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ChIP-Seq analysis

Figure shows transcription factor binding at the mouse mm9 PLXND1 gene. Figure shows transcription factor binding at the mouse mm9 PLXND1 gene. ChIP-Seq combines chromatin immunoprecipitation (ChIP) with sequencing to identify the binding sites of DNA-associated proteins (e.g. transcription factors) and histone modifications genome-wide.

The following files can be provided with ChIP-Seq projects:

  • Primary QC report (general QC metrics on sequencing quality for each sequenced sample)
  • FASTQ (raw sequence data) and BAM (alignment) files for each sample
  • Peak calling output files (list of ChIP-enriched regions identified)

Bespoke downstream ChIP-Seq analyses*:

  • Secondary QC report (a set of QC metrics to assess the enrichment of the IP and the reproducibility of the experiment)
  • Peaks annotated with nearest gene information
  • Analysis of peak distribution with respect to genomic features
  • Differential binding analysis
  • Gene ontology and functional pathway enrichment analysis
  • Known and de novo motif search
  • Customised ChIP-Seq downstream analyses

* Please note that bespoke analyses might be subject to availability and resources, please contact us for more information.