Differential Gene Expression in Airway Smooth Muscle Cells

I've attached RNA-seq raw counts, sample metadata, and gene annotations from the public airway dataset. Install any tools you need to analyze differential gene expression. Compare dexamethasone-treated vs untreated human airway smooth muscle cells.

Produce a PCA plot showing sample clustering, a volcano plot of differentially expressed genes, and a summary report.

Date: May 18, 6:12 PM

• Set up the DE analysis environment and ran an initial DESeq2 analysis.
• Analyzed gene expression differences and produced PCA, volcano, and report files.
• Reviewed the research plan and ran the analysis notebook.
• Drafted the gene expression comparison report and delivered figures plus the results file.

Results:

• PCA of airway samples (dex vs control)
• Volcano plot: dexamethasone vs control
• Airway dex vs control: DE analysis report

The dataset contains paired control and dexamethasone-treated RNA-seq libraries from four primary human airway smooth muscle (HASM) donor lines (N61311, N05261…

Full DESeq2 results (per-gene log2FC, padj, symbol, description):

Ran PyDESeq2 on the eight samples — PCA, volcano, a written report, and the full per-gene results table are delivered. 2,728 genes hit padj < 0.05; PC2 cleanly separates treated from control across all four donors.

Visuals:

• PCA of airway samples (dex vs control)
• Volcano plot: dexamethasone vs control
• Airway dex vs control: DE analysis report

PCA Analysis:

Principal components on the top 500 variable genes (log2 normalized counts). PC1 (31% variance) separates donor cell lines; PC2 (28%) cleanly separates dexamethasone-treated from untreated samples across all four donors, indicating a reproducible drug response.