CD73 KO vs WT RNA-seq Analysis with Kallisto and Sleuth

I built this project to run a reproducible RNA-seq comparison between CD73 knockout (KO) and wild-type (WT) samples using a practical Kallisto + Sleuth workflow.

Project repository: omics/Project

The work is inspired by the paper: Knock-out of CD73 delays the onset of HR-negative breast cancer by reprogramming lipid metabolism and is associated with increased tumor mutational burden.

Why this matters

CD73 has an important role in tumor biology and lipid metabolism. Reproducing this analysis in an independent pipeline helps:

• validate published findings
• identify significant transcript-level changes between KO and WT groups
• support downstream pathway and mechanism-focused analysis in cancer research

Dataset and biological context

• SRA BioProject: PRJNA933922
• Organism/reference used in pipeline: Mus musculus (GRCm39)

What this pipeline does

1. Download sequencing runs from SRA.
2. Convert and compress FASTQ files.
3. Build a Kallisto index from Ensembl cDNA reference.
4. Run kallisto quant with bootstrap estimates.
5. Run Sleuth likelihood-ratio testing (~1 vs ~condition).
6. Export significant transcripts (qval <= 0.05) and generate result plots.

Outcome

This project provides a structured and reusable transcriptomics workflow to study CD73-driven expression changes, with direct relevance to HR-negative breast cancer biology and downstream pathway interpretation.