PAT-ChIP
PAT-ChIP
PAT-ChIP is a variation of ChIP-Seq, optimized for the analysis of chromatin derived from FFPE samples. The distinguishing features of this method are dewaxing with a xylene substitute (Histolemon, Carlo Erba) followed by both MNase digestion and sonication. FiT-seq introduces further refinements to this method.
Pros:
- Works on FFPE samples
Cons:
- Long protocol takes 4 days
- Low yield
- Sonication may introduce sequence bias 1
- PAT-ChIP: Fanelli M., Amatori S., Barozzi I. and Minucci S. Chromatin immunoprecipitation and high-throughput sequencing from paraffin-embedded pathology tissue. Nat Protoc. 2011;6:1905-1919
- FiT-Seq: Cejas P., Li L., O'Neill N. K., et al. Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles. Nat Med. 2016;22:685-691
- 1. Teytelman L., Ozaydin B., Zill O., et al. Impact of chromatin structures on DNA processing for genomic analyses. PLoS One. 2009;4:e6700