title: Carroll_ChIP_exo
design: Carroll_ChIP_exo
library_construction_protocol: The liver material was isolated from three adult (three month) C57/BL6 males obtained from Charles River UK. The investigation was approved by the ethics committee and followed the Cambridge Institute guidelines for the use of animals in experimental studies under home office license PPL80/2197. All tissues were treated post mortem with 1% formaldehyde as previously described (Schmidt et al., Methods 48(3) July 2009 doi:10.1016/j.ymeth.2009.03.001). The ChIP assays were performed as previously described (Schmidt et al., 2009). Protein-bound DNA was immunoprecipitated with antibodies against COT2/COUP-TFII (R&D Systems, PP-H7147-00), FoxA1 (Abcam, ab5089), ER (Santa-Cruz, sc-543), FoxA2 (Santa-Cruz, sc-6554) and P300 (Santa-Cruz, sc-585).  For the ChIP-exo library preparation, the immunoprecipitated chromatin was end-repaired, ligated to the TruSeq P7 exo-adapter, nick repaired, digested with the lambda and the RecJf exonucleases. The digested DNA was extracted, second-strand synthesised with the P7 primer, ligated to the TruSeq P5 exo-adapter and finally amplified with 18 PCR cycles. A 2% agarose gel was used to select 200-300 bp DNA fragments.
attributes.tag: Experimental Factor: immunoprecipitate
attributes.value: FoxA1
attributes.tag: Experimental Factor: organism
attributes.value: Mus musculus
attributes.tag: Experimental Factor: protocol
attributes.value: ChIP-exo