Additional file 2 of Universal NicE-seq for high-resolution accessible chromatin profiling for formaldehyde-fixed and FFPE tissues

Additional file 2: Supplementary Table 1: HCT116 UniNicE-Seq matrix for library with different amounts of enzyme. Note 25 and 50 U NicE-seq labeling reactions were incubated at 37 °C at 800 RPM. Supplementary Table 2: Quality control metrics of UniNicE-seq libraries applied to two human cell lines K562 and MCF7 in comparison to libraries made on and off beads with either with 5mdCTP or dCTP in the dNTP mix. We examined percentage of mitochondrial reads (“%mito”), number of total peaks and promoter peaks (+/- 500 bp of TSS) and enrichment of signal at TSSs (“FRiP (TSS peaks)”). Two technical replicates were conducted for each sample. All the values were calculated from a subsample of 11 million de-duplicated alignment pairs. Supplementary Table 3. Quality control metrics of UniNicE-seq libraries applied to mouse kidney tissues. 25 K fixed cells were compared with 25 K, 10 K, 1 K, 0.5 K and 0.25 K unfixed cells. Supplementary Table 4. a. Quality control metrics of UniNicE-seq libraries applied to human adult lung tissues. b. Quality control metrics of UniNicE-seq libraries applied to different human adult and fetal tissues.* *Here the replicates are merged together and downsized to 50 M aligned pairs for the downstream analysis. Supplementary Table 5. Quality control metrics of UniNicE-seq libraries applied to human FFPE liver tissue sections. Supplemental Table 6. External ChIP-seq data sets of various human and mouse tissue and cell types in this work.

附加文件2：补充表1：不同酶用量的文库所用HCT116细胞的UniNicE-Seq测序矩阵。注：25 U与50 U的NicE-seq标记反应体系于37℃、800转/分钟条件下孵育。补充表2：针对两种人类细胞系K562与MCF7构建的UniNicE-seq文库的质控指标，与在磁珠上及磁珠外使用dNTP混合液中添加5mdCTP或dCTP构建的文库进行对比。本研究分析了线粒体读段占比("%mito")、总峰数与启动子峰数(转录起始位点TSS上下游500bp区域)，以及TSS处的信号富集度("FRiP（TSS峰）")。每个样本设置两个技术重复，所有数值均来自1100万条去重比对读段对的子样本计算所得。补充表3：应用于小鼠肾脏组织的UniNicE-seq文库质控指标。将25000个固定细胞与25000、10000、1000、500及250个未固定细胞进行对比。补充表4：a. 应用于人类成人肺组织的UniNicE-seq文库质控指标；b. 应用于不同人类成人与胎儿组织的UniNicE-seq文库质控指标。*注：本部分将重复样本合并，并下采样至5000万条比对读段对用于后续分析。补充表5：应用于人类福尔马林固定石蜡包埋(FFPE)肝脏组织切片的UniNicE-seq文库质控指标。补充表6：本研究中使用的各类人类与小鼠组织及细胞系的外源ChIP-seq数据集。