Rat aorta ageing Ma et al. Cell 2020
Aorta / vessel slice of the first multi-tissue rat ageing atlas with caloric restriction
(Ma et al., Cell 2020; PMID 32109414, GEO GSE137869).
The parent study profiled ~210,000 cells/nuclei across 9 tissues (aorta, BAT, BM, brain, kidney, liver, muscle, skin, WAT)
and reported that CR reverses ~25% of ageing-regulated genes, with S100A8 / Ybx1 as inflammation switches.
This page analyses the Rank001 nohomo_norm object actually in hand: a log-normalised aorta slice
(Tissue = Vessel). Young / Old / CR labels are not present in this object and were not imputed.
The paper-level 9-tissue landing is Data1454 / GSE137869 Rat CR Aging. Data1455 is this Rank001 aorta slice (the file named in the deploy request). Data0557 remains the older per-tissue QC card for the same folder.
UMAP overview
Left→right: Leiden clusters · aorta cell type · n_genes. Computed on the log-normalised Rank001 object (HVG 2000, 30 PCs, Leiden 0.6). No age overlay — the labels are absent.
Cell types
Annotation by per-cluster mean expression of canonical aorta / vessel markers (endothelium Cdh5/Vwf/Cldn5, smooth muscle Acta2/Myh11/Tagln, fibroblast Col1a1/Dcn/Pdgfra, pericyte Rgs5/Pdgfrb, macrophage Cd68/Aif1/C1qa, T/NK, B, neutrophil S100a8/S100a9, mesothelium).
| Cluster | Cell type |
|---|---|
| 0 | Fibroblast |
| 1 | Fibroblast |
| 2 | Smooth_muscle |
| 3 | Macrophage |
| 4 | Endothelial |
| 5 | Smooth_muscle |
| 6 | B_cell |
| 7 | Fibroblast |
| 8 | Macrophage |
| 9 | Fibroblast |
| 10 | T_NK |
| 11 | Fibroblast |
| 12 | Fibroblast |
| 13 | Macrophage |
| 14 | Endothelial |
| 15 | Fibroblast |
| 16 | Smooth_muscle |
| 17 | Macrophage |
| 18 | B_cell |
| 19 | Macrophage |
| Cell type | Cells | % |
|---|---|---|
| Fibroblast | 11,206 | 47.1 |
| Smooth_muscle | 4,633 | 19.5 |
| Macrophage | 3,662 | 15.4 |
| Endothelial | 1,993 | 8.4 |
| B_cell | 1,589 | 6.7 |
| T_NK | 731 | 3.1 |
Composition
Aorta slice composition after QC. Counts and percentages are from the annotated Leiden map, not from imputed age groups.
Inflammation / CR-switch genes
Paper-highlighted switches and inflammatory genes (S100a8/S100a9, Ybx1, Ccl2, Il1b, Icam1/Vcam1, Cdkn1a) scored as mean log-normalised expression per annotated cell type. This is a cell-type panel, not an Old-vs-Young contrast.
| Cell type | S100a8 | S100a9 | Ybx1 | Ccl2 | Cxcl1 | Cxcl2 | Il6 | Tnf | Il1b | Nfkb1 | Cdkn2a | Cdkn1a | Icam1 | Vcam1 | Sele |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| B_cell | 0.041 | 0.042 | 0.445 | 0.757 | 0.618 | 0.108 | 0.157 | 0.006 | 0.203 | 0.039 | 0.057 | 0.174 | 0.282 | 0.069 | 0.002 |
| Endothelial | 0.028 | 0.064 | 1.728 | 0.78 | 1.25 | 0.206 | 0.476 | 0.013 | 0.109 | 0.175 | 0.004 | 0.626 | 0.864 | 0.422 | 0.264 |
| Fibroblast | 0.028 | 0.023 | 1.554 | 0.953 | 1.101 | 0.169 | 0.425 | 0.01 | 0.115 | 0.173 | 0.01 | 0.468 | 0.54 | 0.89 | 0.004 |
| Macrophage | 0.093 | 0.097 | 1.603 | 1.936 | 2.252 | 2.779 | 0.078 | 0.292 | 1.649 | 0.29 | 0.025 | 0.607 | 0.641 | 0.165 | 0.004 |
| Smooth_muscle | 0.029 | 0.015 | 1.84 | 0.246 | 0.343 | 0.07 | 0.085 | 0.003 | 0.049 | 0.16 | 0.002 | 0.508 | 0.204 | 0.61 | 0.004 |
| T_NK | 0.057 | 0.059 | 0.993 | 0.604 | 0.445 | 0.081 | 0.101 | 0.045 | 0.142 | 0.186 | 0.038 | 0.213 | 0.262 | 0.054 | 0 |
Cluster marker genes (top)
Wilcoxon marker genes per Leiden cluster on the HVG subset, displayed as gene symbols.
| Cluster | Cell type | Top markers |
|---|---|---|
| 0 | Fibroblast | C1s · Gpx3 · Igfbp6 · Pla2g2a · Cebpd · Scara5 · Gpc3 · Serpinf1 · Fmo2 · Clec3b |
| 1 | Fibroblast | Col3a1 · Col1a1 · Col1a2 · Fbn1 · AABR07068316.1 · Serpinf1 · Adamts2 · Pcolce · Cpz · Pdgfrl |
| 2 | Smooth_muscle | Col18a1 · Flna · Myl9 · Cald1 · Ppp1r14a · Tagln · Tpm1 · Myh11 · Mylk · Acta2 |
| 3 | Macrophage | Lyz2 · Ctsz · Aif1 · Fcer1g · Tyrobp · Cybb · Tmem176b · Cyba · Cd68 · Tmem176a |
| 4 | Endothelial | Fabp4 · Esam · Emcn · Cd320 · Ramp2 · Plvap · Ly6e · Anxa3 · Apoe · Lrg1 |
| 5 | Smooth_muscle | Nov · Acta2 · Tagln · Cnn1 · Tpm1 · Lmod1 · Myh11 · Ppp1r14a · Hspb1 · Myl9 |
| 6 | B_cell | Mzb1 · AABR07034739.1 · AABR07034739.2 · Sec11c · Igh-6 · AABR07065625.1 · Cd79b · Jchain · AABR07051642.1 · Sdf2l1 |
| 7 | Fibroblast | Fibin · Timp3 · Prelp · Slc29a1 · Serpinf1 · LOC108348172 · Alpl · Foxs1 · Gadd45b · Kazald1 |
| 8 | Macrophage | C1qb · C1qc · Pf4 · C1qa · Folr2 · Alox5ap · Lyve1 · Mrc1 · Ninj1 · Tf |
| 9 | Fibroblast | PCOLCE2 · Uap1 · Lrrn4cl · Clec3b · AABR07044388.2 · LOC100911932 · Nbl1 · Tnfrsf11b · Gfpt2 · Igfbp5 |
| 10 | T_NK | Rac2 · AABR07017902.1 · Laptm5 · Ptprcap · Coro1a · Cd3e · Lat · Cd3g · Limd2 · Btg1 |
| 11 | Fibroblast | Sod2 · Il6 · Mt2A · Gadd45b · Cxcl1 · Timp1 · Ccl2 · Icam1 · C1s · Igh-6 |
| 12 | Fibroblast | Tm4sf1 · Clu · Ehd4 · Icam2 · Gja5 · F11r · Sbspon · Vwf · Mmrn2 · Cavin2 |
| 13 | Macrophage | RT1-Db1 · Cd74 · RT1-Ba · RT1-Da · Napsa · Gm2a · RT1-Bb · Lsp1 · Cfp · Ifi30 |
| 14 | Endothelial | Cldn5 · Cavin2 · Mmrn1 · Ramp2 · Tgm2 · Emcn · Ecscr · F11r · Egfl7 · Lrg1 |
| 15 | Fibroblast | Stmn1 · Cdkn3 · Spc24 · Cks2 · Prc1 · Hmgb2 · LOC100359539 · Cdca3 · Cenpw · Pttg1 |
| 16 | Smooth_muscle | Mustn1 · Tinagl1 · Fabp4 · Bcam · Des · RGD1564664 · Tpm1 · Myl9 · Sncg · Rasl11a |
| 17 | Macrophage | Tyrobp · Napsa · Glipr1 · Gmfg · Lst1 · Coro1a · Lyz2 · Fcer1g · Il1b · Sod2 |
| 18 | B_cell | Rac2 · AABR07065625.1 · RT1-Ba · RT1-Da · RT1-Db1 · Cd74 · Rilpl2 · LOC100910270 · AABR07034739.1 · Limd2 |
| 19 | Macrophage | Hba-a2-1 · LOC100134871 · Hbb · Hba-a2 · LOC103694857 · Alas2 · LOC689064 · Lgals5 · Hba-a3 · Car2 |
Source and related views
The 575 MB Rank001 object stays on the compute host. Sibling per-tissue cards from the same paper remain in the rat species table (Data0557 Aorta and ranks 002–009).
Open 9-tissue Rat CR Aging analysis ↗ Open LACA data card ↗ Open existing aorta QC card (Data0557) ↗ Open rat species view ↗ GEO GSE137869 ↗ Cell paper ↗