LACA · Longevity & Aging · Aging Atlas · GSE137869 (Rat · caloric restriction)
Single-cell · Rat Aging + Caloric Restriction
GSE137869 Rat CR Aging Atlas
Multi-tissue single-cell atlas of ageing and caloric restriction in the rat
(Ma et al., Cell 2020). Young (Y) and old (O) ad-libitum animals plus old CR
animals across aorta, BAT, bone marrow, brain, kidney, liver, muscle, skin and WAT.
This page summarises the combined Rank0001 object: tissue / sex / diet labels recovered
from study barcodes, Young vs Old ageing contrast, and CR vs Old reversal.
74,060 / 74,592 / 75,403Young / Old / CR
UMAP overview
Balanced subsample across Young / Old / CR. Left→right: age–diet group · tissue · sex.
Tissue and group coverage
Nine tissues. Diet groups recovered from study barcodes: Y = young AL, O = old AL, CR = old caloric restriction. Brain and muscle empty-tissue barcodes were remapped from GEO 10x sample sheets.
| Group | Cells |
|---|
| Young | 74,060 |
| Old | 74,592 |
| CR | 75,403 |
| Sex F | 114,431 |
| Sex M | 109,624 |
| Tissue | Cells |
|---|
| WAT | 32,278 |
| BAT | 29,783 |
| Muscle | 28,883 |
| Skin | 26,817 |
| Brain | 25,947 |
| BM | 24,733 |
| Aorta | 24,168 |
| Liver | 20,051 |
| Kidney | 11,395 |
Young / Old / CR composition
Absolute cell counts by tissue and age–diet group, plus within-tissue fractions. Per-tissue LACA cards already exist for the nine QC slices (Data0557–Data0574).
| Tissue |
CR |
Old |
Young |
total |
| WAT |
9,813 |
10,079 |
12,386 |
32,278 |
| BAT |
10,273 |
12,176 |
7,334 |
29,783 |
| Muscle |
8,685 |
9,322 |
10,876 |
28,883 |
| Skin |
11,275 |
8,339 |
7,203 |
26,817 |
| Brain |
7,232 |
9,339 |
9,376 |
25,947 |
| BM |
8,285 |
8,754 |
7,694 |
24,733 |
| Aorta |
6,663 |
7,513 |
9,992 |
24,168 |
| Liver |
7,766 |
5,738 |
6,547 |
20,051 |
| Kidney |
5,411 |
3,332 |
2,652 |
11,395 |
Differential expression — Old vs Young
Wilcoxon rank-sums on a balanced ~80k-cell subsample (old AL vs young AL) after CP10K + log1p. Cross-tissue DE is exploratory — composition shifts contribute to the signal.
Up in Old (aged ↑)
| Gene | log2FC | padj |
|---|
| AABR07060872.1 |
2.25 |
0.0e+0 |
| Chi3l1 |
2.33 |
0.0e+0 |
| Slpi |
1.97 |
0.0e+0 |
| Igh-6 |
3.17 |
0.0e+0 |
| H3f3b |
0.7 |
7.8e-286 |
| Mcemp1 |
2.34 |
1.8e-277 |
| Oas1a |
2.05 |
1.1e-190 |
| Ifit3 |
2.09 |
2.2e-188 |
| AABR07065625.1 |
0.81 |
2.9e-160 |
| Tf |
0.76 |
1.7e-153 |
| Oasl |
1.63 |
4.7e-151 |
| Osm |
1.63 |
4.6e-117 |
Down in Old (aged ↓)
| Gene | log2FC | padj |
|---|
| Col3a1 |
-2.38 |
0.0e+0 |
| Col1a1 |
-2.37 |
0.0e+0 |
| Col1a2 |
-2.26 |
1.6e-220 |
| Eln |
-2.51 |
1.9e-187 |
| Fn1 |
-1.19 |
3.0e-155 |
| Hspa1a |
-0.72 |
1.0e-143 |
| Nov |
-2.23 |
3.6e-143 |
| Postn |
-1.56 |
9.2e-143 |
| Ogn |
-1.49 |
3.3e-139 |
| Acta2 |
-3.74 |
1.2e-134 |
| Mfge8 |
-0.89 |
2.9e-117 |
| Tagln |
-3.16 |
6.5e-110 |
Caloric restriction vs Old — reversal
CR vs old AL on the same subsample. Paper report: CR reverses about a quarter of ageing-regulated genes;
chronic inflammation is shared across tissues; S100A8 / Ybx1 behave as switches.
Here, 398 / 475 ageing DE genes (padj<0.05, |log2FC|>0.25) flip sign under CR
(83.8%).
Up in CR vs Old
| Gene | log2FC | padj |
|---|
| RT1-Bb |
1.77 |
7.3e-244 |
| Hspa1a |
0.92 |
1.4e-189 |
| Gpx3 |
1.03 |
4.0e-187 |
| Gsta1 |
1.04 |
1.0e-134 |
| RT1-Db1 |
0.78 |
1.2e-104 |
| C1qc |
0.56 |
1.9e-93 |
| Cd74 |
0.63 |
3.2e-92 |
| C1qb |
0.52 |
2.1e-77 |
| Cyr61 |
0.89 |
6.7e-75 |
| Dcn |
0.72 |
4.0e-63 |
Down in CR vs Old
| Gene | log2FC | padj |
|---|
| Slpi |
-1.72 |
0.0e+0 |
| Chi3l1 |
-1.47 |
3.7e-203 |
| Mcemp1 |
-1.47 |
1.5e-144 |
| Tf |
-0.7 |
5.4e-139 |
| AABR07065625.1 |
-0.71 |
1.5e-91 |
| Mmp8 |
-1.21 |
9.8e-74 |
| Hp |
-1.03 |
9.1e-73 |
| Igh-6 |
-1.04 |
5.2e-65 |
| Ifit3 |
-1.08 |
1.3e-58 |
| H3f3b |
-0.2 |
7.3e-57 |
| Gene | Age LFC (Old vs Young) | CR LFC (CR vs Old) | Age padj |
|---|
| LOC100360095 |
-24.51 |
17.02 |
8.3e-3 |
| AABR07051708.1 |
7.1 |
-3.41 |
1.3e-6 |
| Acod1 |
4.38 |
-2.24 |
5.5e-12 |
| Cnn1 |
-4.55 |
1.56 |
1.3e-62 |
| Ifit1bl |
3.45 |
-1.87 |
1.7e-85 |
| Acta2 |
-3.74 |
1.19 |
1.2e-134 |
| Mzb1 |
2.09 |
-2.05 |
1.5e-13 |
| Actg2 |
-4.43 |
0.88 |
2.0e-38 |
| Mcemp1 |
2.34 |
-1.47 |
1.8e-277 |
| Chi3l1 |
2.33 |
-1.47 |
0.0e+0 |
| Slpi |
1.97 |
-1.72 |
0.0e+0 |
| Igh-6 |
3.17 |
-1.04 |
0.0e+0 |
| Myl9 |
-3.24 |
0.95 |
4.6e-101 |
| Myh11 |
-3.45 |
0.89 |
1.0e-65 |
| AABR07034739.2 |
1.7 |
-1.65 |
4.4e-7 |
| Nov |
-2.23 |
1.17 |
3.6e-143 |
