Sequencing
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Contents
Technology
The GTC offers Next-Generation sequencing on the Illumina platform. We have two GAII systems and one HiSeq2000. We offer full service sample processing including library prep service with the SPRIworks system from Beckman.
Pricing
For pricing information - Click Here
Sample Submission Guidelines
Please use our sample submission forms found here. Internal users should use the online form, external users should download the excel form.
Users may submit libraries prepared with Illumina adapters or dsDNA for library prep service.
User prepared libraries should be gel-purified and provided UNDILUTED in EB. Please submit 5uL of undiluted sample. We will determine the concentration by RT-PCR and make the appropriate dilutions. Excess sample will be retained in our freezers for potential future re-run. Users are also strongly encouraged to retain a portion of their samples in case of emergency.
For library prep service please submit 5uL of dsDNA (RNA samples will need to be reverse transcribed first). We will provide all reagents for adapter ligation and enrichment.
GTC will provide sequencing primers for libraries prepared with standard Illumina adapters. If custom sequencing primers are required they must be provided at the time of sample submission.
Data
Images acquired from the solexa sequencer are processed through the bundled solexa inage extraction pipeline to get the sequence and quality score for each base. The data is aligned to a reference genome, if requested, using an ELAND algorithm. An in-depth QC report is included in the package.
- Coming soon - Details on the final data package*
Turnaround Time
Each Genome Analyzer processes 8 samples per run, or 7 samples plus a control. Full flowcells can be run usually within two weeks of submission. Partial submissions of less than eight samples (or 7 with control) are put into a project queue, where they join existing samples or await others before processing. Wait times for partial submissions vary but are generally two weeks or less, depending on demand from other users.
Applications
ChIP-Seq
ChIP-Sequencing (or ChIP-Seq) combines chromatin immunoprecipitation (ChIP) with DNA sequencing allowing researchers to identify the binding sites of DNA-associated proteins.
Small RNA Sequencing
Small RNA discovery provides identification of non-coding RNA to aid in the understanding of gene regulation. It can be helpful in identifying novel small RNA molecules. http://illumina.com/downloads/rnaDGESmallRNA_Datasheet.pdf
mRNA Sequencing
Sequencing the entire transcriptome can reveal valuable information about exon boundaries and splice variants that may be missed by microarray analysis or Digital Gene Expression. Kits for whole transcriptome analysis are expected to be available from Illumina soon.
Denovo Sequencing
De novo sequencing can be done using the Genome Analyzer, although the short read lengths can make assembly challenging, especially in larger genomes. However, advancements are being made to increase read length and improve assembly algorithms. http://illumina.com/downloads/ch2-ILMN_ProdGuide_DNAsequencing.pdf
