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.
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.