Samples8
Cell lines4
Genes tested22,369
FDR < 0.054,000
Which genes change after dexamethasone treatment while controlling for cell line?
The session compared four treated and four control airway smooth muscle samples spanning four cell lines. Its design separated the treatment term from baseline differences between lines.
- Input
- 63,677 gene-level count rows
- Filter
- At least 10 total counts across samples
- Model
- DESeq2 design
~ cell + dex
- Software
- DESeq2 1.40.2 in R 4.3.0
Count filtering, normalization, modeling, and diagnostics
Inspect counts and metadataMatched treatment labels and cell-line identifiers across eight samples.
Filter low countsRetained 22,369 genes with at least 10 total counts.
Fit DESeq2Applied median-of-ratios normalization, a cell-plus-treatment design, Wald tests, and BH correction.
Audit separationUsed variance-stabilized counts for PCA and generated volcano, MA, and heatmap diagnostics.
The treatment contrast produced broad, statistically supported expression changes
4,000 significant genes
At adjusted p < 0.05, 2,193 genes increased and 1,807 decreased.
Stronger thresholds
2,901 genes passed adjusted p < 0.01 and 2,073 passed adjusted p < 0.001.
Visible separation
PC1 explained 48% and PC2 23% of variance, with treated and control samples separating in the report.
Cell line accounted for
The design included cell line directly instead of treating all samples as exchangeable replicates.
Statistical separation is not biological validation
- The dataset contains only eight samples across four cell lines, limiting precision and generalizability.
- The model controls for cell line but includes no additional covariates or interaction term.
- The report does not include pathway analysis, an accession, or an independent validation cohort.
- Differential expression is an association within this experiment; functional claims require orthogonal validation.
Confidence boundary
Strongest for the reported count-level contrast and treatment separation; lower for mechanistic or clinical interpretation.
Reproducibility artifacts recorded in the session
de_results.csvComplete DESeq2 resultsde_significant.csvFDR-significant subsetnormalized_counts.csvNormalized gene countsdeseq2_object.rdsSerialized analysis objectde_config.jsonModel configurationprovenance.jsonExecution provenanceOriginal session report8-page PDF with methods, tables, figures, and recorded runtime of 52.9 seconds.
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