[Data Record 4]: DHPTMs

<b>DESCRIPTION</b><br>This file contains a table for each analysis of Differential Histone Post-translational modifications. Each table contains the following information:<br>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)<br>2) baseMean - average number of reads in region across all samples<br>3) log2FoldChange - log2 fold change between number of reads in treatment condition and in control condition<br>4) lfcSE - standard error of the log2 fold change<br>5) stat - Wald statistic used to calculate the p-value<br>6) pvalue - p-value associated with a particular region<br>7) padj - p-value adjusted using Benjamini &amp; Hochberg adjustment<br><br><b>TABLE DESCRIPTION (ORR)</b><br>This table contains a list of all differential histone post-translational modifications (DHPTMs). Each tab 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). 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. 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.<br><br>The table contains the following columns:<br>1) 'chromosome', 'DHPTM start', 'DHPTM end' and 'Strand' contain the position in the genome where the DHPTM was detected (mm10 assembly) Peak-based tests (marks H3K27ac and H3K4me1) were run as strand-independant, so for such tests column 'Strand' contains '.' for all entries.<br>2) Column 'baseMean' shows the average normalised read counts in each DHPTM.<br>3) Column 'logFC' shows the fold change of the comparison between the conditions in log 2.<br>4) Columns 'pvalue' and 'p-adjust' contain the pvalue and the adjusted p-value according to the FDR test.<br>