ChIP Seq
From Genome Technology Core (GTC) wiki - Sequencing and Microarray
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ChIP-Sequencing (or ChIP-Seq) combines chromatin immunoprecipitation (ChIP) with DNA sequencing, allowing researchers to identify the binding sites of DNA-associated proteins. It can be used as an alternative to promoter or whole genome microarray hybridization or qPCR. http://illumina.com/downloads/ChIP-Seq_DataSheet.pdf
Please see below for further details about the service.
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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.
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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 - ChIP Seq | Sample | Inquire | - |
| Genome Alignment and other analysis | Sample | Inquire | - |
