Analysis

ChIP-Seq

Image of ChIP-Seq

Chromatin immunoprecipitaion followed by sequencing (ChIP-seq) allows in vivo determination of where a protein binds in the genome, which can be transcription factors, DNA-binding enzymes, histones, chaperones, or nucleosomes. ChIP-seq first cross-links bound proteins to chromatin, fragments the chromatic, captures the DNA fragments bound to one protein using the antibody specific to it, and sequences the ends of the captured fragments using next generation sequencing (NGS).

Computational mapping of the sequenced DNA identifies the genomic locations of bound DNA-binding enzymes, modified histones, chaperones, nucleosomes, and transcription factors (TFs), thereby illuminating the role of these protein-DNA interactions in gene expression and other cellular processes. The use of NGS provides relatively high resolution, low noise, and high genomic coverage compared with ChIP-chip assays (ChIP followed by microarray hybridization).

ChIP-seq is now the most widely used procedure for genome-wide assays of protein-DNA interaction, and its use in mapping histone modifications has been seminal in epigenetics research.

The Eugene McDermott Center for Human Growth and Development has been very active in this field of genetic research, providing cutting-edge sequencing, data analysis, and support to the magnitude of researchers at UT Southwestern and beyond. The following is a basic workflow that we employ for the analysis of such data.

Please contact us if you would like more details about the workflow including specific parameters of the software, genome versions used, etc. This publication is a also a great place to start for those who want an accessible introduction to ChIP-Seq analysis. Another great resource is the guidelines written by the ENCODE consortia

McDermott high level ChIP-Seq workflow
High level ChIP-Seq workflow

Files Provided with ChIP-Seq Analysis

The following is a list of files provided with your ChIP-Seq analysis:

  • Raw unprocessed gzipped FASTQ files
  • FASTQC report with basic sequencing quality statistics
  • Mapped BAM files (sorted -> low-qual filtered -> duplicates removed)
  • Wiggle and BigWig tracks
  • ChIP-Seq quality measures (phantompeakqualtools)
  • HOMER generated analysis output files
  • MACS2 generated analysis output files
  • Peak annotations