GSM9022835: MCF7_ChIP-seq input_1 nM E2 30 min_set 1; Homo sapiens; ChIP-Seq
Nuclei were first extracted by inclubation in Farmham lysis buffer followed by centrifugation. Nuclei were then lysed in lysis buffer containing SDS, and sonicated for 8 cycles (30on/off) in a Dyagenode pico sonication device. Shear chromatin was cleared by incubation in dynabeads, protein concnetration measured, and at least 0.5 mg of material used for ChIP assays using the indicated antibody as described. Final ChIP'ed DNA was purified by phenol chloroform extraction followed by ethanol precipitation. ChIP-seq libraries were generated as previously described (Judd J, et al., BioRxiv 2020). Libraries were generated from ChIP'ed DNA or input as described, and subjected to quality control analyses, such as optimizing the number of PCR cycles required to amplify each set of libraries, adapter cleanup by SPRI-bead purification, quantifying the final library yield by Qubit fluorometer (Invitrogen, Q32851), and checking the size distribution of the final library by DNA ScreenTape system (Agilent Technologies, G2964AA, 5067–5584, and 5067–5603). The libraries were barcoded with indices as described using Illumina indexed barcodes and sequenced using Illumina NextSeq (2000) by 100 bp single-end sequencing.