Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [Data Record 7: DMRs]

DESCRIPTION
This data record contains tables of differentially methylated regions (DMRs), where each table contains different compared conditions for each time point (1h or 4w), tissue (CA1 or ACC) and cell type (Neu or Non). Tables with the suffix "_raw" contain all DMRs for adjusted p-value threshold of 0.5, and all other tables contain annotated DMRs for adjusted p-value 0.1 in C-CS tests or for adjusted p-value 0.05 in N-C and N-CS tests. 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.

DATA REPOSITORIES
EPIGENOME BROWSER (https://memory-epigenome-browser.dzne.de/)
Contains the visualisation tracks for the DMRs (i.e. positions of DMRs) under category "DMR-DATA". Sample names include compared conditions (e.g. CxCS compares context with context-shock), time-point, tissue and cell-type separated by dashes. GFF files can also be downloaded for local visualisation.
Figshare
For the annotated DMRs, the tables contain columns "Gene name", "Gene type", "Transcript ID" and "Gene structure", corresponding to the gene name, type (protein_coding, long non-coding, miRNA etc.), ENSEMBL transcript ID and structure (intronic, downstream, etc.) for the nearest gene to each DMR. For all tables, The columns “chromosome”, “DMR start” and “DMR end” contain the position in the genome where the DMR was detected (mm10 assembly). The 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.

DATA GENERATION
The code used to identify DMRs can be found in Figshare (https://dx.doi.org/10.6084/m9.figshare.3146740).