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（CREB结合蛋白）的预处理CUT&RUN测序文件已按有效基因组大小完成标准化。对于每个文件，研究人员借助阴性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扣除该背景信号。 采用MACS2（Model-based Analysis for ChIP-Seq 2）v2.2.7.1对每个生物学重复样本进行峰调用。将所有重复样本间的共识重叠峰视为对应数据集的可重复峰。不同实验组间的重叠峰数量通过R语言中的subsetByOverlaps函数（来自GenomicRanges v1.54.1包，参考文献57）进行计算，并利用biomaRt工具为所有峰注释其最近的靶基因。采用Rsubread v.2.16.0包提取这些基因的启动子区域（转录起始位点TSS上下游1kb范围），并通过deepTools包中的multiBigwigSummary工具对CUT&RUN信号进行定量分析。