Sample deliverable — bulk RNA-seq
A differential expression analysis run end to end on public data (GEO GSE60450, mouse mammary gland). Sample groups were read from the GEO metadata rather than assumed, and the result carries its own biological check.
12samples in series
27,179genes in matrix
16,110genes tested after filtering
2,414up (padj<0.05, |LFC|>1)
2,340down
2 vs 2luminal lactating vs luminal virgin
1 · Design, taken from the source metadata
| Sample | Cell type | Physiological state |
|---|---|---|
| MCL1-DG | basal | virgin |
| MCL1-DH | basal | virgin |
| MCL1-DI | basal | pregnant |
| MCL1-DJ | basal | pregnant |
| MCL1-DK | basal | lactate |
| MCL1-DL | basal | lactate |
| MCL1-LA | luminal | virgin |
| MCL1-LB | luminal | virgin |
| MCL1-LC | luminal | pregnant |
| MCL1-LD | luminal | pregnant |
| MCL1-LE | luminal | lactate |
| MCL1-LF | luminal | lactate |
2 · Sample clustering
Before testing anything, check that samples group by biology. If replicates do not sit together, the differential expression that follows is not worth running.
3 · Differential expression (DESeq2)
| Gene | log2 fold change | adjusted p |
|---|---|---|
Gsdmc | 11.84 | 2.92e-15 |
Csn1s2b | 11.46 | 0 |
Plpp4 | 11.43 | 0.00000653 |
Glycam1 | 11.2 | 0 |
Atp2b2 | 10.68 | 3.59e-213 |
1700042G15Rik | 10.47 | 0.0000421 |
Wap | 10.41 | 0 |
Hephl1 | 10.14 | 1.23e-169 |
Fabp3 | 10.11 | 0 |
Umodl1 | 10.08 | 0.0000887 |
Gm8348 | 9.89 | 0.000127 |
Gm16440 | 9.74 | 1.71e-10 |
4 · The check that matters
A gene list is only trustworthy if it recovers something already known. Comparing lactating against virgin luminal cells should put milk-protein genes at the top — and it does: Csn1s2b, Glycam1, Lao1, Wap appear among the strongest up-regulated genes. We build a check like this into every project, and we tell you when it fails.
What a full project adds
- GO / KEGG / GSEA enrichment on the result, with the background set stated.
- Covariate handling — batch, sex, donor — in the model rather than after it.
- Results tables per contrast, and figures at submission quality.
- The script, parameters and package versions, so the analysis can be re-run.