GSE130664 Primate Ovarian Aging
Single-cell transcriptomic atlas of the ageing cynomolgus macaque ovary (Wang et al., Cell 2020).
Analysis here covers QC, clustering, UMAP, cell-type annotation and an old (OF) vs young (YF) comparison
on the GSE130664_primate_ovarian_aging_counts.h5ad matrix (4 aged + 4 young females; ovarian compartments
OCB / OCS / OM / OO).
UMAP overview
Left→right: Leiden clusters · cell type · age group · ovarian compartment (3369 cells, 14 clusters).
Cell types
Annotation by per-cluster differential markers (paper-consistent primate-ovary cell palette: Oocyte, Granulosa, Theca, Stroma, Smooth muscle, Endothelial, Macrophage, NK/T; plus an ERCC/debris LowQuality class).
| Cluster | Cell type |
|---|---|
| 0 | Stroma |
| 1 | Smooth_muscle |
| 2 | LowQuality |
| 3 | Granulosa |
| 4 | Granulosa |
| 5 | Oocyte |
| 6 | Oocyte |
| 7 | NK_T |
| 8 | Endothelial |
| 9 | Stroma |
| 10 | Theca |
| 11 | Macrophage |
| 12 | Stroma |
| 13 | Stroma |
| Cell type | Cells | Old % | Young % |
|---|---|---|---|
| Endothelial | 119 | 3.5 | 3.5 |
| Granulosa | 781 | 25 | 21 |
| LowQuality | 395 | 8.9 | 15.2 |
| Macrophage | 65 | 0.9 | 3.3 |
| NK_T | 206 | 5.7 | 6.6 |
| Oocyte | 449 | 12.8 | 13.9 |
| Smooth_muscle | 416 | 14.8 | 9.3 |
| Stroma | 867 | 28.3 | 22.5 |
| Theca | 71 | 0 | 4.7 |
Old vs Young composition
Composition shift across ovarian ageing (OF aged vs YF young). Theca and oocyte fractions fall with age; stroma, smooth muscle and granulosa differ as ovarian architecture remodels.
Differential expression — Old vs Young
Wilcoxon rank-sums (all cells); top 50 up/down by adjusted p-value. Antioxidant / stress responses and reproductive markers are key ageing signals.
Up in Old (aged ↑)
| Gene | log2FC | padj |
|---|---|---|
| ND3 | 1.55 | 4.7e-97 |
| EGFR | 1.64 | 9.4e-59 |
| TAGLN | 1.11 | 4.5e-38 |
| ENSMFAG00000035941 | 0.91 | 1.9e-36 |
| APOD | 1.02 | 8.5e-33 |
| GEM | 1.02 | 2.9e-29 |
| FOS | 1.05 | 2.0e-27 |
| EGR2 | 1.06 | 1.5e-22 |
| CLU | 0.74 | 1.9e-21 |
| MYLK | 0.74 | 8.3e-21 |
| CRYAB | 0.91 | 7.2e-19 |
| PPP1R14A | 0.9 | 1.7e-17 |
Down in Old (aged ↓)
| Gene | log2FC | padj |
|---|---|---|
| INHBB | -2.86 | 5.1e-11 |
| COL5A2 | -1.12 | 5.8e-11 |
| TCF3 | -0.69 | 2.4e-9 |
| INSL3 | -1.77 | 2.7e-8 |
| MYH9 | -0.55 | 4.1e-7 |
| FCER1G | -1.61 | 1.8e-6 |
| DNAJC3 | -0.66 | 3.0e-6 |
| DDIT4 | -0.6 | 3.8e-6 |
| ENSMFAG00000042202 | -1.3 | 5.6e-6 |
| LTBP1 | -0.69 | 6.3e-6 |
| VCAN | -1.12 | 8.9e-6 |
| EML3 | -1.28 | 2.5e-5 |
Antioxidant / stress markers (Oocyte · Granulosa · Stroma)
Consistent with the paper: antioxidant capacity declines with age — e.g. GSR (glutathione reductase) is lower in aged oocytes and stroma.
| Age | Cell type | GPX1 | GSR | SOD1 | SOD2 | CAT | GSTP1 | PRDX1 |
|---|---|---|---|---|---|---|---|---|
| Old | Granulosa | 0.263 | 0.036 | 1.09 | 0.338 | 0.141 | 1.626 | 0.751 |
| Old | Oocyte | 2.142 | 0.135 | 2.381 | 0.805 | 0.236 | 0.544 | 1.354 |
| Old | Stroma | 0.557 | 0.036 | 0.948 | 0.397 | 0.183 | 1.597 | 0.864 |
| Young | Granulosa | 0.237 | 0.056 | 0.938 | 0.347 | 0.092 | 1.705 | 0.922 |
| Young | Oocyte | 2.21 | 0.231 | 2.468 | 0.813 | 0.22 | 0.209 | 1.38 |
| Young | Stroma | 0.53 | 0.079 | 0.863 | 0.55 | 0.202 | 1.379 | 0.714 |
Cluster marker genes (top)
Wilcoxon marker genes per Leiden cluster.
| Cluster | Cell type | Top markers |
|---|---|---|
| 0 | Stroma | FOS · C7 · DCN · NUPR1 · TIMP1 · EGFR · MT2 · RPL28 · IFI27 · CCL11 |
| 1 | Smooth_muscle | ACTA2 · TAGLN · MYLK · FOS · CRYAB · RERGL · A2M · ACTG2 · PLAC9 · MGP |
| 2 | LowQuality | ERCC-00108 · ERCC-00003 · ERCC-00043 · ERCC-00060 · ERCC-00145 · ERCC-00009 · ERCC-00111 · ERCC-00022 · ERCC-00095 · ERCC-00092 |
| 3 | Granulosa | GSTA5 · IFI27 · CRHBP · ENSMFAG00000032810 · EGR2 · LDHB · NR5A2 · COL4A3 · AKAP9 · TCF3 |
| 4 | Granulosa | ERCC-00060 · ACTA2 · GSTA5 · ITLN1 · IFI27 · ENSMFAG00000042202 · ENSMFAG00000035941 · ENSMFAG00000032810 · INHBB · ERCC-00079 |
| 5 | Oocyte | ZP3 · CATSPERG · ENSMFAG00000044379 · CSF1R · CMC4 · SLCO4A1 · ATG7 · PRKAG2 · SMYD3 · POLR3C |
| 6 | Oocyte | ENSMFAG00000044379 · ZP3 · C12orf45 · PCP4 · NCOA3 · SPDL1 · ENSMFAG00000043172 · ATG7 · CCDC178 · SMYD3 |
| 7 | NK_T | GZMB · S100A4 · NKG7 · CCL5 · ANXA1 · GNLY · GZMK · ENSMFAG00000028229 · EGFR · DUSP5 |
| 8 | Endothelial | CD74 · Mafa-DRA · RNASE1 · CLU · APOD · MGP · GBP1 · LPAR6 · PLK2 · IGFBP6 |
| 9 | Stroma | DCN · PPP1R14A · TIMP1 · NUPR1 · C7 · MYLK · REN · FBXO21 · MT2 · CXCL8 |
| 10 | Theca | ENSMFAG00000044591 · ENTPD6 · PIGA · ENSMFAG00000032365 · TTC5 · DHX30 · TTR · AGPAT2 · VAV1 · GPRC5C |
| 11 | Macrophage | AIF1 · FCER1G · TYROBP · LYZ · CD74 · Mafa-DRA · LST1 · CFD · S100A4 · CTSS |
| 12 | Stroma | NPPC · GSN · DCN · TLCD1 · CCL11 · IGFBP6 · OLFML3 · CFD · PLAC9 · MGP |
| 13 | Stroma | ENSMFAG00000037443 · ENSMFAG00000021078 · ENSMFAG00000021158 · ENSMFAG00000003489 · ENSMFAG00000005927 · EFHD1 · FCGR2B · GZMB · TUBB3 · IFI44L |