LIMS User Guide - Core facilities
Contents
1. The file will be saved in our LIMS system under your project RNA isolation No of Samples Source Please specify tissue gt If you select tissue as sample source you need to specify the tissue Qualtiy Measurement Quantification Measurement cDNA Synthesis Can your samples be hazardous il IV Genomics Core Facility Do you want your samples back Button Upload project file gt Use this button if you have additional information that you want to share with us The file will be saved in our LIMS system under your project SNP No of SNPs Assays No of Templates incl controls Assay Need hel pordering assays Template Container No of Template Containers DNA quality have been checked DNA quantification done Can your samples be hazardous Do you want your samples back Button Upload SNP Assay List Button Upload ABI File TQMN_ SNP gt Optional button to upload assay information This must be a file looking like below in the beginning and with information about the SNP assays xxx AB Assay Information File RAR Version 03601500 Number of Assay Information Fields 4 Begin Assay Information Customer Name Order Number Ship DATS aaa Button Upload project file gt Use this button if you have additional information that you want to share with us The file will be saved in our LIMS system under your project QPCR No of templates incl controls gt Include your standard curve samples in the number of templates Total n2. have additional information that you want to share with us The file will be saved in our LIMS system under your project Statistical support Type of data Please specify gt If you select other type of data we want you to specify this Is data generated at Genomics Who was your staff reference gt Only if data was generated at Genomics Study population description gt Please write a short description of your study population Delivery requested Please specify XL xii Genomics Core Facility gt Ifyou select Other as delivery we want you to specify what kind of delivery you request Button Upload project file gt Use this button if you have additional information that you want to share with us The file will be saved in our LIMS system under your project Bioinformatics Type of data Please specify gt For NGS data please specify if it is exome sequencing RNAseq ChlPseg whole genome sequencing methseq gt For Other please specify what data you have Is data generated at Genomics Who was your staff reference Where is data generated gt If data is generated outside Genomics i e BGI GATC SciLife Description of study gt Ifyou want you can add a short summary of your project Delivery requested gt l e analysis data file advice etc Location for data transfer gt Due to firewalls we need to know where the computer use for downloading data is located Button Upload project file gt Use this bu
3. Genomics Core Facility LIMS User Guide 1 Content NC ONTEN assa re ere nen een ee oT eee er A eee Da Seia ao er ee E ce ee ee ci 1 IGT o 0m6 p ORNE ani RR EEEE EEE OR tance sea ced need eagle RO dans cen cians sence RR EE EEEE 2 2 Selo USCr ACC OU a N E E E S 2 de VOCEA ean E Ad 2 Create a new INVOCA COS ras tater a r EE E dap anea bales lee ncgneueneceeaaustareaee 2 4 Create Project REQUEST cccsscssscssscssscecsscessccescoeseesseessceeseeeseeesceuseeeseeesesesctescnesetesssesssesseeeseeeses 4 REQUESL AD aos padirc adiada ds none CEU io bia Nba EO ra pi in pn SE e a sn ci 5 LO CLS Og 5 DECS T O poa nica E E neato sige vastus cece ous yaa ance ana E sou ann T E gt E DNA SONU OI cries css oseevecpscesee A EE A E I E s 5 Ha RNA OON a A 5 M NP oi E E E E E 6 M PE A E E E EE CR 6 V EEANN AG pears SERRO IR RR SC CR RSRS E RR CR RR CORO RR A E E 7 Ma WVU EIE A EA E EAE A E aes 7 vii Sanger SEQUENCING iii a 7 UN NG said aii dai E teu E balers 8 De MCO AY iso ie acuta raed tat txcuncdcta cee SD 9 pS 2 10 159 0 gt eck 6 6 Ce enn EE A MNT ek ne ore ee rrr eR er eRe nn ee ee 9 Xi BIQUINIS rp E E E E 10 xii elfo je laio SPAS go PRP RARO RR E RR DRE RR DE RIR RO DD acces 10 S MS UIE OOO jd sae RAD SAR ERR AP NRO DR RR E uataceeasinnsaseee 11 Create DOOKINE ospasadrirs aaa Gad ani Sano doa uti DECS A SD gi Suse OO Sa GP ans 11 Genomics Core Facility 1 Introduction Genomics Core Facility uses a LIMS syste
4. ant your samples back Button Upload project file gt Use this button if you have additional information that you want to share with us The file will be saved in our LIMS system under your project Sanger sequencing Is optimization needed Need help ordering primers No of templates viii Genomics Core Facility Total no of fragments Sequencing direction Total no of reactions gt This will be calculated automatically when you have filled in no of templates fragments and sequencing direction Starting material Template Container No of Template Containers Region high in GC content Select the steps you want to do VV VV Y Aplification PCR PCR clean up Sequencing reaction PCR Sequencing reaction clean up Sequencing reads in the 3730 Can your samples be hazardous Do you want your samples back Button gt Button gt Button gt NGS Upload genes and exons This button can be used to upload a tab delimited text file with the exons that you want to sequence The file must be without header and on the format below Genel Exonlel Genel Exonl 2 Gene EXonZ sl Where you replace Genel Exon1 1 etc with your own genes and exons Upload list of samples This button can be used to upload a text file with all your sample names in one column like below The file must be without header SampleID 1 SampleID_2 SampleID_3 Upload project file Use this button if you have addi
5. bout when the project starts and who is responsible for the project Below you find more information about what we want you to fill in Fields with blue text are mandatory and fields with black text are optional When you are satisfied with your request click the Genomics Core Facility save button in the upper left corner You will then get a confirmation message with your project number Request tab Principal Investigatior Contact person Desired Start of Project Comment gt Ifyou have additional comments you want to add Invoice tab Invoice Address gt After you have selected Principal investigator for your project a list of invoice addresses will show up here If the list is empty you first need to create an invoice address Close your project request and create the invoice address see Create invoice Address in this document When that is done you can create a new project request Name On Invoice gt Ifyou want a different name than yours and your PI s name on the invoice Details tab The information under Details differs between the project types il DNA isolation No of Samples Source Specify source gt If you select Other as source you need to specify the source here Qualtiy Measurement Quantification Measurement Normalization Can your samples be hazardous Do you want your samples back Button Upload project file gt Use this button if you have additional information that you want to share with us
6. m to keep track of samples instruments users and projects To speed up the process we like our users to make project requests and instrument bookings directly in the system This will help us to provide better service to our users If you have questions about our LIMS system don t hesitate to contact the staff 2 Get a user account Send an e mail with the following information to genomics gu se Your name Your e mail address Your phone number Name of your principal investigator E mail to your principal investigator o Rr Phone number to your principal investigator If we receive this on a week day between 9 am and 4 pm we try to send you your log in information within an hour 3 Invoice Address Before you create a project request you need to have an invoice address connected to your principal investigator You only need to do this once for each invoice address you use If you have used Genomics Core Facility later than August 2011 your invoice address is probably already in the system and then you don t need to do this part You can see your invoice addresses under the invoice tab in a project request after you have selected a principal investigator Create a new invoice address Click on New invoice address under User info User info Change password SE dit user information Edit invoice address aNewinvoice address Genomics Core Facility A new window will open where you can fill in the invoice informa
7. o of genes assays gt Include your endogenous controls housekeeping genes in the total number of genes Replicates Total no of reactions gt This will be calculated automatically when you have filled in no of templates genes and replicates Template Container No of template containers QPCR method Is optimization needed gt This question is only relevant if you will use SYBR Green as method RNA quality checked yi vii Genomics Core Facility RNA quantification done Standard curve No of Applied TLDA cards No of custom TLDA cards Need hel pordering primers Can your samples be hazardous Do you want your samples back Button Upload project file gt Use this button if you have additional information that you want to share with us The file will be saved in our LIMS system under your project Fragment No of templates incl controls No of PCR products fragments Pooling No of Markers gt Ifyou want pooling Template Container No of Template Containers Is optimization needed Need help ordering assays Can your samples be hazardous Do you want your samples back Button Upload project file gt Use this button if you have additional information that you want to share with us The file will be saved in our LIMS system under your project MLPA No of Templates incl controls No of kits Template Container No of Template Containers Is optimization needed Need help ordering assays Can your samples be hazardous Do you w
8. olation RNA isolation SNP QPCR Fragment DNAISOLATION aM LPA Recent File Edit ltem Project sSanger sequencing G NGS Summary Samples Results Items Microarray Summary Info Request Details Invoice Internal s a For help click the internet icon at the bottom left Statistical support PP Principal Investigator A Bioinformatics Created By A_KULL Contact person j Updated On 06 18 2012 Bioanalyzer Owner A_KULL Desired Start of Project 0618 2012 E Other Closed No Status Incomplete Comment Above is also an image of how our project template looks Information for the request should be entered under the summary tab H Summary Samples Under the summary tab you will find four additional tabs Summary Info FE rm Request Invoice Details Internal For help click the Int Princinal Invastinator The Request and Invoice tabs are common for all project types They contain information about what customer user requests the project when you want to start and what invoice address you want to use The Details tab differs between the project types and here we collect the information we need for the specific project type For information about what information we want you to fillin under the details tab please scroll down in this document to the project type you selected The internal tab is where the Genomics staff to enter information a
9. tion Customer lt lt c lt Please enter your invoice information gt gt gt Invoice Address Id lt lt lt Invoice ID is the name that you can choose in the drop down list Invoice Address in project manager gt gt gt Invoice Recipient O Ansv Nr Faculty Institution Department K Lua Nr mr Customer gt Click the magnifying glass and select your Principal investigator Invoice address Id gt Give this address an ID that helps you remember what address it is The ID can be for example the reference responsibility lua number or something similar Invoice Recepient Ansv nr gt lf Invoice Recipient is University of Gothenburg then Ansv nr is mandatory Faculty Institution Department Lua Nr gt If Invoice Recipient is Sahlgrenska University Hospital then Lua Nr is mandatory Omr gt If Invoice Recipient is Sahlgrenska University Hospital then Omr is mandatory Ref Nr Address 1 gt Use this field together with Address 2 and Address 3 to fill in your address gt If Invoice Recipient is something else than GU or SU it is mandatory to specify an address Address 2 gt Use this field together with Address 1 and Address 3 to fill in your address Address 3 gt Use this field together with Address 2 and Address 3 to fill in your address Genomics Core Facility 4 Create Project Request Under New Project select the type of project you want to request New Project DINA is
10. tional information that you want to share with us The file will be saved in our LIMS system under your project No of samples Species to sequence Applications gt If you select Other please specify the application in the comment field Library Prep Sample Prep Kit Method Which instrument Comment IX Genomics Core Facility gt If you want to add additional information Location for data download gt Dueto firewalls we need to know where the computer use for downloading data is located Please specify gt If you selected Other as location for data download we need you to specify where you are located Can your samples be hazardous Do you want your samples back Bioinformatics service Comment gt Ifyou have additional comments about the bioinformatics service requested Delivery requested gt l e analysis data file advice etc Button Upload project file gt Use this button if you have additional information that you want to share with us The file will be saved in our LIMS system under your project Microarray Is optimization needed Need help ordering assays No of samples Control incl in no of samples Type of array Application gt Mandatory if you select SNP expression och methylation bead arrays Please specify gt Mandatory if you select custom bead array Can your samples be hazardous Do you want your samples back Button Upload project file gt Use this button if you
11. tton if you have additional information that you want to share with us The file will be saved in our LIMS system under your project Bioanalyzer No of samples Chip Bring own chip and reagents Can your samples be hazardous Do you want your samples back Button Upload project file gt Use this button if you have additional information that you want to share with us The file will be saved in our LIMS system under your project 10 Genomics Core Facility 5 Instrument booking Instruments computers for data analysis and licenses for IPA are booked in our LIMS calendar Open the calendar by selecting Book instrument on the main page Book instrument Create booking 1 Select the day you want to book by clicking in the white part of that calendar day You can see that a day is selected on the nn signs Select Edit Book instrument from the menu or click P in the menu bar 3 Fillin information about your booking and click OK You have to fill in a reference from Genomics An e mail will automatically be sent to the reference for him her to confirm your booking Lab Instrument Date 08272012 Start Time End Time Name Telephone Genomics Reference Comment OK Cancel 11
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