnnoccnncccnnccnnnccnnncccnnoccnnnccnnnccnnness 7
54. cted in Section 2 9 Warning When performing microplate position calibration solo pin or solo dispenser mode is required CapitalBio Corporation 40 SmartArrayer M Chapter 6 System Configuration Step 1 Choosing Location Well Number In the Location Section choose Well A24 for the 136S 48S or choose Well A24 Well A12 for the 136D 48D according to the different type of microplates because the 136D 48D supports both the 384 well plate and the 96 well plates then calibrate the Current Position Parameters The X W axis Y axis and Z axis coordinates will be displayed in the corresponding text box If it is the initial time the initial values are all set to 0 Step 2 Initialization of the Axes Confirm that the Z axis X axis also if 136S D is in the home position If it 1s not in the home position send it to the home position by clicking on the Z Home button X Home also if using the 136S D microarray workstation Step 3 Adjustments Move the X axis W axis instead if the 136S D Y axis and Z axis by slowly moving step by step and carefully watching until the pin or dispenser is located at well A12 or A24 on the microplate thereby ensuring proper sample uptake Warning When moving the axes always be aware of the position of the print head and pins dispensers Make sure that the planned routines of all the moving components are clear of any obstacle before you apply actual movement to avoid potentia
55. e Delay time refers to the time required while the pins contact the slide when spotting Lifting stroke refers to the distance the pin moves upward relative to the record of the Z axis position calibration when spotting Dropping stroke refers to the distance the pin moves downward relative to the record of the Z axis position calibration when spotting Step 5 Minimum Relative Humidity Min RH refers to the minimum relative humidity that should be used within the microarray workstation It is dependent on the characteristics of the sample CapitalBio Corporation 55 SmartArrayer M Chapter 7 Spotting or Dispensing 7 4 4 Dispensing Process Process of Dispensing tab only applies to 136D 48D as shown in Figure 7 8 de Microarray Setting Sample Sequence ie Process of Dispensing Cleaning Sample Uptake Protocol a Mode Full sample cr a FS Dry_1 Pre dispensing Times 2a time us 250 Dispense Time us Channel 1 a0 ooo Channel 2 Channel 3 Channel 4 so Channel 5 Options o EL Channel 6 iw on times i Add TAR po y ae la i El _Open Channel 8 pso O W Dry times 1 a Save PET bs 3 Figure 7 8 The dispensing parameters setting interface Step 1 Cleaning The cleaning section describes the cleaning method of the system The cleaning protocol is the iteration of five steps Rinse Drain Rinse Drain Dry The number of cycles of this iteration is dependent on the sample characteristics Sample
56. e glass slide sonicator and for loading and unloading of the pins are identical Before loading or replacing pins ensure that the Z and Y axes are in the home position and then open the upper enclosure of the microarray workstation When loading unloading or replacing pins users must wear lab gloves and try not to touch the tip and stem of the pins by hand in order to avoid contaminating and or destroying the pin Users must also protect the pin tip which can easily become blunt due to collisions with other objects 68 SmartArrayer M Chapter 9 Operation amp Maintenance To place the pins in the pin holes in the pin holder correctly and safely the operator should hold the cap of the pin by the right hand and place the tip in the hole in the upright position direction The user must not shake the pins After placing the pins the operator must slide the pin along the pin hole slowly In succession with the aid of a tweezers the operator can rotate the pin in the hole and make sure the cap of the pin enters the slot which prevents large angle rotation of the pin while spotting Use the tweezers to lift the pin up slightly Then move the tweezers away and see whether the pin can slip downward along the hole freely or not If not the operator must unload the pin from the pin holder and clean the pin and or the pin holder because dust may adhere to the surface of the pin stem and or the hole of the pin holder To unload the pins from
57. e of ventilation Users must not block or cover the vent of the fans Blockage will cause the temperature to rise and may result in damage to the arrayer possibly causing electric shock and fire Warning Users are not allowed to cover the vent of the fan in the platen of the CapitalBio SmartArrayer Otherwise the temperature will rise and result in damage to the arrayer possibly causing electric shock and fire 1 6 Moving Parts The CapitalBio SmartArrayer contains moving parts which may lead to a mechanical hazard 1f users do not follow the instructions manufacturer has provided or moving parts may cause injury to users The protective housing is designed to protect users from exposure to the moving parts during operation CapitalBio Corporation 4 SmartArrayer Chapter 1 Important Safety Information Warning Users are not allowed to gain access to the interior of the arrayer during operation The protective housing of the arrayer is designed to protect users from the hazardous moving parts under operation 1 7 Water The CapitalBio SmartArrayer has some components such as the Sonicator Humidifier and the Working Water Tanks which for operations must be filled with some water For details see Section 9 3 1 8 Sample Requirements Applications to fabricate nucleic acid or protein microarrays on CapitalBio SmartArrayer are possible with either the contact pin printing module or the non contact di
58. eesensaeeeeeeeeeeeeesessseeessnsnaaeeeeeeseeeeeees 2 Table HH Environmental Require MENIS serran casos aa ssa casa oases 7 Table HI Minimal dimensions of the instruments ui 7 Table IV icc trical anput Patti GS rt A A AA AA A 8 Table V Recommended UPS specifications cccccccccssssssessssesesseseseeesessseseeseeeseeesseeeeeeeeeeeeeeeeeeaas 8 Table VEC Oia puter FCG Cn NiS see esa ee el 9 Table VP ACKSd DO ASAS iaa 10 Table VIII Procedure for changing from spotting to dispensing modules ccccnnnnnooooooconnnononcnnnnnos 17 Table EX Sample Wp lak ie 10 desata ralla cie 57 Table X Protocol for replacing water for sonicate wash cccccccnnnnooooooononcnononnnnncnnnnnnnanananononononnnnnnos 70 Table XT Troubleshooting tor 136S and AS ainia 73 Table XII Troubleshooting for 136D and 48D 00oooooooooocccccnccncccnnnnonoononnnnnnnnnnnnonononnnnnnnnnnno non nnnnnnnnnnnnnnnos 74 Table HEIS Condi On ae a Dtos El Table XIV SmartArrayer 48 Number of Spotting Slides Spotting Time c cccccccessessessssseeseeeeee 77 Table XV SmartArrayer 48 Number of Slides Dispensing Time cccccccccscsscscsssscsesecesserseseeeeeers 77 Table XVI SmartArrayer 136 Number of Slides Spotting Time c c ccccsccscsssessssssssessseseeseseeeeee 78 Table XVII SmartArrayer 136 Number of Slides Dispensing Time oooocnicnonininiononinincononininicuoncnons 78 Table XVIII SmartArrayer 48 Number of Sample Spotting Time
59. equirements Table III Minimal dimensions of the instruments Models Dimensions Length mm Width mm Height mm Warning The SmartArrayer series microarray workstation should be placed in a room which has appropriate space to operate conveniently Place the computer at the left side of the microarray workstation and leave enough space between them CapitalBio Corporation 7 SmartArrayer Chapter 2 Hardware Installation 2 2 3 Power requirements Make sure the power supply meets the requirements appropriate for the relevant model 48S 48D 136S 136D The requirements of each model are listed in the following table Table IV Electrical input ratings For the series of EU Parameter Model 48S 136S NDM Frequency Hz 50 50 50 Rating voltage V 230 230 230 Maximum input current A 3 0 3 5 0 2 Rating power kW 0 69 0 805 0 046 Fuse A 6 3 6 3 0 315 For the series of NA Parameter 485S 136S NDM Frequency Hz 60 60 60 Rating voltage V 100 120 100 120 100 120 Maximum input current A 5 0 oD 0 4 Rating power kW 0 55 0 605 0 044 Fuse A 8 8 1 0 Comment the electricity rating for the 48D and 136D respectively is the sum of the power supply of the 48S and 13658 and the rating input electricity of the NDM To avoid or reduce losses caused by an accidental power cut we advice users to equip the microarray workstation with a UPS constant voltage power source The recommended voltage parameter
60. fit loss operation interruption business interruption business information loss and any other pecuniary loss arising from the use of this System or inability to use this System CapitalBio does not guarantee the stability of this System if you install other software in the process of using this System on the same computer This system may only work and function with properly under correct usage CapitalBio s total liability to you for any damages and or losses for any causes whatsoever under the terms of this Agreement will be limited to the actual amount paid by you for this System Termination of License If you breach any terms or conditions of this Agreement CapitalBio shall have the right to terminate the license at any time If CapitalBio decides to terminate this license you must immediately destroy no more than three 3 days after the termination this System and any copies of any documents of this System or return them to CapitalBio CapitalBio Corporation 11 SmartArrayer Applicable Laws This System shall be protected by the Copyright Law of the People s Republic of China and relevant international intellectual property protection treaties which have been acceded to and enforced in the People s Republic of China This Agreement shall be governed by the law of the People s Republic of China If you have any question with respect to this Agreement please contact CapitalBio Address CapitalBio Corporation 18 Life S
61. g technology SmartArrayer 4 0 is the updated application software for CapitalBio SmartArrayer series microarray workstations There are corresponding user interfaces for different workstation types and work applications 0 4 Conventions Table I below lists the abbreviations and alternative names used frequently in the user manual Table I Abbreviations and alternative names Microarray Alternative name of CapitalBio SmartArrayer 48 and CapitalBio workstation SmartArrayer 136 48S CapitalBio SmartArrayer 48 equipped with spotting unit pin printing 48D CapitalBio SmartArrayer 48 equipped with non contact dispensing unit 136S CapitalBio SmartArrayer 136 equipped with spotting unit pin printing 136D CapitalBio SmartArrayer 136 equipped with non contact dispensing unit NDM Non contact Nano Dispense Module NDM Dispensing Non contact droplet dispensing Spotting Contact printing or pin printing 0 5 Where to get help Our staff at CapitalBio Corporation wants to help with any questions or comments you might have regarding the system its software and other components Feel free to contact CapitalBio Corporation in the following ways CapitalBio Corporation 2 SmartArrayer Chapter 0 Preface Address CapitalBio Corporation 18 Life Science Parkway Changping District Beying 102206 P R China Tel 86 10 80725793 Fax 86 10 80726782 Website http www capitalbio com Email techsupport capitalbio
62. g unit and refreshing system liquid for the sonicator bath 9 2 Daily operations Before loading the unit with plates or slides or replacing the pins and refreshing the water in the sonicator basin lift the upper enclosure and place it on the top of the frame Note Before performing the above operations make sure the power status of the microarray workstation and computer is set to off Figure 9 1 How to open the covers of 136S and 136D models The 384 or 96 well plate surface should be placed in the plate bracket in the lower plate area and pressed downward to fasten the plate via the moveable frame Be careful to place the plate in the proper direction CapitalBio Corporation 67 SmartArrayer M Chapter 9 Operation amp Maintenance Figure 9 2 Load well plate To load the slides into the plates push the moveable frame back and place the glass slide into the concave areas the barcode of the slides should be placed near the moveable frame and then the moveable frame should be loosened to attach the slide CapitalBio Corporation Figure 9 3 Load slide Warning The water volume in the sonicator should be about 2 3 of the inner capacity of the basin After adding water to the sonicator the sonicator needs to be placed on a marble workbench and be placed in contact with the positioning plate For models 48S and 48D and for 136S and 136D the methods protocols and notes for installing the microplat
63. haracters cane Figure 6 3 Setting the password interface Warning After any modification on the configuration panel please click on the OK button to validate your change 6 3 Position Calibration Position calibration refers to determining and recording the locations of several components of the microarray workstation which are critical to different steps in spotting or dispensing operations Position calibration should be carried out after any instrumentation changes or maintenance to ensure that precise location is determined and avoids any potential problems e Position calibration consists of determining the following coordinates for pin movements relative to the positions of the slides microplate rinsing drying and sonicator modules e For the 48S the position of 1 slide should be calibrated while for the 1365 the positions of both the 1 and the 73 slide which is the 1 slide on the second platen should be calibrated e For the 136D or 48D the system liquid position should be set as the same as the sonicating position in the 1365 or 48S e For the 136D or 48D the pre dispensing position should be set and the sample source could be either the 96 well plate or the 384 well plate e For the 1365 the position calibration page of the configuration panel is as shown in Figure 6 4 CapitalBio Corporation 34 SmartArrayer M Chapter 6 System Configuration System configuration Position Calibration Motio
64. he microarray workstation e Turn on the microarray workstation press the device startup button prior to the linked computer e Turn on the control box power if using the NDM Then turn on the computer linked to the microarray workstation e Launch the microarray workstation application software 5 2 3 Shutdown System Steps Turn off the computer linked to the microarray workstation Turn off the power switch which is on the rear panel of the microarray workstation Turn off the control box power if using the NDM Turn off the vacuum pump 5 3 System Startup Click the Start at the left bottom corner on the desktop menu of the Windows operating system Select Program gt CapitalBio gt SmartArrayer4 0 gt SmartArrayer4 0 or click the shortcut SmartArrayer4 0 to start the microarray workstation application software After system startup the following action is required for a self test which checks the system control card and the serial port communication CapitalBio Corporation 31 SmartArrayer M Chapter 5 Getting Started oe fe NBR Capital Bio Corporation E ARNO SmartArrayer 48 Microarray Spotting System Loading settings 2006 01 V4 0 Figure 5 1 System self test interface Once the self test is successfully completed the main interface of the software will appear Warning If a message box appears please shut down the microarray workstation and contact the technical support engineer to h
65. imensions of the barcode on the slide should be taken into account when determining PY e Modifying OX might reduce PX automatically likewise OY to PY The upper bound of PX or PY should not exceed the slide dimension while the lower bound relates to pin dispenser patterns e Modification of PX or PY might affect array settings Figure 7 5 Slide parameters Step 3 Slides In this section you can specify the number of the slide to start at the number of the slide to finish at and the sum of slides to be spotted on At least one slide must be reserved for pre spotting by the 136S 48S For example using the 48S if you desired 40 spotted slides and CapitalBio Corporation 51 SmartArrayer M Chapter 7 Spotting or Dispensing needed 3 prespotting slides the required total number of slides on the arrayer platen is 43 Step 4 Array Settings One spot constitutes one feature on the slide Parameters such as spot distance sum of spots array spacing and sum of arrays provide information about the dimension and layout of features on the slide Spot distance refers to the displacement of the same pin dispenser between successive spotting actions It should be modified according to spot size and will usually be 180 400um Sum of spots Array spacing refers to spacing between borders of neighboring arrays Sum of arrays should be no greater than the Maximum sum of arrays The latter could be calculated according to array spacing a
66. iration time for air refers to the time required to inhale air Drying time refers to the time required for vacuum drying after taking up sample or system liquid Warning It is recommended to modify the aspiration time and dispensing pressure according to the viscosity and surface tension characteristics of the sample When all dispensers are equipped the dispensing pressure should be no less than 3kPa and the dispensing time no less than 0 25ms Operation Guide e Access the Dispensing Parameters page on the Configuration Panel as shown in Figure 6 8 Specify the parameters applying to the cleaning or the dispensing procedures respectively in the corresponding text boxes You can always restore the parameters to the manufacturer s default setting by clicking on the Default button System configuration Position Calibration Motion Setting Pressure Dispense Uther Cleaning Dispense Aspiration pressure kPaj 5 00 Aspiration pressure kPa 4 00 Aspiration time s 4 00 Aspiration time For system Fluid 5 Dispense pressure kPa 20 00 Aspiration pressure For air kPa Dispense time 5 2 00 Aspiration time For air 5 Aspiration time For Went time 5 3 00 sample s Drying time ts 2 00 Dispense pressure kPa Drying time 5 Detault Open Backup Figure 6 8 The interface for setting Dispensing parameters 6 7 Other Options Other pages provide access to other important par
67. l the driver for the motion control card The driver can be found on the SmartArrayer 4 0 software disk Place the SmartArrayer 4 0 software disk into the CD ROM or DVD ROM and then browse the driver folder to find the setup exe file Run the setup exe and follow the instructions After successfully installing the driver shut down or restart the computer 2 9 Hardware Mark Conventions In general the top right hole shown in the following figure is referred to as the Ist hole for the pin in the software setting and the hardware installation Accordingly the top right corner of the slide is referred to as 0 0 position when you hold the slide longitudinally near the end with the barcode The layout and definitions of these conventions for the 136S and the 136D are shown in the following figures Figure 2 7 and 2 9 The layout and definitions of these conventions for the 48S and the 48D are shown in Figure 2 8 In the view at the left side of the 136S and the 136D workstation Fig 2 7 the slide at the top left corner of the upper platen is the Ist slide and the slide at the top left corner of the lower platen is the 136th slide The source microplate should be fixed into its bracket on the lower platen with the number P24 well at the bottom right corner of the bracket and the number A24 well should correspond to the Ist pin Accordingly the top right hole of the vacuum drying unit 1s assumed to be underneath the Ist pin
68. lly disastrous collisions Step 4 Calibration In the Current Position Parameters section confirm that the checked boxes in front of the X axis or W axis if 136S D Y axis and Z axis coordinates are all ticked Click on the Calibrate button and confirm calibration when notified to save the axes position to the hard disk The corresponding coordinates in the Calibrated Position Parameters section will be updated and then the Z axis has moved to the home position 6 3 6 Pre dispensing Position Calibration The Pre dispensing Position Calibration Position applies only to the 136D 48D It refers to determining and recording the Z axis coordinate when pre dispensing just over the well holding the sample liquid immediately after taking up the sample Only the Z axis coordinate is concerned Step 1 Choosing the Pre dispensing Location In the Location Section choose Pre dispense and then calibrate the Current Position Parameters The Z axis coordinates will be displayed in the corresponding text box The X W axis and Y axis coordinates are invalid If it is the initial calibration the initial values are all set to 0 Step 2 Initialization of Axes Confirm that the Z axis X axis also if 136S D is at the home position If not send the Z axis to the home position by clicking on the Z Home X Home also if 136S D button CapitalBio Corporation 41 SmartArrayer M Chapter 6 System Configuration Step 3 Adjustments Move the
69. n Setting Other Figure 6 4 The 1365 position calibration interface For the 48D the position calibration page of configuration panel is shown as Figure 6 5 CapitalBio Corporation 35 SmartArrayer M Chapter 6 System Configuration System configuration Position Calibration boton Setting Pressure Dispense Other Options Rinse C Dry C System Liquid C ist Slide 0 Pre dispense C Wo A12 Well Calibrated Pos Parameters tmm D000 Y 0 000 Current Pos Parameters mn E 0 000 mt Y 0 000 W Z 0 000 Save Jogging rr 4 Step TO b IS Step 6 Y Lett Y Right to Calibrated pos Step Lp Down to Calibrated poz x Home Y Home Horne Open Backup Cancel Figure 6 5 Interface for position calibration of the 48D Warning Axis velocity and acceleration are fixed when calibrating For axes X W and Y velocity is 20mm s and acceleration is 200mm s for axis Z velocity is 10mm s and acceleration is 100mm s 6 3 1 Rinsing Position Calibration Rinsing Position Calibration involves the Y and Z coordinates but not the X coordinate It ensures that all 32 pins for the 136S or 48S or 8 dispensers for the 136D or 48D are immersed simultaneously in the rinsing solution held by the rinse dry station and are rinsed thoroughly by flowing distilled water The position of the rinse dry station is described in Section 2 9 Step 1 Choosing Rinse Lo
70. n slowly in incremental movements and carefully watch until the pin head or dispenser reaches the desired location above dispenser based system or just contacting spotting system the slide surface Step 6 Calibration the Z position In the Current Position Parameters section confirm that the checked box in front of the Z axis coordinates is selected but the ones in front of the X and Y axis coordinates are not ticked Click on the Calibrate button and confirm the calibration position when notified to save it to the hard disk The corresponding coordinates in the Calibrated Position Parameters section will be updated by the time the Z axis has moved to the home position Step 7 Calibration of other slide positions as required For the 136S D models the calibration of the 73 slide is also required When performing these calibrations steps 1 to 6 are to be repeated with all the operations performed on the X axis substituted with operations on the W axis 6 3 5 Microplate Position Calibration The microplate position refers to the X Y Z axis coordinates when the pin or dispenser drops into the wells of the microplate to uptake sample The Microplate Position Calibration ensures that the uptake volume of sample is adequate and consistent among the all the pinheads or dispensers The coordinates of the well A24 for the 384 well plate or A12 for the 96 well plate should be used for calibration The location of the microplate is depi
71. n the platen enclosure and workbench Clean the humidifier sonicator and water tanks Remove any liquid spills from the workbench surface 2 6 Debugging e Before starting up the system Check the cable and tubing connections again Make sure that the photoelectric stop slide stay is away from the motion limit sensor Warning Check the workbench and make sure there are no obstacles to obstruct the movement of the printing head Clean the wash water tank and sonicator wash tank and refill distilled water into distilled water tank e Test the instrument step by step Install debugger software Startup the microarray workstation following the instructions in Section 5 2 2 and startup the debugger software Warning Set the velocity for each axis at 20mm s and the acceleration at 100mm s Check the forward and backward movement of each axis O Listen to whether there are any abnormal noises produced by the axes or by other equipment while moving or stopping Test the rinse sonicate wash vacuum dry drain and EMS functions separately e Test the system Install application software startup the hardware and software Calibrate the key positions and prepare the samples and slides The calibration methods can be found in Section 6 3 Runa protocol and make a microarray If there are problems please refer to other chapters including the trouble shooting chapter CapitalBio Corporati
72. nd redo all position calibrations For detailed instructions of each operation please see Section 2 7 and Section 6 3 1 13 Service Service is conducted by the technical support team of CapitalBio Corporation or authorized agencies only Consult CapitalBio Corporation or authorized agencies for repair instructions See Where to Get Help in the Preface for more information CapitalBio Corporation 6 SmartArrayer Chapter 2 Hardware Installation Chapter 2 Hardware Installation 2 1 Summary The chapter will introduce hardware installation requirements and installation procedures and inspection details debugging switching of dispensing module and spotting module and hardware mark conventions 2 2 Requirements 2 2 1 Environmental requirements The SmartArrayer should be placed in a clean room that meets the environmental conditions Spotting or Dispensing environmental requirements described in the following table Table II Environmental Requirements Site Requirement Indoor Use Cleanliness degree 10000 class meets or exceeds GMP requirements Temperature Range 5 30 C Relative Humidity Range Up to 50 Altitude Up to 2000m Because the microarray workstation is a precision instrument please keep the environment as clean as possible Install the microarray workstation away from sunlight ventilation ducts and any other devices that may cause significant change in temperature and humidity 2 2 2 Space r
73. nnnnnnnnnnnnnnnnn non nnnnnnnnnos 51 PraurS JS tdo Paramore rtorras hee 51 FISULS Sample ein ta o Be a cases 52 Figure 7 7 The spotting parameters setting Interface ceimice i 54 Figure 7 8 The dispensing parameters setting INter aCO oooooooooocnnnnncncnnnnnnnannnnnnnonnnnnnnncnnnnnananano non nnnnnnnnss 56 igure 7 9 Ve Slide preview UMC ACS A A A A 58 Fioure 10 The sample preview Miter aCe essa dd 59 Prouro 7ell The ronning stite interactions dd 61 Fieure 7 12 The continue ophon alter Pause e 62 CapitalBio Corporation I SmartArrayer Figure 8 1 The reprinting on missing spots Setting IMter aCe oooooncnoooooooonnnnnccnonononanonnornnnnnnnnnnnnccnnnnnnnnnnos 64 Figure 8 2 The interface for tagging Sample occccccnnnnnnnonononononnnnnnnnnnnnnnnanonnnn non nnnnnnnnnncnnnnnnnnnnnnnnnnss 64 Figure 8 3 Examples of sample attention Marks cccccnnnnnnooooonononnnononncnnonnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnss 65 Figure 8 4 The sample marker information file format ooocccccncnnnccncnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnns 66 Figure 9 1 How to open the covers of 1368 and 7136D models ccccccnnnnnnonooonononcnnnnnnnncnnnnncnnnnnnannn nooo 67 Risuts 9 2 bodd We IED Ale scan as de td cd orto 68 Pirar o Load Slide e e e A 68 Fiore 9 4 Loadine or UNLOAD iia a ER AAA E A A 69 CapitalBio Corporation IV SmartArrayer Table I Abbreviations and alternative names ccccssssccccccceceeccesees
74. o SmartArrayer through any other openings except that is needed to perform the function of the CapitalBio SmartArrayer Removing the housing may damage the CapitalBio SmartArrayer components and result in hazardous exposure to hazardous voltage or moving parts If the protective housing is damaged users are instructed to halt all use until a certified technician has inspected the instrument 1 3 Power Supply Cable Cord The manufacturer of the CapitalBio SmartArrayer provides the user with the power supply cable cord The cord is PVC insulated with an area of 0 75mm the voltages of which are up to and including 450V 750V Users are not allowed to replace the power supply cable with different rating or it may result in electric shock even cause fire and damage the arrayer Warning We suggest that users do not replace the power supply cord provided by the manufacturer If needed contact the technical support team for the CapitalBio SmartArrayer Replacing the power supply cable with another cable of a different rating may result in electric shock or even cause fire and damage the arrayer 1 4 Fuses See Chapter 2 2 3 Warning Replace only with same type and rating fuses otherwise it may result in electrical hazard or even dangerous fire Turn off electrical power at source 1 5 Fan before attempting to remove or replace the fuses There is a fan in the CapitalBio SmartArrayer for the purpos
75. o the 136D 48D There are parameters for pressure and time that are required for different stages of the work flow The parameters are already set by the manufacturer before packing The dispensing parameters consist of two groups of parameters used during the cleaning and dispensing procedures There are 3 consecutive steps in the Cleaning Procedure pumping in out circulating water through the channel Rinsing washing out liquid droplets that adhere to the inner side of the channel with high flows of water Draining blowing out liquid droplets that adhere to the inner surface of the dispenser by high pressure air and Drying drying the inner surfaces by negative air pressure The first group of parameters applied to these steps in the cleaning procedure The second group of parameters applied during the dispensing procedure They are as follows Aspiration pressure refers to the pressure applied to take up the sample or the system liquid preparations Aspiration pressure for air refers to the pressure applied to inhale air to separate sample and system liquid Dispensing pressure refers to the pressure applied to dispense the sample through the dispenser orifice onto the slide surface Aspiration time for sample refers to the time required to take up the sample Aspiration time for system liquid refers to the time required to take up the system liquid CapitalBio Corporation 44 SmartArrayer M Chapter 6 System Configuration Asp
76. of distilled water in the humidifier 111 1 4 Please refer to Chapter 9 Passage 3 for detailed operation instruction about 111 4 1 111 4 3 111 1 5 Before running any spotting protocol manually keep the water circulating through the rinsing position for about one minute and then perform corresponding cleaning operation via the preparation panel from software to wash the pin head or dispenser head 111 1 6 After being left idle for long time the instrument should be calibrated again before it is put to work again 111 2 On Run Maintenance If you launch a spotting protocol which lasts long time more than 24 hours etc you probably have to check 1 1 1 3 intermittently during the protocol is running 111 3 Post Run Maintenance 111 3 1 Perform corresponding cleaning operation via the preparation panel from software to rinse the pin head or dispenser head 111 3 2 Manually keep the water circulating through the rinsing position for about one minute to wash away the residuals in the basin tank 111 3 3 Check if there is any spillage on the workbench and wipe it away 11 3 4 Clean the pins and unload them from the pin holder cover the dispenser head with dispenser enclosure after microarray fabrication processes if the instrument will not be used again within several hours Scheduled Maintenance 111 4 Weekly Maintenance 111 4 1 Check if the pin can drop neatly and swimmingly during spotting If not please unload it and sonicate
77. omputer WARNING This computer program is protected by copyright law and international treaties Unauthorized duplication or distribution of this program or any portion of it may result in severe civil or criminal penalties and will be prosecuted to the masimum extent possible under the law Cancel Figure 3 1 Installation welcome interface CapitalBio Corporation 23 SmartArrayer Chapter 3 Software Installation Step 2 Choose the hardware model j SmartaArrayer 4 0 ala E omarArrayer Software Install Please install software depend on the hardware CapitalBio Smart raver 48 Micro rray Spotting System Spotting CapitalBio Smart rraver 48 Micro rray Spotting System Dispensing CapitalBio Smart rraver 136 Micro rray Manufacturing System Dispensing Figure 3 2 Software Control System Choice Interface Warning The interface allows you to choose the appropriate software for your instrument you must choose the right software to install Otherwise 1t may cause damage to the instrument Step 3 Choose the target folder to install j SmartArrayer 4 0 Select Installation Folder The installer will install Smart rayer 4 0 to the following folder To install in this folder click Next To install to a different folder enter it below or click Browse Folder C Program Files CapitalBio SmartaArrayer 4 04 Disk Cost Install Smart rraper 4 0 for yourself or for anyone who
78. on 15 SmartArrayer Chapter 2 Hardware Installation 2 7 Switching between Spotting and Dispensing Function To switch to the 136D 48D from the 136S 48S the NDM has to be linked through the corresponding cable connectors and the tubing connectors in addition to replacing the spotting module with the dispensing module Notice that there are tubing and cables that need to connect with the dispensing unit and the connection plate for the 48S The serial port labeled Serial of the NDM should be connected with the serial port of PC and the dispense control port should be connected to the same labeled port on the 136D 48D See Table IX The NDM has two tubing connectors namely Pressure Inlet and Pressure Outlet with the Pressure Outlet tubing connector connecting with the Air tubing connector of the 136S 48S and the Pressure Inlet tubing connector connecting with the pressure supply Dispense control port Pe Power input jack i _ Serial port Ha Pressure inlet Figure 2 7 The rear panel of NDM CapitalBio Corporation 16 SmartArrayer Chapter 2 Hardware Installation Power switch Power input jack Vacuum pump power jack Humidifier power jack Dispensing control jack Dispensing tubing tie in Motion control il Figure 2 8 The rear panel of 48S The following Table shows how to exchange the pin head module with the dispenser head module Table VIII Procedu
79. otting results High motion speed and some moving parts have become loose Insufficient sample Increase sample uptake time Inconsistent spot sizes after several spots High sample viscosity pone the set drop number per Surrounding environ Ensure the temp RH environment conditions slide conditions and high purity of sample quality sample are all correct and are quality etc No preview result File operation S Preview after saving Preview before saving saved xls files fOtherenors o Cont Ca ta Table XII Troubleshooting for 136D and 48D Following the software installation Unreliable connection instructions disconnect the cable and between the cable and motion control card and then Error light ON motion control card reconnect them and fasten the connection Sensor Damage or the Contact CapitalBio to replace the One or more axes If head placed Exit software shut down the PC shut Same as System running Restricted motion of pin s in their guide hole s Irregular array Contact CapitalBio Poor quality of spots Abnormally high speed high di Initialization exceed the sensor limits manually in the down the system and then place the position incorrect position axes between the corresponding beyond limits when Home sensors and the position limit power off sensors One of more axes do not move and stay between the Home sensor and the position limit sensor Wrong
80. oxes in front of the Y and Z axis coordinates are selected but the ones in front of the X and W axis coordinates are not ticked Click on the Calibrate button and confirm the calibration when notified to save the position to the hard disk The corresponding coordinates in the Calibrated Position Parameters section will be updated by the time the Z axis moves to the home position 6 3 4 Slide Position Calibration Slide Position Calibration applies to the X axis W axis the Y axis and the Z axis coordinates The X Y Z axis coordinates of the 1 slide are required for all models in addition the coordinates of the 73 slide are only required for the 136S D models The location of the slides is depicted in Section 2 9 The X axis W axis and Y axis coordinates of the upper left corner should be used for calibration The calibration of the Z axis coordinates should also be performed For the pin based system the Z axis coordinate is justified for calibration when the pinhead contacts the slide while for the dispenser based system the desired position is when the dispenser pin hovers at 1 2mm above the slide Warning When performing slide position calibration solo pin or solo dispenser mode is required Step 1 Choosing location of the 1 slide Choose the 1 Slide in the location section and then calibrate the current Position Parameters for the X axis Y axis and Z axis coordinates The coordinates will be displayed in
81. pitalBio Corporation l SmartArrayer Chapter 0 Preface control technology to control the movement of X Y Z and W axes and move the printing pins or dispensing head to set positions to spot or dispense sample droplets and meet the requirements of high precision and high velocity printing for microarray fabrication Both Telechem pin printing technology and CapitalBio non contact dispensing technology patents pending are able to be used in the CapitalBio SmartArrayer series microarray workstations This flexible technology enables CapitalBio SmartArrayer series microarray workstation users to have access to more applications than other brands These applications include the ability to fabricate microarrays of nucleic acids proteins antigens and other biomolecules on preformed chip surfaces of glass plastic or membranes Our highly efficient combinatorial cleaning of dispensing pins consists of sonication rinsing and drying can decrease or prevent most potential cross contamination among samples The humidifying unit and HEPA filter help to improve the fabrication quality of the microarrays 0 3 2 Series CapitalBio has developed two types of microarray workstations the CapitalBio SmartArrayer 48 and the CapitalBio SmartArrayer 136 with throughputs of 48 and 136 slides respectively All CapitalBio SmartArrayer series microarray workstations can adopt both pin printing technology and non contact droplet dispensin
82. pots on the slide Slide info slides for spotting slides for pre spotting and unused slides are each labeled with different colors as well as text descriptions There is no pre spotting for pre spotting in the 136D 48D Slide Preview al Sample Previews Slide vi Total spots per slide eee slide Into Sum of pre spotting slides H Array s Slides for pre spotting No used slides Slides for spotting Figure 7 9 The slide preview interface CapitalBio Corporation 58 SmartArrayer M Chapter 7 Spotting or Dispensing 7 5 2 Sample Preview Sample Preview help users to estimate the sample spots distribution on each slide according to the current microarray settings and sample sequence as shown in Figure 7 10 In addition tools for exporting GAL files are accessible on this page Save Info Click the Save Info button to save the distribution information of spots on the slide as an Excel file A dialog will pop up for the user to customize the file name and path Tag Sample Click the Tag Sample button to import an Excel file holding record of the sample ID and tag pairs to prepare sample information for exporting GAL files The imported Excel file can be edited and arranged in a special format with stand alone Microsoft Excel application or generated by Tag module of this software system see Figure 7 10 A dialog will pop up for user to select the proper Excel file Save Tagging Info button will
83. ppendix Il Aspiration Volume and Aspiration Time Table XXII Aspiration volume of 10 glycerol under different conditions Aspiration volume of 10 glycerol under different conditions 25 0 5KPa 20 0 AKPa 15 0 3KPa 10 0 Aspiration volume microliter sah o 0 0 0 0 2 0 4 0 6 0 8 1 1 2 Aspiration time s Table XXIII Aspiration volume of 30 glycerol under different conditions Aspiration volume of 30 glycerol under different conditions 25 0 20 0 5KPa 19 4KPa 3KPa 10 0 Aspiration volum micro liter 5 0 0 0 o O N 2 D gt O D 0 8 _ N Aspiration Time s CapitalBio Corporation 81 SmartArrayer M Appendix II Aspiration Volume and Aspiration Time Table XXIV Aspiration volume of 50 DMSO under different conditions Aspiration volume of 50 DMSO under different conditions 25 0 5KPa 15 0 4KPa 3KPa Aspiration volume microliter 5 0 0 0 0 0 2 0 4 0 6 0 8 1 1 2 Aspiration time s CapitalBio Corporation 82 SmartArrayer M Appendix III Routine Maintenance Appendix Ill Routine Maintenance 111 1 Pre Run Maintenance 111 1 1 Refresh system liquid for dispensing system or distilled water in the basin of the sonicator for spotting system 111 1 2 Make sure there is adequate reservoir in the distilled water tank and adequate space for drainage in the waste water tank 111 1 3 Make sure there is plenty of reservoir
84. r back in the positioning plate plug in the power cable Then press it close to the positioning plate Refill the distilled water into the sonicator bath Be careful to avoid spilling water on the workbench Humidifier The humidifier should be refilled with distilled water regularly Confirm the microarray workstation is not in operation and then unscrew the bolts on the rear plate of the structure with Philips head screwdriver to open the rear plate The humid gas tubing and power cable of the humidifier should be unplugged and the upper part of the humidifier should CapitalBio Corporation 70 SmartArrayer M Chapter 9 Operation amp Maintenance be pulled out and refilled with more distilled water After that place the upper part of the humidifier back in the correct position plug in the gas tubing and power cable and then install the rear plate again Water Tanks The distilled water tank and the waste water tank should be refilled or emptied based on actual operational usage Before undertaking this operation confirm that the microarray workstation is not in operation and then open the rear plate Empty the waste water tank and fill distilled water into the distilled water tank After completion the tank should be placed in the tank card plate Please make sure that the connection between the distilled water inlet pipe and the distilled water tank and the connection between the outlet pipe and the waste water tank are in pl
85. re for changing from spotting to dispensing modules Step No Schematic Drawing Description Move the Z axis to home position To unload the pins from the pin holder the operator should use the tweezers to lift the pin up by one hand and then slip the pin out from the pin hole slowly and with care Store the pins carefully The operator should use the screwdriver to unload the pin head module from the Z axis CapitalBio Corporation 17 SmartArrayer Chapter 2 CapitalBio Corporation 18 Hardware Installation Insert the dispensing head module Fasten the dispensing module Adjust the dispensing head to level Plug in the control cable Screw fasten the control cable Loosen the connector from the dispensing unit SmartArrayer Chapter 2 Hardware Installation 10 Connect the tubing to the connector Link other cables and tubing see the 11 above content in this section Once the dispensing module has been replaced by the spotting module the position of the dispensing spotting module has to be adjusted slightly to be completely level by using a spirit level to assure perfect motion between the pin dispenser tip and the glass slide surface The calibration methods can be referred to in Section 6 3 Warning Key position calibration must be done before running any protocol 2 8 Control Card Driver Installation After the installation of the workstation hardware the next step is to instal
86. re shown below CapitalBio Corporation 12 SmartArrayer Chapter 2 Hardware Installation Vacuum pump power 7 a jack Humidifier IU jack Dispensing control jack tie in Figure 2 5 The connection plate at the back of the frame The 48S includes the frame body and enclosure with similar attachments to the 1368 One of the major differences between the 48S and the 1365 is that the 48S has only one printing roller with 48 slide capacity while the 1365 has two printing rollers with 136 slide capacity The second difference is the shape of the control panels which for the 48S is fixed on the outside of the frame body at the top front right side The shapes of the EMS button and the Startup button are also different Similarly the 48D is a combination of the 48S and the NDM while the spotting module is replaced by the dispensing unit and the cables and tubing are connected CapitalBio Corporation 13 SmartArrayer Chapter 2 Sonicator Hardware Installation Z axis Rinse Vacuum dry F l A EMS button A Control panel X axis Figure 2 6 The 48S instrument components 2 5 Attention Items of Installation Warning Make sure the power input is the same as the rated power requirements Refer to Section 2 2 3 e UPS Uninterrupted Power Supply is recommended CapitalBio Corporation Warning Connect the cables and tubing according to the requirements stated in the user manual
87. rough no less than 2 cleaning cycles prior to switching to printing a new sample source and the number of washing cycles must be increased more when printing samples of higher viscosity or higher CapitalBio Corporation 5 SmartArrayer Chapter 1 Important Safety Information concentration Note Stand alone cleaning protocols should be completed before shutting down the system to ensure complete cleanliness for subsequent use 1 10 Emergency stop button The EMS Emergency Stop button can be found on the front panel of the 136S and the 136D model microarray workstations In the 48S and the 48D models the EMS button located in the both sides of the body of the machine Warning Press the EMS button 1f the microarray workstation functions incorrectly or needs to be shut down prematurely The EMS button needs to be reset before the microarray workstation can be restarted 1 11 Protection locks The protection locks locate on both sides of the equipment It provides safety protection for operators Warning The locks are necessary for the operators Do not unlock them while the arrayer is running If you do need to do it please pause or halt the arrayer first 1 12 Switch between pin printing and dispensing system When switching pin printing and dispensing systems users should confirm that the application software is compatible with the hardware subsystem Then users must newly configure the system parameters a
88. rray size and spotting area determined by PX PY Step 5 Sample Replicates Sample Replicates define how many spots will be done with the same sample in an array The maximum could be greater than the product of the X and Y sum of spots namely the total sum of spots in an array Step 6 Array Replication Array replication is a switch indicating whether the sample sequences of arrays are consistent 7 4 2 Sample Sequence In a Sample sequence tab you can plan the sampling method from microplates and arrange the sequence as shown in Figure 7 6 dl Clear all Paste Move Blank area selection Delete all down Clear out Me Microarray Setting dl Sample Sequence p Prodess of Spotting Delcte eam 36 4 well plate Bearers SA MAENES AE KET RSE HEE Ea H anan a nn Jnana O A ae faman O ee lt maa Eaa T HEHHEHE O PPT 0010 000 01000 0 00 0 O O A O A O A A Sum of sample block TTT PT y sum of sample Sum of selected sample block Sum of selected sample Sample insertion settings Figure 7 6 Sample setting CapitalBio Corporation 52 Sample selection info 3 K L5 6 3 G H 6 J LJ 6 3 K L7 8 3 E F9 10 3 G H9 10 31 39 10 3 K L9 10 NULL 3 E F11 12 MULL 3 6 H11 12 MULL 3 l J1 1 12 3 K L11 12 3 E F13 14 3 G H13 14 3 l J1 3 14 3 K L13 14 3 E F15 16 3 G H15 16 3 l J1 5 16 3 K L15 16 3 E F1 7 18 mn Set sample as NULL or vice vers
89. s related to the sample display slide and the Y direction textbox If the array is not replicated the X direction textbox is gray and disabled Input the index of the replicate spot within the replicate list to indicate from which replicate spot the spotting dispensing procedure should be brought back to The index is related to the sample display Slide and Y and X direction textbox Select the Forward to Last Position option to move to the last position where it used to be before the last operation and then continue spotting or dispensing This function only applies just after the Back operation Step 3 Click on the Yes button and take action If users select Pause after the cleaning option to halt the system after completion of the wash operation the Pause button will change to the Resume button and the Stop button will be enabled Step 4 While the system is halted click the Resume button to resume spotting or dispensing 7 6 4 Stop Select pause spotting model f Continue Wash Re uptake sample Ss iw C Pause after cleaning ai Backward Sample i Slide 76 Y direction x direction O Replication i cn Figure 7 12 The continue option after pause You can either select the Exit option when prompted for next action or click the Stop button when the system is halted CapitalBio Corporation 62 SmartArrayer M Chapter 8 Additional Software Features Chapter 8 Additional Software Features 8 1 O
90. sample will be taken up again directly e Select the Exit option to break away from the current loop of spotting dispensing If the spotter is in the home position after the washing checkbox is selected the wash operation will be executed and then the axes will be taken to the home position before exiting e Select Pause after the cleaning option to halt the system after the wash operation If the Cleaning First checkbox is selected the wash operation will be executed prior to the Continue operation launched by users eo Select Backward option to go back to a certain position and continue the spotting dispensing CapitalBio Corporation 61 SmartArrayer M Chapter 7 Spotting or Dispensing Input the index of a sample group within the sample list in the Sample textbox to appoint which sample group the spotting dispensing procedure should be brought back to Input the Slide Index in the Slide textbox to designate which slide the spotting dispensing procedure should be brought back to Input the index of the Y direction vector in the Y Direction textbox to designate from which vector the spotting dispensing procedure should be brought back to The index is related to the sample display and slide textbox If the array is not replicated the Y direction textbox is gray and disabled Input the index of the X direction vector in the X direction textbox to designate from which vector the spotting dispensing procedure should be brought back to The index i
91. spensing 5aartArrayer No position calibration or parameter setting section found in system setting file inil Please check 1t Figure 6 1 The system setting required note This chapter below describes the following procedures position calibration axis velocity and acceleration setting slide configuration pressure and dispenser setting only for the dispensing module other option settings and backing up and restoring settings 6 2 Access System Configuration Warning The parameters described below are crucial Incorrect Revision or incorrect alteration could cause disastrous outcomes and damage to the instrument It is recommended that only a qualified and authorized administrator gains access to modify these settings and parameters In order to ensure that the settings and parameters are protected password protection is available The correct password should be filled in the text box Password as shown in Figure 6 2 and then click on the button OK to access the configuration panel Immediately after installation the initial password is arrayer It is strongly recommend resetting it with a new one as shown in Figure 6 3 CapitalBio Corporation 33 SmartArrayer M Chapter 6 System Configuration Input password Password Change ves Cancel Figure 6 2 Input the password interface Hew password Current Password New password Confirmation Pe Password should be composed of 3 15 c
92. spensing module The properties of the sample are an important factor influencing the production of the microarray and the quality of microarray chips To fulfill the quality specification samples should comply with the following requirements Note All of the samples and buffer must be water soluble to ensure that they could be rinsed out completely with the distilled water No corrosive components should be present in the sample The pre treatment procedures such as filtration and purification are indispensable to eliminate large particles in the sample and avoid circumstances of high viscosity or clotting The viscosity of the sample solution should be at a low or moderate level to avoid undesirable consequence such as jammed nozzle blocked pin and cross talk caused by incomplete cleaning A level of viscosity lower than 40 glycerol is recommended For protein the concentration should not be higher than Smg mL Note When an innovative sample and buffer system is about to be applied exploratory tests for the better printing or dispensing conditions are compulsory 1 9 System Cleaning When an innovative sample and buffer system is about to be applied exploratory tests for the most effective cleaning protocol are compulsory It is recommended to use fluorescent labeled reagent in such experiments to evaluate the effectiveness of the cleaning procedures When using the spotted array protocols the pins should be passed th
93. spotting dispensing tasks Note To get detail information of all operations users can read the following three chapters Getting Started System Configuration Spotting or Dispensing Warning Whenever a new system is installed or the system is moved to a new place or some changes are made to the hardware or the software it is mandatory that you to do a spotter dispenser calibration to ensure that the system functions correctly 4 2 Launch the System Turn on the vacuum pump Turn on the switch which is on the rear panel of the microarray workstation Turn on the microarray workstation press the device startup button prior to turning on the linked computer Turn on the control box power 1f using the NDM for 136D 48D Then turn on the computer linked to the microarray workstation Launch the microarray workstation application software 4 3 Configuration For safety Users should configure the system immediately after installation or switching the spotting module to the dispensing module or vice versa Current configurations are then stored and will be used for routine spotting or dispensing operations The system does not need to be configured again for subsequent routine operations Users can go directly to normal running operations preparation when the machine is used again If the spotting or dispensing operations at some later stage become inaccurate the system should be re configured Access system configuration
94. ss the Motion Setting page on the Configuration Panel as shown in Figure 6 6 e Drag the scrollbar to adjust the velocity or acceleration of the corresponding axis CapitalBio Corporation 42 SmartArrayer M Chapter 6 System Configuration System configuration Position Calibration Motion Setting Other Figure 6 6 Velocity parameters setting interface 6 5 Pressure parameters setting The Pressure Parameters page applies only to the 136D 48D These parameters are used by the control cassette to generate the proper pressure They are already set by the manufacturer before packing Operation Guide e Access the Pressure Parameters page on the Configuration Panel as shown in Figure 6 7 Specify the positive and negative pressure respectively in the corresponding text boxes You can always restore them to the default setting of the manufacturer by clicking on the Default button CapitalBio Corporation 43 SmartArrayer M Chapter 6 System Configuration System configuration Position Calibration Motion Setting Pressure Dispense Other Positive Pressure Time Factor Detault Fine Tuning Tuning Time ris Time ms 20 00 Precision 1 Precision 0 30 Negative Pressure Time Factor Default Fine Tuning Tuning Time ms Time ms 150 00 Precision Precision 0 30 Figure 6 7 Dialogue box for setting Pressure parameters 6 6 Dispensing parameters setting The dispensing parameters page applies only t
95. suesanevansrencuesdeesuensmencuaedeenduer sm enc ues deesteaeemactancesechoacenaaet 24 Pigure 3 4 Conto installation interia E italia 25 Figure 3 NS ta ALO SAC ei EEG 235 Figure 3 6 Installation complete interlace misean a a A 26 Figure Sa System selt test interia consi e 32 Pitre S22 The Matrintertac IO AA A cd 32 Fioure 6 1 The system serine required MOE A A Wnaeees 33 Fiure o2 Input tbiepissword mMer acia AAA Add 34 Fiure 6 35 Settine thepassword Merla eserine e a td 34 Figure 6 4 The 736S position calibration interface cccccssccccccccceeesssseseessseneeeeeeeeeeeeeeesseseesssnsteeeeees 35 Figure 6 5 Interface for position calibration of the 48D ooccccccnnnnnoooononooonnnnnnnnncnnnnnnnnnannnn nono nnnnnnnss 36 Figure 6 6 Velocity parameters setting IM ema seat wtescladexictdeevceastesiueennetinen tehdctaanetivnn Dac savectuakinelacers 43 Figure 6 7 Dialogue box for setting Pressure parameters oooooccccccccnncnonononononnnnnnnnnnncnononnnnnnnnnnnnnnnnnnnnoss 44 Figure 6 8 The interface for setting Dispensing parameters ooooccccnnncnnnnnoononnnnnnnnnnnnnnnncnnnnnnnnnnnnnnnnnnnnss 45 Figure 6 9 The interface for setting Other Options ersun ena aira a E a EN E Aa E aa 46 Figure 7 1 Preparation before Spotting a A O 47 Fioure 7 gt The Pin array setting Mtera Eoin a EE E ERASE AAEE 50 PIQUES 723 Pecon oUa Otilia 51 Figure 7 4 The 2 2 Dispensing head configuration oooonnoooocconnnnnonononnnononanonononnnnnnnn
96. t on keeping the pin head immersed into the sample preparation Its optimum differs from sample to sample and could be customized Spots per uptake refers to the maximum number of spots that should be done per uptake It differs from sample to sample Step 3 Pre spotting Settings The pre spotting refers to the procedure to deposit certain excess amounts of spotting solution onto the pre spotting slide immediately after initial up take of samples for the purpose of spot uniformity In this section the parameters indicate how many slides how many spots and how much distance spacing between pre spots should be used in the pre spotting operation Sum of slides refers to the amount of slides that will be used for pre spotting In the Slide Preview tab see Section 7 5 1 you will be informed about how many pre spotting slides will be needed If you do not have many slides to spot more slides could be set as pre spotting slides Sum of spots it is dependent on the sample characteristics Distance refers to the displacement between two neighboring pre spots Pre spots are larger than working spots so the distance should be greater It is also dependent on the sample characteristics It should not be too small otherwise contamination between samples could be brought into the pre spotting procedure Step 4 Z Motion Settings of Spotting Parameters herein should be optimized according to sample characteristics to ensure the proper performanc
97. tamination due to other Following the software installation instructions disconnect the cable and motion control card and then reconnect them and fasten the connection Contact CapitalBio to replace the damaged sensor with a new one Exit software shut down the PC shut down the system and then place the axes between the corresponding Home sensors and the position limit sensors Contact CapitalBio Same as software ini one or more axes exceed Release EMS button exit software shutdown computer and system and then restart the system Contact CapitalBio Remove the any contamination and wash the pins and holders thoroughly or check if properties of the sample meet the sample requirements Water flood at the wash Waste water tank is Empty the waste water tank station full CapitalBio Corporation 73 SmartArrayer M Chapter 10 Troubleshooting Tubing connected to Lower the height of the waste tubing the wash station clogs to remove air bubble and restore flow Lots of air bubbles enter Lack of water for eeh nie Mak the wash station wash Increase RH setting One or more pins fails Missing spots to fall after being lifted while last spotting Irregular spot shapes High motion speed Reduce motion speed Pin holder misaligned Adjust holder using a spirit level Aggregation of adjacent Insufficient Lc ae Increase number of preprinting spots spots preprinting Sp
98. the copyrights specified in the paragraph above If this System contains documents only in electronic format you may print copies of the documents You may not delete any copyright statements of this System You warrant that you will copy any copyright statement when you make a copy of this System or any portion of this System in accordance with this Agreement You agree to refrain from doing any illegal copying of any forms of this System and or any parts of this System Post Sales Warranty CapitalBio warrants that within ninety 90 days after the selling of this System this System shall not have any material defects or technical defects subject to the condition that this System is used in its normal manner of operations In the event that a defect is confirmed by CapitalBio CapitalBio only shall be responsible for replacing the defective software This is the only remedy available for you If the defect is caused by or arising from any accident abuse or mistake the above mentioned post sales warranty shall be invalid Exemption from Liability Except for the contents specified in the above paragraphs you shall not have any other post sales warranties of this System Limitation of Liability Subject to the scope of applicable laws specified in this Agreement in no event shall CapitalBio and its agents and sales persons be liable for any special incidental indirect or consequential damages and or losses including but not limited to pro
99. the pin holder the operator should use the tweezers to lift the pin up by one hand and then cautiously slip the pin out from the pin hole slightly Warning Clean the pins and unload them from the pin holder after the microarray fabrication process if they will not be used again within several hours Move the dispenser enclosure onto the dispensing module after the microarray fabrication process if they will not be used again within several hours Do not routinely plug and unplug the connectors cables and tubing of the microarray workstation in or out Figure 9 4 Loading or unloading pins For the 48S and the 48D the method protocol and notes for installing the microplate glass slides sonicator and loading unloading of the pins are the same as those of the 136S and the 136D 9 3 Maintenance Sonicator The distilled water in the basin of the sonicator bath is required to be replaced everyday or more often Confirm that microarray workstation is not in any possible motion status before the following steps listed in the table below CapitalBio Corporation 69 SmartArrayer M Chapter 9 Operation amp Maintenance Table X Protocol for replacing water for sonicate wash Step No Schematic Drawing Description Open the upper enclosure and unplug the power cable of the sonicator Carefully take the sonicator out from its positioning plate Empty the water in the basin of the sonicator Place the sonicato
100. tion Dispense time refers to the duration of each Dispense operation measured in micro seconds Step 5 Minimum Relative Humidity Min RH refers to the minimum relative humidity that should be used in the microarray workstation It is dependent on the sample 7 4 5 Backup amp Load Setting File You can access the Save and Load buttons on the top toolbar to backup and restore the editing protocols Warning It is recommended that you save the protocols before you run spotting application CapitalBio Corporation 57 SmartArrayer M Chapter 7 Spotting or Dispensing 7 5 Spotting Preview Click on the Preview button on the left and access the spotting preview panel There are two tabs Slide preview and sample preview Slide preview 1s the first to display 7 5 1 Slide Preview Slide Preview provides a visual aid for users as shown in Figure 7 9 In this section according to the protocol planned the simulation of the spotting pattern on the slide will be displayed to help users confirm whether the protocol and configuration are correct thus reducing the possibility of mistakes In addition you can adjust the slide sum placed one time see Section 7 4 3 Total spots per slide refers to the total sum of spots per slide calculated from microarray settings Sum of pre spotting slides refers to an estimation based on the microarray settings and only applies to the 136S 48S Slide View depicts the distribution of the s
101. ttachments such as the humidifier and the vacuum pump as shown in the above Figure 2 1 The 136D is a combination of the 1365 and the NDM while the spotting module is replaced by the dispensing module and the cables and tubing are connected The frame forms the base of the workstation and stably supports the total weight of the equipment The humidifier vacuum pump and water tanks shoulde be placed behind the frame The body includes four axes fixed on to the workbench The enclosure covers the body to form a closed and clean environment for microarray fabrication There 1s control panel at the front of the instrument with the startup buttons for the workstation five status indicator lights and an EMS button EE y i oh me Iittala i i I Pad A Cues t MA be AY MEM A Humidifier Sonicator Peristaltic pump Figure 2 2 Accessories Fuller details of the instrument body are shown in the following figures The upper platen 1s connected with the slide block of the X axis and the lower platen is connected with the slide block of the W axis and they move in the left and right directions The pins or dispensers in the spotting dispensing units move up and down It is assembled on the slide block of the Z axis The X and W axes are fixed on the workbench and the Z axis is fixed on the Y axis which moves forward and backward The axes are controlled by the application software via a motion control card which should
102. tting Operation Guide e Click the Pin Rinse button and push it down to a depressed appearance as Pin Rinse The Y axis and Z axis are moved to a rinsing position and rinsing starts Meanwhile the rinse indicator continues to be illuminated e Click on the Pin Rinse button again to pop it up to a released appearance The pins or dispensers are lifted along the Z axis and rinsing stops Meanwhile the rinse indicator light turns off 7 3 1 3 Vacuum Vacuum refers to the operation to power up the pump prior to spotting Operation Guide e Click the Dry button and push it down to a depressed appearance to begin Drying and start the vacuuming Meanwhile the dry indicator light is lit up e Click on the Dry button again to pop it up in a released appearance and stop vacuuming Meanwhile the dry indicator light turns off 7 3 1 4 Dry Move the pins or dispensers to the location indicated by the drying position calibration record and dry them in the inhalant holes on the wash dry station prior to spotting Operation Guide e Click the Pin Dry button and push it down in a depressed appearance for Pin Dry The Y axis and Z axis are moved to the drying position and drying starts Meanwhile the dry indicator continues to be illuminated e Click on the Pin Dry button again to pop it up to a released appearance The pins or CapitalBio Corporation 48 SmartArrayer M Chapter 7 Spotting or Dispensing dispensers are lifted along the
103. ttings previously saved by selecting a sas file CapitalBio Corporation 46 SmartArrayer M Chapter 7 Spotting or Dispensing Chapter 7 Spotting or Dispensing 7 1 Overview The most common spotting dispensing procedure is described in this chapter to guide you to successfully do slide spotting dispensing operations Warning Most discussion in this chapter uses the 136S D system for examples For the NDM the same operations are required to a great extent except some description of spotting operations are substituted with printing and some additional settings are unique to NDM 7 2 System Startup e Power the system according to the instructions depicted in Section 5 2 e Launch the software system according to instructions depicted in Section 5 2 and access the main User Interface 7 3 Prepare You can access the preparation panel by clicking on the Prepare button on the left It is the default first page displayed immediately after the software system is launched as shown in Figure 7 1 The instructions on this page are common to both the 136S 48S systems Fg CapitalBio Smart rrayer 136 Nicroarray Manufacturing System Spotting E _ CapitalBio A smartArrayer 136 r ing M Cleaning according to the selected cleaning protocol file l L Rinse File P Pin Rinse Progress Dr UY PinDry LI Sonicate Pin Sonicate ther Load Slide
104. values for the UPS for all models are listed in the following table Table V Recommended UPS specifications Parameter Model 48S 48D 136S 136D UPS electrical source power kW 1 5 1 5 UPS power supply time after power cut minutes 2 2 4 Electromagnetic compatibility EMC requirements Warning A good EMC environment is critical for operation of the microarray workstation as electromagnetic fields may lead to unpredictable results The Electromagnetic property of microarray workstation must be according with the requirements of EMC directive about CE the FCC Partl5 and ICE 003 directive CapitalBio Corporation 8 SmartArrayer Chapter 2 Hardware Installation The following cautions should be considered Keep the microarray workstation away from high electromagnetic discharge equipment such as pacemakers electric welding equipment etc Site the microarray workstation away from equipment such as refrigerators centrifuges etc that frequently consume high power upon starting up Keep the microarray workstation away from any strong magnetic fields Do not connect too many power cables to the same junction box to which the arrayer is connected Do not plug in or pull out any other equipment connections to the same junction box while the arrayer is running 2 2 5 Computer requirements Computer requirements Table VI Computer requirements CPU Pentium 4 2 0GHz or higher Memory 512M or more Disk space 40G or
105. verview There are some additional features in the software reprinting tagging sample etc Reprinting also called selective spotting dispensing means to re spot at missing spot positions The information for sample groups slides arrays and replicates involved in the spotting dispensing procedure base in the microarray settings defined previously is needed to be specified Or you can also use Reprinting to refine your spotting task just before the procedure starts to do part of the plan and leave the remaining spots temporarily incomplete The Tag function is a complement to the protocol It provides facilities to generate GAL files to save information for sample sequence tag and location distribution on the slide 8 2 Steps of Reprinting Step 1 On the run page click the Reprint button to access the reprinting pop up dialog as shown in Figure 8 1 Step 2 Set the range to the reprinted e Select starting and ending sample indexes from the Sample lists to specify the sub sample sequence list for reprinting between the selected ranges e Select starting and ending slide indexes from the Slide list to specify the sub slide sequence list for reprinting between the selected ranges e Select indexes of starting and ending Y direction vectors from the Y Direction drop lists to specify the sub array for reprinting between the selected ranges The index selection only applies to circumstances when arrays are replicated e Select indexes of st
106. vides instructions on how to install the SmartArrayer Software Installation application software and the device drivers Provides instructions on how to prepare a microarray chip To get apo s detailed information users can see the following three chapters Tutorial i j Getting Started System Configuration Spotting or Dispensing Chapter 5 Provides instructions on how to run the spotting system for a test Getting Started immediately after the hardware and software installation oe a Provides instructions on how to configure the system parameters Configuration before spotting or dispensing o de Provides instructions on how to successfully do slide spotting or f dispensing operations Dispensing Chapter 8 Additional Software Provides descriptions of additional software features Features Chapter 9 Operation amp Provides information on routine maintenance for quality service Maintenance Chapter 10 Provides answers to frequently asked questions and solutions to Troubleshooting frequently encountered problems 0 3 Functions and Series 0 3 1 Functions CapitalBio SmartArrayer series of microarray workstations are used for fabricating bio molecular microarrays spotting or dispensing several to tens of thousands of kinds of bio chemical samples precisely onto set positions on preformed microarray chips CapitalBio SmartArrayer series of microarray workstations utilizing precise robotic motion Ca
107. wn in Section 2 9 Step 1 Choosing Sonicate Location Choose Sonicate in the location section then calibrate the current position parameters for the Y axis and the Z axis but not the X W axis coordinates The position parameters will be displayed in a corresponding text box If it is the initial calibration the initial values are all set to 0 Step 2 Initialization of the Axes Confirm that the X axis W axis also if using the 136S D and the Z axis are in the home position If not send them to the home position by clicking on the X Home W Home or Z Home button Step 3 Adjustments Move the Y axis and the Z axis gradually step by step and carefully watch the axes until the pins are sonicated thoroughly in the sonicator bath or that the dispensers take in the system liquid properly It is necessary to immerse the pins in the sonicating solvent or the dispensers in the system liquid a bit deeper than into the sample to ensure completely cleaning the surface area in contact with sample CapitalBio Corporation 38 SmartArrayer M Chapter 6 System Configuration Warning When moving the axes always be aware of the position of the print head and pins dispensers Make sure that the planned routes of all the moving components are clear of any obstacles before you apply actual movement to avoid any potentially disastrous outcomes Step 4 Calibration In the Current Position Parameters section confirm that the checked b
108. y of this System in a computer readable format for the purpose of making a copy or a managing file on a single computer 3 You can only use this System in a multi user environment or a network system under one of the following conditions It is authorized by this Agreement to be used in a multi user environment or a network system or CapitalBio Corporation 1 SmartArrayer you have purchased the use license for every related computer License Restrictions 1 You will not assign the license of this System to others 2 You will not conduct any reverse engineering decompiling or disassembling of this System 3 You will not copy or assign this System or any portion of this System 4 This System is granted to license as a whole You will not disassemble this System and use its parts and components on more than one computer 5 This Agreement shall not grant you any legal rights relating to any trademarks or service trademarks of CapitalBio 6 You will not rent lease or lend this System to anyone Copyrights All copyrights of this System including but not limited to the copyrights of any photographs pictures cartoons videos recordings music words additional programs printed materials and any copies of this System are exclusively owned by CapitalBio and except for the limited license to use this System granted to you CapitalBio reserves all rights titles and interests in and to this System You are not permitted to use

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