Dataset of Sir proteins impede, but do not prevent, access to silent chromatin in living Saccharomyces cerevisiae

The supplementary dataset of Sir proteins impede, but do not prevent, access to silent chromatin in living Saccharomyces cerevisiae.ChIPexo_seq_GSE147927The bigwig files of the fragment occupancy of ChIP-seq analysis of GSE147927 (Badjatia et al. 2021; Rossi et al. 2021) for visualization in IGV.Published ChIP-seq data (GSE147927 were pre-processed by fastp/0.24.0, then aligned to the sacCer3 or the YHP827 genome using Bowtie2 v2.5.3 (-X 5000 --very-sensitive --no-discordant --no-mixed --no-unal). Aligned reads were filtered using SAMtools v1.21 (-f 0x2 -F 0x300 -q 1). Read occupancy was calculated using BEDTools v2.31.1. We calculated the average occupancy of nuclear chromosomes (excluding chrXII) and normalized the ChIP-exo seq data to the average occupancy (set to 1.0).MEcoGII_Footprint_GSE243114Bigwig files of nucleosome protection (0-100%) measured by M.EcoGII for wild-type nuclei from GSE243114 (Dennis et al. 2024). 0% means full nucleosome depletion in nuclei and 100% means all the sequenced genomes are protected by nucleosomes.MNase_GSE69400Bigwig files of MNase data from GSE69400 (Ocampo et al. 2016).MiscrDNA and X element data of the paper. See Misc/README.md for details.

酿酒酵母活细胞中Sir蛋白（Silent Information Regulator）阻碍但未阻断沉默染色质访问的补充数据集。
ChIPexo测序（ChIPexo-seq）数据集GSE147927：本部分包含GSE147927（Badjatia等，2021；Rossi等，2021）的ChIP-seq分析片段占有率bigwig文件，用于IGV（Integrative Genomics Viewer）可视化。已发表的GSE147927的ChIP-seq数据已通过fastp/0.24.0进行预处理，随后使用Bowtie2 v2.5.3（参数：-X 5000 --very-sensitive --no-discordant --no-mixed --no-unal）将测序reads比对至sacCer3或YHP827基因组；使用SAMtools v1.21（参数：-f 0x2 -F 0x300 -q 1）对比对后的reads进行过滤；通过BEDTools v2.31.1计算reads占有率。本研究计算了核染色体（不含chrXII）的平均占有率，并将ChIPexo-seq数据归一化至该平均占有率（设为1.0）。
MEcoGII足迹数据集GSE243114：本部分包含GSE243114（Dennis等，2024）中野生型细胞核经M.EcoGII检测得到的核小体保护率（0-100%）bigwig文件。其中0%代表细胞核内核小体完全缺失，100%代表所有测序基因组均被核小体保护。
MNase测序（Micrococcal Nuclease sequencing, MNase-seq）数据集GSE69400：本部分包含GSE69400（Ocampo等，2016）的MNase数据bigwig文件。
本数据集还包含本文的其他rDNA与X元件数据，详细信息请参见Misc/README.md文件。