User Guide for the Genetic Analysis Laboratory Information
Contents
1. my primer2 lo e Payment type External customers select from PO number Visa or MasterCard Enter the PO number in the box beside the payment type If paying by credit card submit the card number and expiry date to us with your samples don t enter into the LIMS Internal customers with University of Calgary accounts will see several boxes asking for their PeopleSoft account information e Principal Investigator This is the person listed in your user profile e Comments to Lab Use to alert us to any special handling or billing requirements e Sample Name A name is required for each sample The sample name has specific restrictions the name cannot be longer than 20 characters and can only contain legal characters o Legal characters are a z A Z 0 9 and o Illegal characters are any other characters o Do NOT use underscore _ or period characters The Index Fillx fill x number of rows Fill 2X or Alternate fill rows in pairs and Clear buttons are used to simplify filling in multiple rows with names that are sequentially numbered e Template Name Use to identify the type and identity of the template submitted e Template size bp Used to record the size of the template submitted This information is particularly important for PCR fragments since the amount required for sequencing depends on the length of the PCR products e Primer Name Select from a pull down list of available stock primers see below or2. 4277 or dnalab ucalgary ca Economy In a final volume of 12 uL H20 Premixed DNA and Primers Plasmid or PCR DNA DNA 0 1 ug per 1000 base pairs if plasmid use total size i e vector plus insert Primer 3 2 pmol BAC or other large DNA templates 1 2 ug of template and 6 13 pmol of primer Please contact us for more information on sequencing large templates For Full Service samples only we provide the following standard primers at no cost Please check the primer sequence with that of your vector to ensure they are the same Some companies have made changes without changing the name of the primer Preferred sample microtubes and 96 well plates When submitting samples to us in tubes our preferred format is a strip of 8 PCR tubes so we can array the tubes in a 96 well format and use our 8 channel pipetters If you are submitting samples in a 96 well plate format than our preferred plates are the Eppendorf twin tec 96 well full skirted PCR plates Eppendorf 951020401 which are available from VWR 47744 116 The Sequencing Laboratory can also be contacted by phone 403 220 4503 or e mail dnasegq ucalgary ca for assistance Our complete contact information is located on our web site at www ucalgary ca dnalab contact_us Placing an Order Submitting samples for sequencing is a two part process 1 The order must be created on line by using the Enter DNA Sequencing Requests hyperlink on the main dnaLIMS User Tools p
3. Calgary AB T2N 4N1 z 403 220 4503 UCDNA Home Page User Commands Logout Plasmid Prep Request Form Payment Type PO Number v PO 1 2345 DNA Provided Liquid bacterial culture Glycerol stock v Number of Plasmid Preps 5 Total Number of Primers Total Number of Reactions Principal Investigator Richard T Pon No Validation response means all required fields are filled in Sample Name earn More Plasmid Prep Information Primer Qtearn More Name Size bp Name Tm Fill Clear Fill Fillx Clear Fill Alternate Clear Fill Alternate Clear 7 YF 7 F 7 lt v v v Name Index Fillx Fil x Clear v z v 1 templ prep 1 Plasmid Plasmid 10000 custom vi My Forwvard templ prep 1 Plasmid Plasmid 10000 custom MyReverse i 2 3 temptprep 2 Plasmid 2 v Plasmid custom v My Forward J 6 Plasmid 3 Plasmid3 10000 custom My Fornward 4 templ prep 2 templ prep 3 templ prep 5 10 templ prep 5 2 A Plasmid Prep Request form will appear Completing this form is the same as described above Plasmid5 Plasmid5 10000 custom My Forward v h v Plasmid5 PlasmidS 10000 with the following exceptions o DNA Provided Use the pull d
4. Please note The Login and Password are case sensitive Supported Browsers Learn More The login procedure for existing user accounts is straightforward However please remember that both your user name and your password are case sensitive If you have forgotten your password or user name press the return button on your browser to go back to the opening menu and then select Forgot Your Login Information You will be prompted for your e mail address and your dnaLIMS username and password will be automatically sent to that e mail account UNIVERSITY OF CALGARY A 7 University Core io 29 DNA Services ne Forgot Your Login Enter Your Email Address The dnaLIMS User Tools Menu Once successfully logged in the dnaLIMS User Tools menu will appear This is the main menu for submitting sequencing or fragment analysis requests retrieving results and changing your user profile A UNIVERSITY OF University Core DHA Services CALGARY University of Calgary z fs Unkersiiy Core 2330 Hospital Dr Mii te td DHA Serric s Calgary AB TZN H1 si 403 220 4603 Home Page Logout dnaLIMS User Tools Sequencing Requests amp Results User Profile Sequencing Resources qu ini Li a Change Your Pa ord Contact Info View Your Requests a Change Your Profile a Sample Preparation Guidelines Q Download Your DNA Results a Xplorer Trace and FSA Viewer ell Plate Sequencing i a Logout Supported Browsers 7 Enter Fragment Analysis Req
5. below CALGARY University of Calgary A University Core 3330 Hospital Dr Niu ee SI DNA Services Calgary AB T2N 4N1 403 220 4603 O Homepage Login to Account Create Login Account Forgot Your Login Information Note Selecting the Home Page link will take you to the UCDNA Services home page at www ucalgary ca dnalab Use the Back control on your browser or click on the link in the UCDNA Services home page to return to the dnaLIMS Internet Explorer Version 7 The default settings Internet Explorer 7 disable the use of scripted window prompts However scripted window prompts are used by the coreLIMS to automatically fill in certain fields in the request forms If scripted window prompts are disabled a warning will appear beside the menu bar just like the warnings for a pop up window You may proceed by clicking on this notification and then selecting Temporarily allow scripted windows Alternatively this setting may be permanently changed by going to Tools Internet Options Security and selecting Internet as the zone and then the Custom level button to set the Security level for this zone The Security Settings Internet Zone window will then appear Scroll down almost to the bottom of the list of settings until Allow websites to prompt for information using scripted windows appears Change the selection from Disable to Enable and then click OK gt DNA
6. one sample at a time by Request number e The dnaLliMS system will allow you to delete orders up until the point they are transferred to sample sheets by the laboratory staff However if the samples have already been delivered to the sequencing lab you also need to inform us of any changes e Requests submitted using the 96 Well Plate DNA Sequencing Requests option cannot be viewed or altered by the customer after they are submitted You will receive an error message saying the order was not found in the Sequencing Request Queue because these are automatically advanced to plate status by the dnaLIMS Please contact the sequencing laboratory if any changes or cancellations to these requests are required even if the plate has not been delivered To delete an entire order 1 From the main dnaTools User Tools page select the View Your Requests hyperlink The Search the Sequencing Request Queue page will appear UCDNA Home Page 16 User Commands Logout Search the Sequencing Request Queue Request 1 reaction Order all reactions requested at one time To view ALL your requests in the queue Select Submit To view a Specific Order Select an Order Number below then Submit Requisition or Order Number FO MewAlReweste O Mew Request lt lt a Your Orders View Order Order Samples ns Date 1348 1347 1346 1345 1338 Nov 24 2006 Nov 23 2006 Nov 23 2006 Nov 232006 jf
7. 2 Plasmid2 10000 My Reverse 52 5 1347_5 templ prep 3 Plasmid3 10000 My Forward 55 6 13476 templ prep3 Plasmid3 10000 My Reverse 52 17 13477 templ prep4 Plasmid4 10000 My Forward 55 8 1347 8 templ prep4 Plasmid4 10000 My Reverse 52 9 1347_9 templ prep 5 Plasmid5 10000 My Forward 55 10 1347 10 templ prep 5 Plasmid5 10000 My Reverse 52 Entering DNA Sequencing Requests for Samples in 96 Well Plates This link should only be used to submit samples for our Economy sequencing service i e with the template and primer pre mixed in each well Remember All of the samples will be cycle sequenced together on the same plate Therefore all of the primers have to have similar Tm values Samples for our other services may be submitted in 96 well plate format using the on line request forms for tube submissions as long as the samples are loaded into the wells in ascending column order i e A1 B1 C1 A2 B2 C2 etc Please contact the lab for more advice if you wish to submit samples in 96 well plates for our other services 1 From the main dnaTools User Tools page select the 96 Well Plate DNA Sequencing Requests hyperlink under the Sequencing Requests and Results column 15 UNIVERSITY OF University Core DNA Services CALGARY University of Calgary A 7 University Core 3330 Hospital Dr N s WI DNA Services Calgary AB TZN 4N4 403 220 4503 UCDNA Home Page User Commands Logout 96
8. A Sequencing Requests hyperlink under the Sequencing Requests and Results column in the dnaLIMS User Tools screen UNIVERSITY OF University Core DNA Services CALGARY University of Calgary F University Core 3330 Hospital Dr Nu ts DNA Services Calgary AB TZN 4N4 403 220 4503 UCDNA Home Page User Commands Logout Enter the Number of Reactions to Create Sequencing Requests For Select the Sequencing Type Service Requested Full ss e Economy Special User Prepared Plasmid Prep Sequencin Service Type Full Sample Template and Primer Submitted Separately Economy Template and Primer pre mixed in the same tube User Prepared Customer cycle sequenced the samples Special Samples requiring special conditions pricing or consideration Qa More Plasmid Prep Sequencing Plasmid preparation plus sequencing Set the Service Type to Plasmid Prep Sequencing LIMS will prompt you for the number of plasmids and total primers 2 Apage will appear prompting you to enter the number of reactions to create sequencing requests for i e the number of samples you are submitting and to select the Service Requested Use the pull down menu box to select from Full Economy Special User Prepared or Plasmid Prep Sequencing This information is required to dynamically generate the type and size of request form needed The table below the Service Requested box describes what each type of service is for e Full servic
9. Analyzer is for both sequencing and fragment analysis applications The turnaround time is generally 24 48 hours with a read length up to 1000 bases The results are posted on our secure web server in both text and ab1 file formats General 1 DNA must be ultra clean and in water although some clean up kit buffers are also acceptable i e Guidelines Qiagen elution buffer TE buffers salts phenol ethanol etc interfere with the sequencing reaction 2 Primers must be gel purified and have a Tm between 52 C and 74C 3 Primer sequence must not form dimers nor contain any hairpins If you have trouble sequencing the DNALab has many trouble shooting protocols We are here to help you with all sequencing problems and questions Full Service DNA Please submit the following amount of DNA template per reaction DNA and Primers double stranded 10uL at 0 2 ug uL submitted single stranded 10uL at 0 2 ug uL separately PCR products 10uL at 0 1 ug uL Each user is responsible for checking the purity and template quantity Primer A concentration of 3 2 pmol uL 5 uL of primer per reaction is required Primers should be gel purified before use Please see the UCDNA webpage on designing primers for sequencing Stock KS SK SP6 T3 T7 M13 and pGEX primers are provided at no extra charge Please see below to confirm primer sequence Please contact the University Core DNA Synthesis Laboratory for information regarding primer synthesis at 403 220
10. Novi 2006 w Delete Order Delete Order 2 Locate your order number in the Search Your Orders list box near the bottom of the page Click on the order to highlight it in the list The order number will be placed into the Requisition or Order Number entry box in the middle of the page OK to confirm your intent Select the Delete Order button A window will pop up asking you to confirm the deletion Click 17 UNIVERSITY OF University Core DNA Services CALGARY University of Calgar A University Core 3330 Hospital Dr NYu VQ DNA Services Calgary AB TZN 4N1 ee 403 220 450 UCDNA Home Page User Commands Logout Search the Sequencing Request Queue Request 1 reaction Order all reactions requested at one time To view ALL your requests in the queue Select Submit To view a Specific Order Select an Order Number below then Submit Requisition or Order Number 1 348 O bette Rewest ee Search Your Orders View Order Orde Samples Order Date 48 Nov242006 B 10 Nov23 2006 Nov 23 2006 4 Nov 23 2006 2 Nov 2006 7S Delete Order Note If you select the Delete Request control under Search by Request Number instead of the Delete Order button then you will probably see an error message saying The Requisition Number is not in the Gel Pool The View and Delete Request buttons only work for the Request numbers assigned to individual samples see bel
11. Please use STRIPS of 8 PCR tubes whenever possible If submitting 96 well plates please write ORDER NUMBER on the plate Tube Label Sample DNA Type Size Primer Tm 1 1346_1 my sample1 pTest 20000 M13F 52 2 1346_2 my sample1 pTest 20000 M13R 17 50 3 1346_3 my sample2 pTest 20000 my primert 55 4 13464 my sample2 pTest 20000 my primer2 60 Entering DNA Sequencing Requests for the Plasmid preparation Service 1 If you have requested the Plasmid Prep Sequencing service you be will be First prompted to Enter the Number of Plasmid Preps This is the number of bacterial samples you need plasmids isolated from i e the number of TempliPhi plasmid preparations needed Secondly you will be prompted to Enter the Total Number of Primers for ALL Preps This is the total number of all the sequencing reactions needed For example if submitting 10 bacterial samples to TempliPhi amplification and you want to sequence each plasmid with both forward and reverse primers then the total number of reactions is 10 x 2 20 Third press the Submit button to generate a request form similar to the one shown below If you have made a mistake and generate a form with the wrong number of lines just select the User Commands hyperlink or the Back command on your browser to start over again UNIVERSITY OF University Core DNA Services CALGARY University of Calgary A University Core 3330 Hospital Dr NW A SA DNA Services
12. Sequencing Request Form Windows Internet Explorer Ga y http 136 159 185 32 cgi bin dna seqTableucalgary cgi File Edit View Favorites Tools Help A a amp DNA Sequencing Request Form 2 This website is using a scripted window to ask you for information IF you trust this website click here to allow scripted windows UNIVERSITY OF University Core DNA Services RCA LGARY University of Calgary ree N l A 3330 Hospital Dr NW This notification will AvA Calgary AB T2N 4N1 TE 403 220 4503 appear in IE7 when scripted windows are disabled Full Service Request Form UCDNA Home Page User Commands Logout gt Internet AL100 Internet Options all Security Settings Internet Zone General Security Privacy Content Connections Programs Advanced Settings Enable Select a zone to Yiew or change security settings Prompt Jf 9S Allow status bar updates via script a Ci AS 7 Enable Local intranet Trusted sites Restricted sites Allow websites to prompt For information uSiqg scripted windi Disable Internet This zone is for Internet websites Scripting of Java apple except those listed in trusted and restricted zones Enable Security level for thi ned roon ecurity level For this zone Rare yi amp User Authentication Allowed levels for this zone Medium to High g Logon Medium high Anonymous logon Appropriate for most websites fe fitkarmatk
13. These can then be retrieved by logging back into the coreLIMS and using the View Your Results hyperlink Entering DNA Sequencing Requests for samples submitted in microtubes Note When submitting samples in tubes our preferred format is a strip of eight PCR tubes Large submissions can be submitted in a 96 well plate format Use the 96 Well Plate Sequencing Request hyperlink for requests of 48 or more Economy service samples For smaller Economy submissions in plates or plate based samples for other services the tube based web forms can be used as long as the samples are loaded into the wells in ascending column order i e A1 B1 C1 A2 B2 C2 etc Create a separate order for each 96 well plate so each plate can be labeled with a unique Order number CALGARY University of Calgary A University Core 3330 Hospital Dr NW ee SI DNA Services Calgary AB T2N 4N1 403 220 4503 Home Page Logout dnaLIMS User Tools Sequencing Requests amp Results User Profile Sequencing Resources vy Enter DNA Sequencing Requests a Change Your Password Contact Info View Your Requests Change Your Profile Sample Preparation Guidelines O Download Your DNA Results Xplorer Trace and FSA Viewer a 96 Well Plate Sequencing Requests Logout Supported Browsers Learn More t Enter Fragment Analysis Requests Download Fragment Analysis Results 7 96 Well Plate FA Requests Home Page User Help 1 Select the Enter DN
14. UNIVERSITY OF UNIVERSITY CORE DNA SERVICES CA GARY U niversity Core Genetic Analysis Laboratory I Faculty of M edicine NJ Health Sciences Centre Rm B104A Tel 403 220 4503 Fax 403 283 4907 Email dnaseq ucalgary ca www ucalgary ca dnalab or www sequencing ucalgary ca User Guide for the Genetic Analysis Laboratory Information Management System dnaLIMS Creating a user account and placing orders nidgete 5 cd 0 9 ieereeenenr tan tater Nps Rte iri ec mentee er ett E E ner eee nee ener mere eee ene een eee ae eee 1 ACcCessmag Bi Ute f ho ceee e E E E E ee ere 2 Internet Explorer Version 7 ccccccccsscccseecceeeeeceeecaeeeeaeeeeeueeesaueeseueesseeesaeeesseeessueessaeessseeeseeeeseeessaeessaeeess 3 gen cee ae hee E ee nen ene eee E eee ee ee ee 4 Notes for Creating a new ACCOUNL cccccccccccceececeeeeeeeeeeseneeseeeeseeeeseeeesseeeseeeessaeeseaeesseeeeseesesgeeeseeesseeeens 4 L gIN TOR EXISTING USETE cnn o a a E E N 5 GENG FEID eee enn eee nee ene ee ee ene ee ee ee eee eee 6 Sample Preparation Guidelines ccc cccccccceeeeceeeeaeeeeeeaeeeeeeceeeeeeeseeeeeeesseeeeesseeeeeesaeseeeesseaeeeesaaeeeesaages 6 acelin le Aol ie OTOT tee ahi ah heen eee eter e ale ae one ee ee ET ete ee cee eee ee eee 6 Preferred sample microtubes and 96 well plates ccccccccccceeceseeeeceeeeeseeeeeeseeeeeseeeeessaeeeesaeeeesseeeeess 7 Placing an Order eremo E E E A E E e
15. Well Plate Request Form for Pre Mixed Sample ONLY Primer and template together in each well Enter the Number of Samples in the Plate Enter at least 48 but not more than 96 Samples in Plate Select 2 Enter the number of samples that will be in the plate Any number can be entered as long as it is between 48 and 96 If you have less than 48 samples and want to submit these in a 96 well plate you can use the on line request forms for tube submissions as long as the samples are loaded into the wells in ascending column order i e A1 B1 C1 A2 B2 C2 etc Create a separate order for each 96 well plate so each plate can be labeled with a unique Order number 3 Complete the on line sample form that is generated This is similar to the form for submissions in tubes except that the first column shows the well number Samples must be loaded into the plate in ascending column order i e A1 B1 C1 A2 B2 C2 etc 4 When the on line form is complete press the Submit button Print out the summary report that is generated and label the plate with the Order number that is created Delivery the plate anda copy of the summary report to the Sequencing laboratory Deleting or Viewing a Request after Submission to the dnaLIMS Once the submit button has been pressed it is not possible to edit your request However the View Your Requests hyperlink can be used to delete requests either for an entire order by Order number or
16. age This is the first hyperlink in the left hand column under Sequencing Requests amp Results Once the appropriate sample and billing information has been entered and the Submit button pressed your completed DNA Sequencing Request form with your assigned order number and the details of your request will be displayed You will need to print out this page it shows your order number and the identification numbers required for your samples Your request is not sent to the dnaLIMS until you press the SUBMIT button so you can change cancel or start your request over again at any time just by pressing the Back control on your browser by selecting the User Commands hyperlink to go back to the User Tools page or by closing the web page 2 Then your samples must be labeled using the identification numbers Tube labels specified by the dnaLIMS However samples in 96 well plates must be arranged in ascending column order i e A1 B1 C1 A2 B2 C2 etc These samples along with a copy of the above DNA Sequencing Request form are then delivered to our laboratory If you are paying by credit card write your card number and expiry date onto the DNA sequencing request form Credit card information is not entered into the dnaLIMS Once the samples have been sequenced the results will be uploaded from our DNA sequencer and stored in the dnaLIMS system You will receive an automatic e mail notification that your results are available
17. choose custom if you are supplying a custom primer 11 Standard Primer List Netscape UCDNA Stock Primers IMIG reverse 28mer Jozoa acc cca Taa caa trr cacacacoa a fe Terminator far ecracr mar tecteasces Ww w Ts promoter fozes CGCAATTARCCCTCACTAAAG iat w SP6 promoter Josss23 ear Tracer cacacratae hW W pex sprime osz ccc cac cre cat ere Tcaeas n e e Primer Tm If you are using a custom primer then the primers Tm must be supplied calculate this as 4 x G C 2 x A T Tm The primer Tm is required to determine the optimum cycle sequencing conditions and it should be within 52 and 74 e Clear The Clear button allows you to start the request form over again e Validate Table The Validate Table button checks to see if all required fields have been completed If no error message occurs then all fields are present e Submit Pressing the Submit button is required to send your order to the dnaLIMS Do not press this button until you are sure the form is complete and accurate You can change cancel or start the request over again at any time before you press Submit To return to the dnaLIMS User Tools page select the User Commands hyperlink or use the Back command on your browser You can also exit from your browser at any time to abort a request 4 When the Submit button is pressed a completed request form showing your order number and the identification numbers required fo
18. e For samples where the template and primer are submitted as separate tubes and the sequencing lab needs to quantitate and mix them together This service is primarily for researchers new to sequencing or having only occasional sequencing needs More experienced users should consider our less expensive Economy service The Full service is also recommended for difficult templates where a variety of sequencing conditions may need to be evaluated e Economy service This is our most common service where the customer has combined the correct amounts of template and primer in a single tube or well Also known as our premixed service e Special service This service should only be selected for requests that are not automatically priced by the dnaLIMS So if you have a special requirement extra charges may apply or quote from us select this service Be sure to indicate the special consideration required in the Comments field of the request form e User prepared We only accept user prepared samples from a very few customers primarily companies who need to follow validated protocols because of the risk to our instrument from poorly prepared samples You must arrange for this service in advance if required e Plasmid Prep Sequencing This service is our plasmid preparation service Cell to Sequence where we use TempliPhi to amplify and isolate the plasmid to be used as a template The bacterial source can be glycerol stock cul
19. e N 7 Entering DNA Sequencing Requests for samples submitted in microtubes c ccccecsssseeeeeseeeees 8 Entering DNA Sequencing Requests for the Plasmid preparation Service cccccceeceseeeeceeeeeeeees 12 Entering DNA Sequencing Requests for Samples in 96 Well Plates 0 cc cecccceccceeeeeeeeeesaeeeeaeees 14 Deleting or Viewing a Request after Submission to the dnaLlIMs 0 oe eccccceeceeeeeeeeeeeseeeesaeees 15 IG GCIETE an entire Order argc ceasing aa ced en cet esas eetaadee uawetoaphieaeand Aa 15 To Delete or View Individual Samples in an Order ccccccccccccceeeeeeeceeeeeeeseeeeeeeseaeeeeesseeeeeesseeeeeeas 17 File Login and Ordering dnaLIMS User Guide doc 2007 12 17 Introduction A lab information system has been implemented for the automated DNA sequencing and fragment analysis services Our dnaLIMS system is based upon the coreLIMS produced by dnaTools www dnalools com and will be used to log user submissions monitor and streamline sample information as samples are processed within the lab and provide secure storage and data retrieval This system is installed on a dedicated server in the secure server room in the basement of the Math Sciences building and it is backed up and protected by the University of Calgary s Information Technology department Data is also mirrored on a duplicate server for additional protection The dnaLIMS system replaces th
20. e secure Web File Server WFS system previously maintained by the MedlT department The dnaLIMS system offers much faster data transfer greater storage capacity and reduces the turnaround time between sample submission and receipt of data We use the dnaLIMS to automatically notify users by e mail as soon as the raw sequencing results are produced regardless of the time of day Since most automatically produced results are quite satisfactory this enablea earlier access to your data Our lab staff will still review all sequencing results and perform manual adjustments when required but this may not happen until the next working day 3330 Hospital Drive N W Calgary AB Canada T2N 4N1 e www uCcalgary ca dnalab Accessing the dnaLIMS The dnaLIMS system can be accessed using any internet browser such as Internet Explorer or Netscape Communicator at www sequencing ucalgary ca or by using the links on the UCDNA Services web pages at www ucalgary ca dnalab Users of Internet Explorer 7 should see the note at the end of this section about enabling scripted window prompts Supported Browsers dnaLIMS works with the following browser versions IE 6 Netscape 6 Safari Lit To view chromatograms your computer requires the Java Run Time Environment of 1 4 or greater Obtain the JRE from PC s java sun com getjava Mac OS X www apple com java_ click on java 1 4 1 update User Help The opening menu for the dnaLIMS system is shown
21. formation for your institution s Billing Address i e your Financial Services Dept will most likely be different than the address and contact information for the Shipping Information i e your lab s information e If you are funded from more than one institution and each institution must be billed separately than you should create a Login ID for each institution e The Validate Form button confirms that all required fields have been filled in dnaLIMS User Profile Tool The dnaLIM login account was created The Login was Created Home Page Login Tool Copyright c 1998 2006 by dnaTools All Rights Reserved After the above information is entered the Submit button must be selected A window verifying that all of the required fields have been completed will appear Select OK to send your information to the dnaLlIMS A confirmation window will then appear Future changes to your contact or billing information can be done by using the Change Your Profile option in the User Tools menu Similarly your password can also be changed at anytime with the Change Your Password option Login for Existing Users UNIVERSITY OF University Core DNA Services CALGARY University of Calgary A E University Core 3330 Hospital Dr NW 39 DNA Services Calgary AB T2N 4N1 403 220 4503 Home Page Logout DNA Sequencing Ordering and Sequence Retrieval System Please Login Login Name Password
22. ic lanan amlu in Take anak zane Prompts before downloading potentially unsafe lt content Takes effect after you restart Internet Explorer Unsigned ActiveX controls will not be downloaded a ES Reset custom settings Reset to medium high default Custom level Reset all zones to default level First Time Users First time users need to create their own personal login account by selecting the Create Login Account link DNA sequencing results can only be retrieved using your Login ID and Login password Your Login ID also identifies your status as either an Internal University of Calgary External other academic hospital or government researchers or Industry commercial user Industrial users are subject to a different fee schedule An example of the New Account Setup page is shown below UNIVERSITY OF CALGARY A University Core Ys DNA Services ins ee New Account Setup for dnaLIMS Login Information Required Fields Login Name mmmouse AAACASA Password i dees Re Type Password FirstName mickey LastName mouse Email Address mmouse mouseltd com Affiliation Select the Affiliation Type before filling in Contact Info Affiliation Industry Internal UofC External NonUofC Academic PI Disney Walter Last First Name ofthe Senior Researcher for your lab or project Contact Information Bill
23. ing Information Accounts Payable Shipping Information Name mickey mouse Name mickey mouse Institution gt Mickey Mouse Industries Ltd Institution Mickey Mouse Industries Ltd Dept Accounts Payable Dept Dept of Molecular Biology Address 100 Mouse Hole Lane Address 101 Mouse Hole Lane Address 2 Address 2 Science amp Technology Bldg City Calgary i City Calgary Province State AB Canada Province State AB Canada Country Country Postal Code Zip T2N1N4 Postal Code Zip T2N 2N2 Phone 403 123 4567 Ext u Phone 403 220 1234 Ext Fax Fax Email acctspayable mouseltd com Email mmouse mouseltd com Copy Billing to Shipping Clear Billing Clear Shipping Copy Shipping to Billing Validate Form Notes for creating a new account e Required fields are denoted with a e Capital letters in your First and Last Name are converted to lowercase by the system to simplify searching e Be sure to enter your e mail address correctly Among other things this is the address that will be used to send you your password in case you forget it e The Copy Billing to Shipping and Copy Shipping to Billing buttons can be used to avoid typing similar information twice into the Billing Information and Shipping Information columns However the address and contact in
24. or a particular Request number by pressing the Back button on your browser or by the View Your Requests hyperlink from the main dnaTools User Tools page Enter the Request number for the sample you wish to view or delete into the box labeled Requisition or Order Number Under Search by Request Number select either the View Request or Delete Request button Select the Submit button to either view or delete that sample from your order Once a sample has been deleted it cannot be restored to the dnaLlIMS
25. ow UNIVERSITY OF University Core DNA Services CALGARY University of Calgary A University Core 3330 Hospital Dr NW Ko ES DNA Services Calgary AB T2N 4N1 Pee 403 220 4503 UCDNA Home Page User Commands Logout Display DNA Sequencing Requests Return to View your Requests Bottom of Page Cannot process your wiew delete Sequencing Request The Requisition Number 1343 is not in the Gel Pool Please review the Req s of your entries in the Gel Pool 4 Click on the Submit button near the top of the Search the Sequencing Request Queue page Your entire order will be deleted Once an order has been deleted it cannot be restored to the dnaLIMS To Delete or View Individual Samples in an Order 1 From the main dnaTools User Tools page select the View Your Requests hyperlink The Search the Sequencing Request Queue page will appear 18 Locate your order number in the Search Your Orders list box near the bottom of the page Click on the order to highlight it in the list Click on the Submit button near the top of the page A table of all your outstanding requests will appear The first column will show the unique Request number assigned to each sample as a hyperlink Tip If you want to view or delete more than one sample make a note of the Request numbers so you don t need to keep coming back to this page Return to the Search the Sequencing Request Queue page by either clicking on the hyperlink f
26. own menu to identify whether your bacterial samples are from eson Meese e liquid culture or glycerol stock or in the form of plaques colonies o The request form will contain a column called Plasmid Prep Information with a pull down 13 menu listing the products from the TempliPhi amplifications as Plasmid1 Plasmid2 Plasmid3 etc You will need to label your bacterial samples as Plasmid1 Plasmid2 etc to correspond to this form You can have up to six different sequencing reactions i e six primers run from each plasmid preparation Be careful to ensure that each sequencing reaction is named correctly for the plasmid and primer chosen o When complete press the Submit button to send your request to the dnaLIMS 3 When the Submit button is pressed a completed request form showing your order number and the identification numbers required for your tubes will be displayed Print out one copy of this page to be submitted with the samples and one copy to be kept for your records However do not label each of your samples with the individual Tube Label numbers shown on your form i e 1346 1 1346 2 etc Instead label your samples with the Plasmid numbers indicated in the DNA Type column Place the samples and a copy of the print out in a suitable package for delivery to our lab If you are paying by credit card your credit card number and expiry date should also be added to the re
27. quest form or make arrangements for this information to reach our lab by other means 14 Menus Logout The Requests are entered your Order Number is 1347 DNA SEQUENCING REQUEST FORM ATTENTION Please print two copies and turn one copy in with your samples Order No 1347 University Core DNA Services Contact Name pon richard University of Calgary TE 3330 Hospital Dr NW Email mtpon ucalgary ca Calgary AB T2N 4N1 Principal Investigator Richard T Pon 403 220 4503 Department Biochemistry amp Molecular Biology Building 3350 Hospital Drive Room HM 179 Phone 403 220 4225 Service Type Plasmid Prep DNA Provided Glycerol Todays Date Nov 23 2006 Cost Reaction 20 Number of Plasmid Preps 5 Plasmid Prep Cost 30 Payment Method PO 12345 Comments Example of a plasmid prep request The order contains 10 Samples Please write your NAME and ORDER NUMBER on the outside of the bag rack that you put your samples in and label the individual PCR tubes with the assigned tube label eg 1071_1 1071_2 1071_3 etc Please use STRIPS of 8 PCR tubes whenever possible If submitting 96 well plates please write ORDER NUMBER on the plate Tube Label Sample DNA Type Size Primer Tm E 1347_1 templ prep 1 Plasmid1 10000 My Forward 55 2 1347_2 templ prep 1 Plasmid1 10000 My Reverse 52 EA 1347_3 templ prep 2 Plasmid2 10000 My Forward 55 4 1347_4 templ prep
28. r each of your tubes Tube Label will be displayed Print out one copy of this page to be submitted with the samples and one copy to be kept for your records Label each of your samples with the individual numbers shown on your form i e 1846 1 1346 2 etc and place the samples and a copy of the print out in a suitable package for delivery to our lab If you are paying by credit card your credit card number and expiry date should also be added to the request form or make arrangements for this information to reach our lab by other means 12 hienus Logout The Requests are entered your Order Number is 1346 DNA SEQUENCING REQUEST FORM ATTENTION Please print two copies and turn one copy in with your samples Order No 1346 University Core DNA Services Contact Name pon richard University of Calgary 3330 Hospital Dr NW Calgary AB T2N 4N1 Principal Investigator Richard T Pon 403 220 4503 Email mtponq ucalgary ca Department Biochemistry amp Molecular Biology Building 3350 Hospital Drive Room HM 179 Phone 403 2204225 Service Type Full Todays Date Nov 23 2006 Cost Reaction 20 Payment Method PO 12345 Comments Enter any special requirements here The order contains 4 Samples Please write your NAME and ORDER NUMBER on the outside of the bag rack that you put your samples in and label the individual PCR tubes with the assigned tube label eg 1071_1 1071_2 1071_3 etc
29. ture media or a small piece of a plaque Each plasmid preparation produces enough template for up to six different sequencing reactions i e you can sequence with up to six different primers 10 3 Enter a value from 1 to 384 for the number of sequencing reactions Tip if you have more than 48 reactions it s easier to submit your samples as a 96 well plate request Depending upon the service you have selected a customized request form will appear with one line for each sample UNIVERSITY OF University Core DNA Services CALGARY University of Calgary University Core 3330 Hospital Dr Nui oe Calgary AB TZN 4N1 403 220 4503 Ra ae SI bee aa UCDNA Home Page User Commands Logout Full Service Request Form Payment Type PO Number k PO 1 2345 Principal Investigator Richard T Pon Comments to Lab Enter any special requirements here No Validation response means all required fields are filled in Sample Name Q Learn More Template Information Primer earn More Si Name Name Size bp Name Tm Index Fillx Fil 2 Clear Fill Clear Fill Fillx Clear Fill Alternate Clear ill Alternate Clear v 7 v 7 7 F F 7 J gt J 1 mysamplel Plasmid pTest 20000 M13F j M13F 2 my sample1 Plasmid pTest 20000 M13R 17 M13P 17 3 imy sample2 Plasmid pTest 20000 custom v Imy primer1 4 my sample2 Plasmid Y pTest 20000
30. uests ve 96 Well Plate FA Requests Home Page User Help E Done Internet Getting Help On the bottom of this page is a User Help hyperlink which provides rudimentary on line help from dnaTools in the form of an online dnaTools User Manual However the on line help provided by dnaTools is quite dated and not always relevant to our installation Other help information will be placed on our facility website www med ucalgary ca dnaservices as we create it Alternatively you can contact the DNA sequencing staff by phone 403 220 4503 or e mail dnaseq ucalgary ca Sample Preparation Guidelines The dnaLIMS User Tools main menu contains a link in the right hand column called Sample Preparation Guidelines which displays details of how to prepare samples required template and primer concentrations required sample volumes and other details It also lists the stock primers we provide at no charge for full service sequencing and information about preparing samples for fragment analysis Please contact the sequencing lab staff dnaseq ucalgary ca for detailed assistance on any matter UNIVERSITY OF University Core DNA Services CA LG ARY University of Calgary A University Core 3330 Hospital Dr NW ae ONA Services Calgary AB T2N 4N1 403 220 4503 UCDNA Sample Preparation Guidelines The DNA sequencing lab uses standard automated sequencing methods We use a 3730 ABI DNA sequencing instrument The 3730 Genetic
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