RNA-seq analysis of CX3CR1 microglia under high-fat diet (HFD) and chow conditions (SRP530013)

This repository contains processed data, analysis scripts, and computational environment information for RNA-seq analysis of CX3CR1-positive microglia isolated from male mice under chow and high-fat diet (HFD) conditions (SRA project: SRP530013). The workflow includes gene-level quantification, differential expression analysis (DESeq2), principal component analysis (PCA), and gene set enrichment analysis (GSEA) using Hallmark and Reactome pathways. Raw sequencing data were processed in a Linux (WSL Ubuntu) environment using SRA Toolkit, FastQC, MultiQC, Cutadapt, and Salmon. Downstream analyses were performed in R using tximport, DESeq2, and fgsea. The repository includes: curated metadata and sample annotations reproducible R scripts for analysis heatmap-ready expression matrices complete computational environment information The sample SRR30509639 was excluded from part of the analysis due to outlier behavior.This analysis is associated with a manuscript currently under submission.