title: GSM8242194: BTS11_1_Input; Homo sapiens; ChIP-Seq
library_construction_protocol: Native chromatin immunoprecipitation-sequencing libraries were generated for BTS11 and CT29 cells grown in technical replicates using ULI-nChIP-seq method as previously described (Hanna et al., 2018). Briefly, cells were washed in PBS and 20,000 cells were resuspended in Nuclei isolation buffer (Sigma).  Cells were lysed in 0.1 % Triton X-100 and 0.1 % deoxycholate. Chromatin was then digested to mononucleosomal fragments by MNase enzyme (NEB) at 21 °C for 7.5 minutes. Chromatin was then split into 4 reactions, immunoprecipitated overnight at 4 °C using antibodies for H3K4me3 (Diagenode, C15410003), H3K27me3 (Diagenode, C15410195), H3K36me3 (Diagenode, C15410192) or H3K9me3 (Diagenode, C15410056), with 10% taken for input controls. Following salt washes, DNA elution and purification with SPRI beads, sequencing libraries were generated using the MicroPlex Library Preparation kit by Diagenode (C05010001), as per the manufacturer's instructions. Samples were then multiplexed and sequenced by 50 bp paired end on the Illumina NextSeq2000.  Three replicates of H3K36me3 were excluded due to poor enrichment. These data were analysed alongside published CUT&Tag, CUT&Run and ChIP-seq datasets, where available. In this study, we used H3K4me3, H3K27me3 and H3K9me3 ChIP-sequencing from naïve and primed hESCs (GSE75868) (Theunissen et al., 2016); H3K4me3, H3K27me3, and H3K9me3 CUT&RUN or CUT&TAG from hTSCs (CT27 and CT29) (GSE200763) (Frost et al., 2023); H3K4me3 and H3K36me3 CUT&RUN from hTSCs (GSE196221) (Zhou et al., 2023); H3K4me3 and H3K27me3 ChIP-sequencing from 2nd trimester cytotrophoblast (GSE127288) (Kwak et al., 2019).