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:

• HiC-bench platform (chipseq–standard pipeline)

The following select publication have used our analyses:

• Ntziachristos P, Tsirigos A, Weistead GG, Trimarchi T, Bakogianni S, Xu L, et al. Contrasting roles of histone 3 lysine 27 demethylases in acute lymphoblastic leukaemia. Nature. 514(7523):513-7.
• Benitez J, Ma J, D’Antonio M, Boyer A, Camargo M, Zanca C, et al. PTEN regulates glioblastoma oncogenesis through chromatin-associated complexes of DAXX and histone H3.3. Nature Communications. 2017:8:15223.