Difference between revisions of "Sequencing"
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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. | 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 = | ||
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| + | 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. | ||
= Applications = | = Applications = | ||
| − | = ChIP-Seq = | + | == ChIP-Seq == |
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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. | |
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Revision as of 12:47, 20 August 2010
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GTC has two Illumina Genome Analyzers 2.0. Each sequencer can process up to 16 samples per week, with a data yield of 20-30 million reads per sample. Read lengths are 36 to >100 bases in single or paired-end formats.
Templates are “sequenced” by incorporating fluorescently labeled nucleotides with Illumina's proprietary “Sequencing-By-Synthesis” technology. A detailed description of this process can be found here: http://illumina.com/pages.ilmn?ID=203
Sample Submission Guidelines
Users are required to prepare their own sequencing libraries. Samples should be gel-purified and provided UNDILUTED in EB.
Users should 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.
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 interative ELAND algorithm. An in-depth QC report is included in the package.
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.
Frequently used applications of Illumina sequencing include:
- ChIP Seq
- Small RNA Sequencing
- Digital gene expression
- Whole Transcriptome Analysis
- Genome sequencing and resequencing
- Paired End Sequencing
- Genotyping: Protocols are being developed for detection of SNPs, chromosomal rearrangements and other genotyping applications.
Protocols
Protocols for all of the supported technologies can be found on the Illumina website, or by contacting Illumina at (800) 809-4566. http://illumina.com/pagesnrn.ilmn?ID=70#252
