Genomics Core | Services, Prices and Forms

ABI 3730xl

The Genomics Core is equipped with a State-of-the-Art Applied Biosystems 3730xl DNA analyzer and employs experienced, well-trained personnel to handle sequencing projects. Information on how to prepare samples, how to submit samples and how to access and interpret the results is given in the various files below:

1. Introduction and general information on preparing DNA samples, designing primers and primers available through the Genomics Core
2. Information on sample submission formats
3. Information on how to submit your samples.
   Note:
   For each sample submission (individual samples or 96-well plates) two forms need to be filled out. Form one contains the sample and primer names and needs to be put in the online Dropbox folder. Form two contains some overlapping information but also has the billing infomation and is submitted with the samples. Links to these forms are given below.
4. To connect to the Dropbox folder:(PC path = \\lri-fs01\GenomicsCore\dropbox, Mac path = smb://lri-fs01/genomicscore/dropbox).
5. Individual Sample submissions:
   • Genomics Core sample sheet for individual sequence sample submissions (to be filled out and put in the Dropbox folder)
   • Genomics Core sample submission form for individual sample submissions (to be filled out and submitted with the samples)
6. 96-well Plate Sample submissions:
   • Genomics Core sample sheet for 96-well plate sample submissions (to be filled out and put in the Dropbox folder).
   • - Genomics Core sample submission form for 96-well sample submissions (to be filled out and submitted with the 96-well plate).
7. Accessing and interpreting DNA sequencing results.
8. Information on pricing

General:

Illumina Beadstation

• Clients purchase micro-array directly from Illumina and have them shipped to the Core. Contact the Core for the shipping address, product ordering information and information on available product discounts.
• Payment information (activity number, PO, credit card information) needs to be provided before data can be released.
• Illumina website: http://www.illumina.com/

Services:

Gene Expression Profiling Services
• Clients provide the Core with arrays (human, mouse, or rat; see above) and total RNA (minimum of 1 microgram, 10 ul @ 100 ng/ul). The Core will perform an RNA quality control step, process the RNA samples if they pass, hybridize to the arrays and produce relevant output files (at the Cleveland Clinic the Core can install the Illumina GenomeStudio software on a PC in your lab).
• Supported products: Whole genome gene expression arrays and whole genome DASL products.

Genotyping Services:
• Clients provide the Core with arrays (Infinium or GoldenGate; see above) and DNA (generally 10 ul @ 50 ng/ul). The Core will process the DNA samples, hybridize to the arrays and produce relevant output files (at the Cleveland Clinic the Core can install the Illumina genomeStudio software on a PC in your lab).
• Supported products: (most) Infinium and all Goldengate products.

Methylation Services:
• Clients provide the Core with arrays (Infinium HumanMethylation27; see above) and DNA (10 ul @ 50 ng/ul). The Core will process the DNA samples, hybridize to the arrays and produce relevant output files (at the Cleveland Clinic the Core can install the Illumina genomeStudio software on a PC in your lab).
• Supported products: Infinium HumanMethylation27.

General:

Illumina GAIIx

• Clients provide the Core with Sequencing Libraries (include Bio-analyzer picture with concentration) or purified RNA and/or DNA samples to be used in library preparation protocols. Contact the Core for the shipping address and amounts.
• Payment information (activity number, PO, credit card information) needs to be provided before data can be released.
• Illumina website: http://www.illumina.com/

Services

• Sequencing Finished Libraries: when providing finished sequencing libraries please provide 3-4 ul @ 100 nmol/l or more.
• Generating Sequencing Libraries: the Core can generate all standard (bar-coded) libraries (mRNA-SEQ, CHIP-SEQ, small RNA-SEQ, DNA-SEQ as well as Targeted re-sequencing libraries using the Agilent SureSelect enrichment system).
• As the protocols for making sequencing libraries is subject to change please contact the Core about the exact amounts of RNA / DNA needed (rough guidelines would be 1-10 micrograms of total RNA for standard mRNA/small RNA SEQ libraries, 30-100 ng of enriched DNA for CHIP-SEQ and 3-10 micrograms of DNA for (targeted) DNA-SEQ libraries.
• Output Files: standard output files are the sequence.txt file (no mapping to Genome) and the export.txt file (mapping to Genome). If requested CASAVA projects can be generated for visualization in the Illumina GenomeStudio software.