ChIP Seq

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Marson A, et al. Cell 2008


Chromatin Immunoprecipitation Sequencing (ChIP-Seq) combines ChIP with DNA sequencing, allowing researchers to identify the binding sites of DNA-associated proteins. It can be used as a more cost effective and higher quality alternative to whole genome microarray hybridization.

Sample Submission Guidelines

Users are required to prepare their own libraries for sequencing by following the corresponding Illumina Protocols. If this is a service that you would like the BMC to perform in the future please visit the Ideas page.

Samples which are ready for sequencing should be gel-purified according to your protocol, and provided as at least 5uL of solution at a concentration of 10 nM in EB/ Tween 0.1%. To calculate your sample’s molar concentration, you must know the average length of your product.

When submitting a sample you must supply the BMC with the molar concentration, average length, and species of origin of all samples.

We encourage all those submitting samples to allow us to run QC to obtain/confirm concentration information. Cyber green and qPCR QC analysis coming soon!

Samples generated using standard kits with Illumina PCR primers can be submitted without sequencing primers. Custom sample preparations using customized PCR primer sequences should be provided along with a complementary sequencing primer.

Sample Submission Forms


Images acquired from the Illumina sequencer are processed through the bundled Illumina analysis pipeline to identify the sequence and quality score for each base. The data can then be aligned to a reference genome, if requested, using an interactive ELAND algorithm. An in-depth QC report of the data is included in the package.

Output Files:

  • sequence.txt
  • eland_query.txt
  • eland_result.txt
  • realign.txt

More information about the output files can be found on the Illumina Pipeline page.

Turnaround Time

Each Genome Analyzer processes 8 samples per run, or 7 samples plus a control. The control is typically used to improve sequence quality. 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 depending on demand from other users. Once the run has begun approximately six days are required for clustering, sequencing, and data analysis for a 36 base pair read. The process requires approximately 5 days for a 25 base pair read.


Illumina sequencing is currently available only for labs associated with the BioMicro Center Core departments. Sequencing is currently available at an introductory price:

                                 Single End Reads (priced per lane):             
                                         7 lanes | 8 lanes                
                                            $610 | $550

ChIP Seq Literature


  1. Paper1 pmid=18692474 <!-mirna 2008->
  1. Paper2 pmid=17558387