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 Histolemon (Carlo Erba) followed by both MNase digestion and sonication. FiT-Seq introduced further refinements to this method.
Pros:
- Works on FFPE samples
Cons:
- • Long protocol takes 4 days
- • Low yield
- • Sonication may introduce sequence bias 1
- CLASH-Seq: Fanelli M., Amatori S., Barozzi I. and Minucci S. (2011) Chromatin immunoprecipitation and high-throughput sequencing from paraffin-embedded pathology tissue. Nat Protoc 6: 1905-1919
- Teytelman L., Ozaydin B., Zill O., Lefrancois P., Snyder M., et al. (2009) Impact of chromatin structures on DNA processing for genomic analyses. PLoS One 4: e6700