RNAseq_Isl1_Knockout

RNA-seq differential expression and pathway analysis for Isl1 knockout vs wild-type mouse allantois (GEO: GSE247182).

Objective

Identify transcriptional and pathway-level effects associated with Isl1 loss using a reproducible R-based analysis workflow.

Workflow

1. QC: FastQC + MultiQC
2. Alignment: STAR (GRCm39)
3. Quantification: featureCounts / Rsubread
4. Differential expression: DESeq2
5. Annotation: biomaRt
6. Enrichment: fgsea (MSigDB Hallmark)
7. Visualization: PCA, MA, volcano, heatmaps

Repository Contents

• RNAseq_lsl1_Knockout.R — end-to-end analysis script
• QC.zip — QC reports
• Figures.zip — visual outputs
• Tables.zip — DEG/enrichment outputs
• Project report.pdf — detailed academic report

Key Findings (summary)

• Significant differential expression profile between KO and WT
• Pathway shifts including EMT/hypoxia-associated signatures
• Distinct genotype clustering on PCA

Tools

R, DESeq2, fgsea, biomaRt, ggplot2, pheatmap, EnhancedVolcano, STAR, FastQC, MultiQC

Reproducibility Notes

• Analysis logic is consolidated in a single script for traceability.
• Figures/tables are bundled for reviewer-friendly inspection.
• Intended as an educational + portfolio demonstration of RNA-seq analysis competency.