Data and analysis code for: Hormonal gating of microglial epigenetic plasticity confers protection from trigeminal neuropathic pain

This record contains the processed data and custom analysis code accompanying the manuscript "Hormonal gating of microglial epigenetic plasticity confers protection from trigeminal neuropathic pain" (Bautista-Abad et al.). Contents data/MeDIP/ — MeDIP-seq analysis inputs and outputs: MEDIPS/edgeR exported tables (400-bp differentially methylated windows and gene-level summaries), Ensembl release 104 annotation for Rnor_6.0 (rn6), JASPAR ESR1/ESR2 position-weight matrices (MEME format) and sequence inputs for the Csf1r motif scan, and provider QC metrics. data/SWC_reconstructions/ — 1,334 Iba1+ microglial arbor reconstructions (SWC), organised by condition (Control, CCI-IoN). data/MorphOMICs/ — MorphOMICs intermediates: selected-cell manifest and Sholl table, reduced coordinates and persistence-image vectors. generated_outputs/ — retained numerical results (MeDIP and MorphOMICs). code/ — MEDIPS/edgeR MeDIP-seq pipeline, Sholl/ramification and MorphOMICs analyses, Csf1r ESR1/ESR2 PWM scan, and Imaris-to-SWC export scripts. Also mirrored at GitHub (https://github.com/alvaroni19/microglia-epigenetics-neuropathic-pain). Released under the MIT license; the dataset as a whole is under CC-BY-4.0. metadata/file_manifest_sha256.tsv — file sizes and SHA-256 checksums. Not included here: MeDIP-seq raw reads (FASTQ) and coverage tracks (WIG) are deposited in NCBI GEO (accession GSE338843). The aligned rn6 BAM files are omitted because of their size (~32 GB) and can be regenerated from the GEO FASTQ files with HISAT2 v2.1.0 (see the archive README).