Expression Seq
From Genome Technology Core (GTC) wiki - Sequencing and Microarray
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We offer a mRNA Sequencing service utilizing the Genome Analyzer System (Solexa) from Illumina. Primarily, we offer:
- Digital Gene Expression Sequencing Service
Digital Gene Expression is similar to SAGE analysis. Sequencing of short mRNA “tags” provides genome-wide expression profiles and is used as an alternative to full-genome microarray hybridization or qPCR. Digital Gene Expression is more sensitive and has a greater dynamic range than traditional microarrays allowing for more accurate quantification and detection of very low abundance transcripts. http://illumina.com/downloads/rnaDGETagProfiling.pdf
- Whole Transcriptome Analysis
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.
Please see below for further details about the services.
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Sample Submission Guidelines
Users are required to prepare their own libraries for sequencing by following the corresponding Illumina protocol. Samples which are ready for sequencing should be gel-purified according to your protocol and provided UNDILUTED in EB.
Users should submit 5uL of undiluted sample. We will calculate 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.
Samples generated using standard kits with Illumina PCR primers can be submitted without sequencing primers. (CAGT can provide standard sequencing primers.) Custom sample preparations using customized PCR primer sequences should be provided along with a complementary sequencing primer.
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 interative ELAND algorithm. An in-depth QC report is included in the package. Sample QC report is here.
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.
Pricing
| Item | Unit | Price Per Unit | Notes |
|---|---|---|---|
| Sequencing - 36 bp Single Read | Sample | ~$850 | Cluster, Sequence, Pipeline |
| Sequencing - 36 bp Paired-End Reads | Sample | ~$1,500 | Cluster, Sequence, Pipeline |
| Sample prep - DGE | Sample | Inquire | - |
| Genome Alignment and other analysis | Sample | Inquire | - |
