GenCore GENOMICS CORE FACILITY. User Guide. Index

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1 GenCore GENOMICS CORE FACILITY User Guide Index. A brief description of the facility 2 2. How to order a service?... 2 a. Registration i. New customer registration ii. Registered customers b. Filling out the requisition 3. How should you prepare your samples?... 4 a. Automatic capillary electrophoresis b. Sequencing reaction and automated capillary electrophoresis (PCR products and plasmids) c. Next Generation Sequencing NGS 4. When and how the results will be delivered.. 6 GenCore Instituto de Investigação e Inovação em Saúde, Universidade do Porto Rua Alfredo Allen, Porto, Portugal Telf: Ext: sequencing@ipatimup.pt

2 . A brief description of the facility The Genomics Core Facility GenCore, initiated at Ipatimup in 2006, is a full service facility dedicated to provide investigators state of the art technological solutions in the field of genomics and high throughput analysis. We offer technical expertise and support with experimental design, protocol development, and data analysis guidance. Training is another crucial aspect of our work. The laboratory is proficient in providing: Sanger/NGS sequencing, exome sequencing; Targeted DNA and RNA sequencing; Small genome sequencing; Metagenome sequencing; Whole transcriptome sequencing; Real-time PCR and digital PCR; Other, upon request. Additionally, due to the very dynamic and rapidly evolving field of genomics, we actively collaborate with different companies in developing NGS related products both for sample preparation and for bioinformatics data analysis. The facility is an Ion Torrent certified service provider. 2. How to order a service? IMPORTANT NOTE: You always need to check the viability of your request with GenCore. a. Registration i. New costumer registration Go to the tab "Prices" on the site and click on. Select Sign up to start your registration and provide the requested data. Click on the Submit button. Access the account you provided when registering and click on the hyperlink to activate it. When your registration is approved you will receive an to validate your login. Choose a password. ii. Registered costumers Go to the tab "Prices" on the site and click on. Enter your address and the password you have used to register. Click "Login". 2

3 b. Filling out the requisition After confirming the viability of your request with GenCore, you will need to fill out a requisition for each service order. In "Service" choose SEQ206 - Sequencing Service. Type your sample names in an Excel file and upload it in "Attach Sample File". When applicable, attach below your Purchase Order/PAD/Budget/Requisition. In "Lines", click on the field "Description", choose the appropriate option from the popup list and complete the fields accordingly: Sanger Sequencing - in "Quantity" put the number of samples to be processed (the price appears automatically). You can order our services in two ways: A. Standard ordering - the service is ordered according to the total number of samples to be delivered, which will be processed on scheduled time (maximum of six business days), with no possibility of samples in credit. The order is billed after service execution. B. Prepaid packages ordering the requested service allows the purchase of a sample pack with one invoice only (with the date of the request). When a request is made, it will be deducted from the prepaid credit, which can be tracked online through history movements. The prepaid credit must be fully executed by the end of the year on which it was requested and the remaining credit will not be refunded. Next Generation Sequencing fill out the Quantity and Unit Price fields according to the quote previously sent by the service. If you need to choose different options, add mores lines by clicking. Click Generate Budget/Pro Forma or "Submit". The Submit option is an order request confirmation. 3

4 3. How should you prepare your samples? a. Automatic capillary electrophoresis The samples for capillary electrophoresis have to be delivered purified, preferably without formamide (sequencing products) and without formamide / size standard (genotyping products). They can be delivered in microcentrifuge tubes, PCR tubes or 96-well plates. Make sure that the tubes / plate are properly sealed and that the identification assigned is easily associable to the list of samples that you have uploaded when you requested the service. The service is not responsible for products delivered in inappropriate conditions (for example, nonspecific PCR products; purification of sequenced product not properly done; poor quality of the sample), so the price value will always be charged, even though the result is not satisfactory, except if the error is inherent to the service (tables & 2). Table Capillary electrophoresis for sequencing products Sequencing Kit Maximum fragment size Price (Euros, VAT not inc.) E [BigDye-V.]* 300bp, 500bp, 700bp or 900bp Z [BigDye-V3.]* 300bp, 500bp, 700bp or 900bp Ready-to-Go samples 3 300bp, 500bp, 700bp or 900bp Other [upon request] 300bp, 500bp, 700bp or 900bp Upon request *Applied Biosystems Life Technologies The length of read is dependent on the quality of the samples. 2 Does not include re-runs unless the error is inherent to the service. 3 Samples are delivered ready to run in AB Genetic Analyzer 330xl and 330 s compatible plates. 4

5 Table 2 Capillary electrophoresis for genotyping products Dye Set Price (Euros, VAT not inc.) D [6FAM;HEX;NED;ROX500]* 2.66 G5 [6FAM;VIC;NED;PET;LIZ500]* 2.66 E5 [dr0; dr6g;dtamra;drox;liz20]* 2.66 Ready-to-Go samples Other [upon request] Upon request *Applied Biosystems Life Technologies Does not include re-runs unless the error is inherent to the service. 2 Samples are delivered ready to run in AB Genetic Analyzer 330xl and 330 s compatible plates. b. Sequencing reaction and automated capillary electrophoresis PCR products and plasmids PCR products and plasmids for sequencing reaction can be delivered in microcentrifuge tubes, PCR tubes or strips, non-purified (PCR products purification is done by the service using an enzymatic procedure). Make sure that the tubes are properly sealed and that the identification assigned is easily associable to the list of samples that you have uploaded when you requested the service. The service is not responsible for products delivered in inappropriate conditions (for example, nonspecific PCR products; poor quality of the sample), so the price value will always be charged, even though the result is not satisfactory, except if the error is inherent to the service. Bring your samples and primers according to table 3. 5

6 Table 3 Sequencing reaction and automatic capillary electrophoresis Type of Minimum DNA Minimum Primer Price (Euros, sample concentration template volume concentration VAT not inc.) PCR product 0ng/µl Plasmid 00ng/µl 0µl 0µM 5.44 Does not include re-runs unless the error is inherent to the service. c. Next Generation Sequencing - NGS Please contact GenCore for more information on price values and sample requirements. The facility in proficient in providing exome sequencing, targeted DNA and RNA sequencing, small genome sequencing, metagenome sequencing, whole transcriptome sequencing, among others. 4. When and how the results will be delivered? The time for delivering the results depends on the type of application. This information will be given when you contact us to check the viability of your request. For automated capillary electrophoresis for: Sequencing products the.ab format files will be sent after being submitted to Applied Biosystems Sequencing Analysis Software v5.2 for quality check (this will enable you to import them to any compatible sequence electropherogram reading program. If you want us to send you the results also in PDF format you need to mention it. Genotyping results non-analyzed *.FSA format files will be sent. These files can be imported to any *.FSA reading program. 6

7 For NGS projects, results are sent in BAM/FASTQ format files. Different file types may be obtainable upon request. Bioinformatics analysis may also be available, depending on the type of project. GenCore sample analysis is related to quality control and does not reflect any data interpretations. Depending on the size, results are sent by or through a DropBox download link. We are in the process of developing a platform allowing you to download your results, meanwhile, for larger file sizes, you may need to collect them at our facilities with an appropriate external disk or similar. If you have any questions or suggestions, please contact us by or phone. GenCore Instituto de Investigação e Inovação em Saúde, Universidade do Porto Rua Alfredo Allen, Porto, Portugal Telf: Ext: sequencing@ipatimup.pt Last revision: February th, 206 7

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