Chromatin Immunoprecipitation Sequencing / High-Throughput ChIP / Exonuclease trimmed ChIP / Multiplexed ChIP

ChIP-Seq is a well-established method to map specific protein-binding sites (Solomon et al., 1988). It has given rise to a vast number of derivatives, such as AHT-ChIP-Seq (Aldridge et al., 2013), BisChIP-Seq (Statham et al., 2012), CAST-ChIP (Schauer et al., 2013), ChIP-BMS (Li et al., 2011), ChIP-BS-seq (Brinkman et al., 2012), ChIPmentation (Schmidl et al., 2015), Drop-ChIP (Rotem et al., 2015), Mint-ChIP (van Galen et al., 2016), PAT_ChIP (Fanelli et al., 2011), reChIP-seq (Truax et al., 2012), scChIP-seq (Rotem et al., 2015), and X-ChIP (Skene et al., 2014). Sequential ChIP-seq (reChIP) can also show the association of different proteins on the chromatin (Elsasser et al., 2015). In this method, DNA-protein complexes are crosslinked in vivo. Next, samples are fragmented and treated with an exonuclease to trim unbound oligonucleotides. Protein-specific antibodies are used to immunoprecipitate the DNA-protein complex. The DNA is extracted, purified, and sequenced, giving high-resolution sequences of the protein-binding sites.


  • Base-pair resolution of protein-binding sites
  • Can map specific regulatory factors or proteins
  • Exonuclease use eliminates contamination by unbound DNA (Zentner et al., 2012)


  • Nonspecific antibodies can dilute the pool of DNA-protein complexes of interest
  • Target protein must be known and be able to raise an antibody


Illumina Library prep and Array Kit Selector


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