Cut&RUN CBP Control Primary Mouse Hepatocytes

Pre-processed CUT&RUN files for CBP were normalized to effective genome size.For each file, background signal was calculated in heterochromatin regions using negativeATAC-seq signal mask, and subsequently removed from the overall coverage. Peak calling on each replicate was performed using MACS252 v.2.2.7.1, and theconsensus overlapping peaks between all replicates were considered as reproducible for thecorresponding dataset. Number of overlapping peaks between conditions was calculated in Rwith subsetByOverlaps (GenomicRanges v.1.54.1)57, and nearest genes were annotated topeaks using biomaRt. Promoter regions of those genes (± 1kb TSS) were extracted using the Rsubread v.2.16.0) package, and the CUT&RUN signal was quantified with multiBigwigSummary from deepTools package.针对CBP的预处理CUT&RUN文件已依据有效基因组大小完成归一化。针对每份文件，研究人员利用阴性ATAC-seq信号掩码在异染色质区域计算背景信号，并随后从总覆盖度中移除该背景信号。 针对每份生物学重复的峰识别（peak calling）采用MACS2 v.2.2.7.1（52）完成；所有生物学重复间的共识重叠峰被认定为对应数据集的可重复峰。不同实验条件间的重叠峰数量通过R语言的subsetByOverlaps函数（GenomicRanges v.1.54.1）57计算得到，并借助biomaRt工具为各峰注释邻近基因。利用Rsubread v.2.16.0软件包提取上述基因的启动子区域（±1kb 转录起始位点（Transcription Start Site, TSS）），随后通过deepTools工具包中的multiBigwigSummary函数对CUT&RUN信号进行定量分析。