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.