ChIP Sequencing | NYU Langone Health

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Applied Bioinformatics Laboratories Services ChIP Sequencing

ChIP Sequencing

The Applied Bioinformatics Laboratories offer chromatin immunoprecipitation sequencing (ChIP-seq) services to researchers. ChIP-seq is a method for genome-wide detection of protein/DNA interactions. The technique uses ChIP and next-generation sequencing to find the DNA-associated proteins binding sites. 

Request a ChIP-Seq Service

To request this service from us, please provide the following:

  • a sample sheet with the corresponding conditions for the samples
  • the organism(s) of the particular study
  • the link to the generated FASTQ data (obtained from NYU Langone’s Genome Technology Center or another sequencing facility)

You receive the following from us:

  • a comprehensive report
  • quality assessment (read quality, alignment statistics, ChIP enrichment plots)
  • individual bigWig files for visualization using a genome browser
  • principal component analysis plot for assessment of sample similarities
  • BED files of identified protein binding peaks
  • distribution of identified peaks in genomic regions of interest (promoters, introns, exons, etc.)
  • annotated peak tables and differential binding analysis (logarithm of fold change, statistics, and normalized peak intensity value of each sample)

Additional or Customized Analyses

We also provide the following analyses:

  • gene-ontology term and pathway enrichment analysis
  • binding motif discovery
  • integration with gene expression (using RNA-seq data, if available)
  • customized plots

 Each of these may be subject to an additional charge.

Additional Resources

Below you can find a link to a computational pipeline that we typically use for our analyses:

The following select publication have used our analyses: