title: GSM5745668: day00.ATAC.Rep1; Homo sapiens; ATAC-seq
library_construction_protocol: ATAC-seq was performed as previously described (PMID: 29434377). ChIP-seq experiments for all histone marks at all time points were performed as previously described (PMID: 22763441). Detailed protocols for ChIP-seq including antibodies used and antibodies validations performed are available at www.encodedcc.org associated with each experiment described here. They can also be found at the links below. Standard ChIP-seq, Tissue fixation & sonication: https://www.encodeproject.org/documents/3125496b-c833-4414-bf5f84dd633eb30d/@@download/attachment/Ren_Tissue_Fixation_and_Sonication_v060614.pdf, Immunoprecipitation: https://www.encodeproject.org/documents/89795b31-e65a-42ca-9d7bd75196f6f4b3/@@download/attachment/Ren%20Lab%20ENCODE%20Chromatin%20Immunoprecipitation%20Protocol_V2.pdf. For RNA-seq, total RNA was extracted with Trizol according to protocol (Thermo Scientific, 15596-026). ATAC-seq libraries were created using Nextera Tn5 transposase with Illumina adapters and PCR-amplified as previously described (PMID: 29434377). ChIP-seq libraries were created as described here: https://www.encodeproject.org/documents/4f73fbc3-956e-47ae-aa2d41a7df552c81/@@download/attachment/Ren_ChIP_Library_Preparation_v060614.pdf. RNA-seq libraries were constructed using standard Illumina TruSeq LT library prep.