Supplemental Material for Cole and Dennis, 2020 (post accept)

<b>Figure S</b><b>1</b><b>. Specific enrichment of MNase-seq fragments at promoters using </b><b>mTSS-Seq, related to all figures.</b>(A) Average plots of sequence-captured GM12878 MNase-seq replicates across the TSS +/- 1000bp, all fragments.(B) Histogram of fragment sizes for GM12878 heavy and light MNase digests(C) Schematic demonstrating targeted enrichment with hg19 SeqCap oligos (mTSS-seq). GM12878 Untreated data for chromosome 20 shown in the UCSC genome browser (genome.ucsc.edu), with multiple magnifications down to a single TSS, CD40, compared to a previously published nucleosome mapping data set from Gaffney et al., 2012. <b>Figure S2. Total nucleosome occupancy of replicate untreated GM12878 cells, related to all Figures.</b>Total nucleosome occupancy was determined for all human promoters centered on the TSS (+/-1kb). Rep 1 and Rep 2 untreated control samples were sorted into quartiles based on maximum signal. <b>Figure S3. Sort of nucleosome occupancy changes dependent on gene expression in GM12878 cells, related to Figure 2.</b>The log₂ratio of the total nucleosome occupancy of 20 minute HKST-treated cells/untreated control cells was sorted into quartiles based on total gene expression (GSM2344230).<b> </b><b>Figure S4. Independent sorts of MNase-sensitivity of untreated and 20 minute HKST GM12878 cells, related to Figure 2.</b>(A) The log₂ratio of light/heavy MNase digest (MNase sensitivity) was determined for all human promoters centered on the TSS (+/-1kb). The MNase sensitivity for the untreated control cells was sorted with k-means clustering (k=7) and the MNase-sensitivity data for 20 minute post-HKST treatment was sorted independently with k-means clustering (k=7). Average sensitivity profiles per cluster are shown below the heatmaps for each time point.(B) Venn diagram representing the unique and shared promoters that are present in the independent sorts of the untreated and 20 minute post-HKST samples. <b>Figure S5. Independent sorts of maximum MNase-sensitivity of untreated, 20 minute, 40 minute, and 60 minute HKST GM12878 cells, related to Figure 3.</b>The log₂ratio of light/heavy MNase digest (MNase sensitivity) was determined for all human promoters centered on the TSS (+/-1kb). The MNase sensitivity for all experimental conditions was sorted into quartiles independently based on maximum sensitivity. Average sensitivity profiles per cluster are shown below the heatmaps for each time point. <b>Table S1. Results of the gene ontology analysis and gene lists for the 20 minute post-HKST -1 sensitive nucleosome cluster, related to Figure S4.</b> <b>Table S2. Results of the gene ontology analysis and gene lists for the untreated control -1 sensitive nucleosome cluster, related to Figure S4</b>

**补充图S1 基于mTSS-Seq在启动子区域特异性富集微球菌核酸酶测序（MNase-seq）片段（与所有插图相关）**
(A) GM12878细胞MNase-seq重复样本的序列捕获平均分布图，覆盖转录起始位点（TSS）上下游1000bp区域，包含所有片段。
(B) GM12878细胞重度与轻度MNase酶切的片段长度直方图
(C) 采用hg19 SeqCap寡核苷酸探针（mTSS-seq）进行靶向富集的原理图。在UCSC基因组浏览器（genome.ucsc.edu）中展示20号染色体的GM12878未处理组数据，经多次放大至单转录起始位点CD40区域，并与Gaffney等人2012年发表的已公开核小体定位数据集进行对比。

**补充图S2 未处理GM12878细胞重复样本的总核小体占据率（与所有插图相关）**
总核小体占据率针对以转录起始位点（TSS）为中心的人类所有启动子区域（±1kb）进行计算。未处理对照组的重复样本1与重复样本2根据信号最大值分为四个分位数。

**补充图S3 GM12878细胞中依赖于基因表达的核小体占据率变化排序（与图2相关）**
以总基因表达量（GSM2344230）为依据，将20分钟HKST处理组细胞与未处理对照组细胞的总核小体占据率的log₂比值分为四个分位数。

**补充图S4 未处理与20分钟HKST处理的GM12878细胞的MNase敏感性独立排序（与图2相关）**
(A) 针对以转录起始位点（TSS）为中心的人类所有启动子区域（±1kb），计算轻度/重度MNase酶切的log₂比值（即MNase敏感性）。对未处理对照组细胞的MNase敏感性采用k-means聚类（k=7）进行排序，并对HKST处理20分钟后的样本的MNase敏感性数据采用同样的k-means聚类（k=7）进行独立排序。每个时间点的热图下方展示了每个聚类的平均敏感性分布图。
(B) 维恩图展示未处理组与HKST处理20分钟后的样本独立排序中所包含的独特与共有启动子。

**补充图S5 未处理、20分钟、40分钟与60分钟HKST处理的GM12878细胞的最大MNase敏感性独立排序（与图3相关）**
针对以转录起始位点（TSS）为中心的人类所有启动子区域（±1kb），计算轻度/重度MNase酶切的log₂比值（即MNase敏感性）。所有实验条件下的MNase敏感性均根据敏感性最大值独立分为四个分位数。每个时间点的热图下方展示了每个聚类的平均敏感性分布图。

**补充表S1 与补充图S4相关的HKST处理20分钟后-1敏感核小体聚类的基因本体（Gene Ontology）分析结果及基因列表**
**补充表S2 与补充图S4相关的未处理对照组-1敏感核小体聚类的基因本体（Gene Ontology）分析结果及基因列表**