1 What is ChIPseq?

Chromatin immuno-precipitation is used to experimentally determine the genomic location of specific protein or protein variants (see figure below). Detection can be done by PCR, hybridization (ChIP-chip) or sequencing (ChIP-seq). The process consists of:

  1. chemically cross-link chromatin (proteins and DNA) [optional in “native ChIP”]
  2. fragment chromatin (< 1kb fragments)
  3. antibody-based enrichment of fragments
  4. purify DNA and sequence
  5. alignment density is a measure of abundance