[Data Record 4]: DHPTMs

This file contains a table for each analysis of Differential Histone Post-translational modifications. Each table contains the following information: 1) coordinates of the target regions (chromosome, start and end positions, with strand information included for analyses for marks H3K4me3, H3K9ac, H3K27me3 and H3K79me3 based on transcription start sites and gene regions, and no strand information for marks H3K4me1 and H3K27ac based on peaks) 2) baseMean - average number of reads in region across all samples 3) log2FoldChange - log2 fold change between number of reads in treatment condition and in control condition 4) lfcSE - standard error of the log2 fold change 5) stat - Wald statistic used to calculate the p-value 6) pvalue - p-value associated with a particular region 7) padj - p-value adjusted using Benjamini & Hochberg adjustment TABLE DESCRIPTION List of all differential histone post-translational modifications (DHPTMs). Each tab of this document contains different compared conditions for time point 1h, tissue CA1, and each cell type (Neu or Non) and histone mark (H3K27AC, H3K27ME3, H3K4ME1, H3K4ME3, H3K79ME3 or H3K9AC). The compared conditions concern the different sets of mouse, N-C compares naïve (N) to context only (C) mice, N-CS compares naive (N) to context shock (CS) mice, and C-CS compares context only (C) to context shock (CS) mice. The columns 'chromosome', DHPTM start', 'DHPTM end' and 'Strand' contain the position in the genome where the DHPTM was detected (mm10 assembly). Each mark is analysed for different DHPTM region set, where H3K27ac and H3K4me1 are analysed for peaks, H3K27me3 and H3K79me3 are analysed for gene bodies and H3K4me3 and H3K9ac are analysed for TSS regions [-500,+1000] bases around the TSS (peak-based tests were run as strand-independant, so for such tests column 'Strand' contains '.' for all entries). Column 'baseMean' shows the average normalised read counts in each DHPTM and column 'logFC' shows the fold change of the comparison between the conditions in log 2. Columns 'pvalue' and 'p-adjust' contain the pvalue and the adjusted p-value according to the FDR test.

本文件为每一项组蛋白差异翻译后修饰（Differential Histone Post-translational Modifications，缩写DHPTMs）分析提供对应表格。每张表格包含以下信息：1) 靶区域坐标：针对基于转录起始位点与基因区域的修饰标记（H3K4me3、H3K9ac、H3K27me3及H3K79me3），将提供染色体、起始与终止位置以及链方向信息；而针对基于峰区分析的H3K4me1与H3K27ac标记，则不提供链方向信息。2) baseMean：所有样本中该区域的标准化reads计数平均值；3) log2FoldChange：处理组与对照组的reads数之比的log2转换值；4) lfcSE：log2倍变化的标准误；5) stat：用于计算p值的Wald统计量；6) pvalue：对应特定靶区域的原始p值；7) padj：经Benjamini-Hochberg方法校正后的校正p值。

表格说明：本文件涵盖所有组蛋白差异翻译后修饰（DHPTMs）的列表。该文档的每个工作表对应一组不同的比较条件，涉及1小时时间点、CA1脑区，以及每一种细胞类型（Neu或Non神经元）与组蛋白修饰标记（H3K27AC、H3K27ME3、H3K4ME1、H3K4ME3、H3K79ME3或H3K9AC）。本次比较的小鼠分组方案如下：N-C为将天然状态（N）小鼠与仅环境暴露（C）小鼠进行对照；N-CS为将天然状态（N）小鼠与环境电击（CS）小鼠进行对照；C-CS为将仅环境暴露（C）小鼠与环境电击（CS）小鼠进行对照。
列"chromosome"（染色体）、"DHPTM start"（DHPTM起始位点）、"DHPTM end"（DHPTM终止位点）与"Strand"（链方向）记录了检测到DHPTM的基因组位置，采用mm10基因组组装版本。
针对每种组蛋白修饰标记，将按照不同的DHPTM区域集开展分析：其中H3K27ac与H3K4me1基于峰区进行分析；H3K27me3与H3K79me3基于基因体区域进行分析；H3K4me3与H3K9ac则基于转录起始位点（Transcription Start Site, TSS）周围[-500,+1000]碱基的区域进行分析。由于基于峰区的检测不考虑链方向，因此此类分析的"Strand"列所有条目均为"."。
列"baseMean"展示了每个DHPTM区域的标准化reads计数平均值；列"logFC"为两组比较的log2倍变化值。列"pvalue"与"p-adjust"分别对应原始p值与基于错误发现率（False Discovery Rate, FDR）校正后的校正p值。