Download Center | Longevity & Aging Cell Atlas

Gene Expression Matrices

Raw count matrices and annotated expression objects, grouped by dataset.

scRNA-seq · TSV.GZ

CancerSCEM Immune Atlas

173 per-sample raw count matrices (genes × cells, gzipped TSV), totalling 1.81 GB.

Browse and download individually below. Browse 173 matrices ↓

bulk RNA-seq · TSV.GZ

gse182409 bulk expression

Gene-level bulk expression matrix with donor scores and longevity gene table.

gene_expression_transposed.tsv.gz6.3 MB gene_index.json160.8 KB longevity_donor_score.tsv4.7 KB longevity_genes.tsv143.5 KB

bulk RNA-seq · TSV.GZ

gse221521 bulk expression

Gene-level bulk expression matrix with donor scores and longevity gene table.

gene_expression_transposed.tsv.gz15.7 MB gene_index.json686.8 KB longevity_donor_score.tsv6.3 KB longevity_genes.tsv307.7 KB

bulk RNA-seq · TSV.GZ

gse255685 bulk expression

Gene-level bulk expression matrix with donor scores and longevity gene table.

gene_expression_transposed.tsv.gz27.7 MB gene_index.json531.4 KB longevity_donor_score.tsv9 KB longevity_genes.tsv326.3 KB

h5ad · AnnData

gse107451_brain_aging

Annotated single-cell dataset (expression matrix + cell/tissue annotations), ready for scanpy / Seurat (via zellkonverter).

155.9 MB ⇩ Download .h5ad

h5ad · AnnData

gse130664_ovarian_aging

Annotated single-cell dataset (expression matrix + cell/tissue annotations), ready for scanpy / Seurat (via zellkonverter).

26.3 MB ⇩ Download .h5ad

h5ad · AnnData

gse130973_skin_aging

Annotated single-cell dataset (expression matrix + cell/tissue annotations), ready for scanpy / Seurat (via zellkonverter).

50.7 MB ⇩ Download .h5ad

h5ad · AnnData

rat_aorta_aging

Annotated single-cell dataset (expression matrix + cell/tissue annotations), ready for scanpy / Seurat (via zellkonverter).

129.7 MB ⇩ Download .h5ad

CancerSCEM count matrices (173 shown)

#	Matrix file	Size	Download
1	AM-036-01-1A.counts.matrix.tsv.gz	21.8 MB	⇩ tsv.gz
2	AM-036-02-1A.counts.matrix.tsv.gz	20.8 MB	⇩ tsv.gz
3	AM-036-03-1A.counts.matrix.tsv.gz	2.5 MB	⇩ tsv.gz
4	AM-036-04-1A.counts.matrix.tsv.gz	27.6 MB	⇩ tsv.gz
5	AM-036-05-1A.counts.matrix.tsv.gz	19.2 MB	⇩ tsv.gz
6	AM-036-06-1A.counts.matrix.tsv.gz	5.4 MB	⇩ tsv.gz
7	AM-036-07-1A.counts.matrix.tsv.gz	13.8 MB	⇩ tsv.gz
8	BRCA-071-13-1A.counts.matrix.tsv.gz	13.1 MB	⇩ tsv.gz
9	BRCA-071-14-1A.counts.matrix.tsv.gz	9.7 MB	⇩ tsv.gz
10	BRCA-071-15-1A.counts.matrix.tsv.gz	16.6 MB	⇩ tsv.gz
11	BRCA-071-16-1A.counts.matrix.tsv.gz	8.7 MB	⇩ tsv.gz
12	BRCA-071-17-1A.counts.matrix.tsv.gz	5 MB	⇩ tsv.gz
13	BRCA-128-01-1A.counts.matrix.tsv.gz	13.9 MB	⇩ tsv.gz
14	CM-036-01-1A.counts.matrix.tsv.gz	8.2 MB	⇩ tsv.gz
15	CM-036-02-1A.counts.matrix.tsv.gz	14.1 MB	⇩ tsv.gz
16	CM-036-03-1A.counts.matrix.tsv.gz	8.2 MB	⇩ tsv.gz
17	CM-036-04-1A.counts.matrix.tsv.gz	22.5 MB	⇩ tsv.gz
18	CRC-073-01-1A.counts.matrix.tsv.gz	5.2 MB	⇩ tsv.gz
19	CRC-073-02-1A.counts.matrix.tsv.gz	4.8 MB	⇩ tsv.gz
20	CRC-073-03-1A.counts.matrix.tsv.gz	5.8 MB	⇩ tsv.gz

Species Atlas Packages

One row per species. The atlas package contains the embedding, cell-type legend, tissue info and config; the cell metadata file is a cell-level table (cell_idx, x, y, cell_type) generated on demand from the embedding. File sizes are measured on disk; transfer size may differ slightly.

What is inside an atlas package?

umap.bin.gz — per-cell binary: little-endian float32 x, float32 y, uint16 cell-type index (10 bytes/cell)
celltype_legend.json — maps the type index to cell-type names, colors and counts
config.json — dataset stats (n_cells, n_celltypes, …)
tissue_info.json — tissue composition of the atlas
genes/ — one <GENE>.bin.gz per exported gene; cell order matches umap.bin.gz row order

Listing 137 public atlas datasets. The manuscript describes 134 species; this table additionally includes extended datasets curated after submission. Legacy / staging builds are excluded. Species names for 87 datasets are pending curation and shown as “pending curation”.

ID	Species	Cells	Cell types	Atlas package	Cell-level metadata
SP013	Bos taurus	1,036,604	75	⇩ tar.gz 7.8 MB	CSV cells.csv.gz
SP014	pending curation	158,163	8	⇩ tar.gz 1.2 MB	CSV cells.csv.gz
SP015	pending curation	14,805	5	⇩ tar.gz 119.6 KB	CSV cells.csv.gz
SP017	Macaca nemestrina	60,146	7	⇩ tar.gz 481.4 KB	CSV cells.csv.gz
SP020	LACA data	799,880	118	⇩ tar.gz 6 MB	CSV cells.csv.gz
SP021	pending curation	720,956	115	⇩ tar.gz 5.3 MB	CSV cells.csv.gz
SP024	Xenopus laevis	242,560	66	⇩ tar.gz 1.8 MB	CSV cells.csv.gz
SP025	Taeniopygia guttata	24,385	8	⇩ tar.gz 197.4 KB	CSV cells.csv.gz
SP026	Lonchura striata domestica	2,220	8	⇩ tar.gz 17.2 KB	CSV cells.csv.gz
SP029	Pogona vitticeps	4,037	10	⇩ tar.gz 32.3 KB	CSV cells.csv.gz
SP030	Ambystoma mexicanum	11,016	8	⇩ tar.gz 87.2 KB	CSV cells.csv.gz
SP037	pending curation	209,615	48	⇩ tar.gz 1.6 MB	CSV cells.csv.gz
SP038	pending curation	21,901	8	⇩ tar.gz 174.2 KB	CSV cells.csv.gz
SP039	Monodelphis domestica	112,800	8	⇩ tar.gz 906.9 KB	CSV cells.csv.gz
SP052	pending curation	3,141	12	⇩ tar.gz 25.9 KB	CSV cells.csv.gz
SP053	pending curation	80,000	13	⇩ tar.gz 607.9 KB	CSV cells.csv.gz
SP055	pending curation	98,241	51	⇩ tar.gz 774 KB	CSV cells.csv.gz
SP056	pending curation	557	50	⇩ tar.gz 4.6 KB	CSV cells.csv.gz
SP057	pending curation	9,632	18	⇩ tar.gz 75.4 KB	CSV cells.csv.gz
SP075	LACA data	1,144,691	131	⇩ tar.gz 8.4 MB	CSV cells.csv.gz
SP080	LACA data	151,382	328	⇩ tar.gz 1.2 MB	CSV cells.csv.gz
SP084	Danio rerio	124,914	49	⇩ tar.gz 972.4 KB	CSV cells.csv.gz
SP085	pending curation	190,817	19	⇩ tar.gz 1.5 MB	CSV cells.csv.gz
SP086	Vicugna pacos	3,216	7	⇩ tar.gz 25.8 KB	CSV cells.csv.gz
SP087	pending curation	40,531	9	⇩ tar.gz 321.5 KB	CSV cells.csv.gz
SP089	Felis catus	109,221	38	⇩ tar.gz 871.4 KB	CSV cells.csv.gz
SP090	Chinchilla lanigera	20,718	8	⇩ tar.gz 162.2 KB	CSV cells.csv.gz
SP091	pending curation	6,400	7	⇩ tar.gz 50.7 KB	CSV cells.csv.gz
SP094	Canis lupus familiaris	116,369	9	⇩ tar.gz 925.5 KB	CSV cells.csv.gz
SP095	Cavia porcellus	30,354	9	⇩ tar.gz 238.3 KB	CSV cells.csv.gz
SP098	Mesocricetus auratus	3,225	6	⇩ tar.gz 25.8 KB	CSV cells.csv.gz
SP101	pending curation	647,801	109	⇩ tar.gz 4.8 MB	CSV cells.csv.gz
SP102	pending curation	9,625	16	⇩ tar.gz 77.4 KB	CSV cells.csv.gz
SP105	Sus scrofa	300,324	57	⇩ tar.gz 2.3 MB	CSV cells.csv.gz
SP106	Columba livia	15,894	10	⇩ tar.gz 125.6 KB	CSV cells.csv.gz
SP107	Oryctolagus cuniculus	103,615	8	⇩ tar.gz 822 KB	CSV cells.csv.gz
SP111	pending curation	661,961	97	⇩ tar.gz 4.9 MB	CSV cells.csv.gz
SP113	pending curation	80,057	29	⇩ tar.gz 628.6 KB	CSV cells.csv.gz
SP115	pending curation	92,559	31	⇩ tar.gz 726.1 KB	CSV cells.csv.gz
SP116	Nannospalax galili	795	14	⇩ tar.gz 6.6 KB	CSV cells.csv.gz
SP118	Gallus gallus	25,486	7	⇩ tar.gz 194 KB	CSV cells.csv.gz
SP121	LACA data	1,245,413	108	⇩ tar.gz 9.2 MB	CSV cells.csv.gz
SP123	Callithrix jacchus	21,184	9	⇩ tar.gz 165.4 KB	CSV cells.csv.gz
SP124	LACA data	525,763	83	⇩ tar.gz 3.9 MB	CSV cells.csv.gz
SP126	Rattus norvegicus	446,858	60	⇩ tar.gz 3.4 MB	CSV cells.csv.gz
SP129	Ovis aries	16,036	6	⇩ tar.gz 129.9 KB	CSV cells.csv.gz
SP130	Trachemys scripta elegans	16,550	9	⇩ tar.gz 129.5 KB	CSV cells.csv.gz
SP1568	pending curation	80,658	34	⇩ tar.gz 624.7 KB	CSV cells.csv.gz
SP1572	pending curation	15,283	11	⇩ tar.gz 124.3 KB	CSV cells.csv.gz
SP1780	pending curation	13,431	7	⇩ tar.gz 108.4 KB	CSV cells.csv.gz
SP1784	pending curation	33,383	6	⇩ tar.gz 271 KB	CSV cells.csv.gz
SP1793	pending curation	32,921	8	⇩ tar.gz 268.2 KB	CSV cells.csv.gz
SP1796	pending curation	14,274	9	⇩ tar.gz 113.3 KB	CSV cells.csv.gz
SP1799	Saimiri sciureus	96,296	7	⇩ tar.gz 779 KB	CSV cells.csv.gz
SP1800	pending curation	25,225	10	⇩ tar.gz 204.2 KB	CSV cells.csv.gz
SP1804	pending curation	24,672	9	⇩ tar.gz 193.4 KB	CSV cells.csv.gz
SP1822	pending curation	46,874	8	⇩ tar.gz 370.2 KB	CSV cells.csv.gz
SP1823	Peromyscus polionotus	44,328	11	⇩ tar.gz 351.3 KB	CSV cells.csv.gz
SP189	Anolis carolinensis	12,366	5	⇩ tar.gz 98.4 KB	CSV cells.csv.gz
SP191	pending curation	17,500	8	⇩ tar.gz 136.6 KB	CSV cells.csv.gz
SP194	pending curation	13,533	8	⇩ tar.gz 105.5 KB	CSV cells.csv.gz
SP197	Petromyzon marinus	15,028	8	⇩ tar.gz 119.6 KB	CSV cells.csv.gz
SP200	pending curation	157,701	7	⇩ tar.gz 1.2 MB	CSV cells.csv.gz
SP201	pending curation	10,004	8	⇩ tar.gz 79.7 KB	CSV cells.csv.gz
SP202	pending curation	796,851	114	⇩ tar.gz 5.9 MB	CSV cells.csv.gz
SP2023	pending curation	27,073	100	⇩ tar.gz 214.7 KB	CSV cells.csv.gz
SP2038	pending curation	10,000	9	⇩ tar.gz 76.6 KB	CSV cells.csv.gz
SP2118	pending curation	70,057	41	⇩ tar.gz 572.2 KB	CSV cells.csv.gz
SP214	Astyanax mexicanus	241,580	10	⇩ tar.gz 1.9 MB	CSV cells.csv.gz
SP215	Oncorhynchus mykiss	16,637	10	⇩ tar.gz 130.7 KB	CSV cells.csv.gz
SP2213	pending curation	573,449	117	⇩ tar.gz 4.2 MB	CSV cells.csv.gz
SP2214	pending curation	53,351	28	⇩ tar.gz 435.6 KB	CSV cells.csv.gz
SP239	pending curation	661,961	89	⇩ tar.gz 4.9 MB	CSV cells.csv.gz
SP244	Tupaia belangeri	129,545	7	⇩ tar.gz 1 MB	CSV cells.csv.gz
SP301	Microcebus murinus	200,389	73	⇩ tar.gz 1.5 MB	CSV cells.csv.gz
SP308	Dasypus novemcinctus	117,311	7	⇩ tar.gz 928.1 KB	CSV cells.csv.gz
SP309	pending curation	81,342	5	⇩ tar.gz 649.2 KB	CSV cells.csv.gz
SP310	pending curation	117,513	6	⇩ tar.gz 935.5 KB	CSV cells.csv.gz
SP311	Aotus nancymaae	49,774	7	⇩ tar.gz 402 KB	CSV cells.csv.gz
SP317	Papio anubis	69,464	7	⇩ tar.gz 562.7 KB	CSV cells.csv.gz
SP318	pending curation	36,862	7	⇩ tar.gz 302.6 KB	CSV cells.csv.gz
SP324	pending curation	288	4	⇩ tar.gz 2.3 KB	CSV cells.csv.gz
SP327	Pleurodeles waltl	8,983	7	⇩ tar.gz 70.9 KB	CSV cells.csv.gz
SP373	pending curation	19,256	7	⇩ tar.gz 150.2 KB	CSV cells.csv.gz
SP374	pending curation	14,841	10	⇩ tar.gz 119.7 KB	CSV cells.csv.gz
SP375	pending curation	16,759	8	⇩ tar.gz 134.9 KB	CSV cells.csv.gz
SP376	Anas platyrhynchos	20,750	11	⇩ tar.gz 163.7 KB	CSV cells.csv.gz
SP389	pending curation	17,036	7	⇩ tar.gz 133 KB	CSV cells.csv.gz
SP406	Carassius auratus	39,882	7	⇩ tar.gz 307 KB	CSV cells.csv.gz
SP421	pending curation	19,691	10	⇩ tar.gz 156.8 KB	CSV cells.csv.gz
SP429	Coturnix japonica	18,920	9	⇩ tar.gz 150.2 KB	CSV cells.csv.gz
SP430	pending curation	38,961	14	⇩ tar.gz 301.8 KB	CSV cells.csv.gz
SP438	pending curation	14,447	5	⇩ tar.gz 111.7 KB	CSV cells.csv.gz
SP447	pending curation	14,568	8	⇩ tar.gz 118.4 KB	CSV cells.csv.gz
SP451	pending curation	275,033	72	⇩ tar.gz 2.1 MB	CSV cells.csv.gz
SP452	pending curation	15,426	9	⇩ tar.gz 118.8 KB	CSV cells.csv.gz
SP454	pending curation	19,619	10	⇩ tar.gz 158.2 KB	CSV cells.csv.gz
SP459	pending curation	13,685	8	⇩ tar.gz 109.2 KB	CSV cells.csv.gz
SP460	pending curation	8,891	17	⇩ tar.gz 70.3 KB	CSV cells.csv.gz
SP471	pending curation	10,000	9	⇩ tar.gz 77.2 KB	CSV cells.csv.gz
SP477	pending curation	15,667	7	⇩ tar.gz 124.4 KB	CSV cells.csv.gz
SP491	pending curation	19,097	7	⇩ tar.gz 151.7 KB	CSV cells.csv.gz
SP492	pending curation	22,975	9	⇩ tar.gz 179.8 KB	CSV cells.csv.gz
SP493	pending curation	4,256	3	⇩ tar.gz 31.2 KB	CSV cells.csv.gz
SP513	pending curation	10,109	1	⇩ tar.gz 81.4 KB	CSV cells.csv.gz
SP520	pending curation	11,891	23	⇩ tar.gz 97.1 KB	CSV cells.csv.gz
SP522	pending curation	5,894	3	⇩ tar.gz 46.9 KB	CSV cells.csv.gz
SP537	Peromyscus maniculatus	46,874	11	⇩ tar.gz 372.6 KB	CSV cells.csv.gz
SP546	Poecilia reticulata	6,325	9	⇩ tar.gz 49.2 KB	CSV cells.csv.gz
SP560	pending curation	12,530	6	⇩ tar.gz 97 KB	CSV cells.csv.gz
SP567	pending curation	24,938	9	⇩ tar.gz 197.2 KB	CSV cells.csv.gz
SP568	pending curation	26,547	10	⇩ tar.gz 211.7 KB	CSV cells.csv.gz
SP569	Serinus canaria	21,115	9	⇩ tar.gz 167.4 KB	CSV cells.csv.gz
SP583	pending curation	16,959	9	⇩ tar.gz 132.4 KB	CSV cells.csv.gz
SP587	pending curation	9,276	6	⇩ tar.gz 75.3 KB	CSV cells.csv.gz
SP598	Xiphophorus maculatus	16,104	10	⇩ tar.gz 128.7 KB	CSV cells.csv.gz
SP622	pending curation	55,698	29	⇩ tar.gz 441.8 KB	CSV cells.csv.gz
SP799	pending curation	16,266	6	⇩ tar.gz 129.7 KB	CSV cells.csv.gz
SP815	pending curation	11,835	7	⇩ tar.gz 92.2 KB	CSV cells.csv.gz
SP816	pending curation	26,005	11	⇩ tar.gz 207 KB	CSV cells.csv.gz
SP820	pending curation	20,894	6	⇩ tar.gz 163.2 KB	CSV cells.csv.gz
SP824	pending curation	16,741	6	⇩ tar.gz 133.8 KB	CSV cells.csv.gz
SP825	pending curation	13,354	7	⇩ tar.gz 107.7 KB	CSV cells.csv.gz
SP839	pending curation	20,996	7	⇩ tar.gz 165.3 KB	CSV cells.csv.gz
SP841	pending curation	11,051	6	⇩ tar.gz 88 KB	CSV cells.csv.gz
SP843	pending curation	22,284	7	⇩ tar.gz 174.5 KB	CSV cells.csv.gz
SP844	pending curation	17,836	6	⇩ tar.gz 138.9 KB	CSV cells.csv.gz
SP859	pending curation	19,144	6	⇩ tar.gz 150.9 KB	CSV cells.csv.gz
SP864	pending curation	14,497	9	⇩ tar.gz 113.9 KB	CSV cells.csv.gz
SP876	pending curation	46,361	13	⇩ tar.gz 377 KB	CSV cells.csv.gz
SP881	pending curation	20,976	9	⇩ tar.gz 170.3 KB	CSV cells.csv.gz
SP884	pending curation	14,428	6	⇩ tar.gz 111.1 KB	CSV cells.csv.gz
SP887	pending curation	31,202	9	⇩ tar.gz 254.3 KB	CSV cells.csv.gz
SP894	Xiphophorus hellerii	8,942	9	⇩ tar.gz 71.1 KB	CSV cells.csv.gz
SP913	pending curation	11,624	10	⇩ tar.gz 92.6 KB	CSV cells.csv.gz
SP914	pending curation	21,132	10	⇩ tar.gz 168.7 KB	CSV cells.csv.gz
SP920	Protopterus annectens	23,920	10	⇩ tar.gz 191.4 KB	CSV cells.csv.gz

Ortholog Mappings

Complete gene-level mapping of all species to human orthologs (OrthoFinder preferentially, supplemented by BioMart and DIAMOND reciprocal best hits). Every assignment is flagged by mapping type; for one-to-many groups the representative retained for cross-species analyses is marked in the retained_in_cross_species column.

CSV.GZ · long table

Full ortholog mapping table

One row per species gene → human ortholog assignment: species gene name/ID, human gene symbol/Ensembl ID, mapping type (one-to-one / one-to-many / many-to-one / missing), source method, source table, and retention flag.

32.8 MB · 2,717,473 assignments ⇩ ortholog_mapping_full.csv.gz

CSV · per-species summary

Per-species mapping summary

Counts and fractions of one-to-one / one-to-many / many-to-one / many-to-many / missing assignments per species, with the source table used.

⇩ ortholog_mapping_summary.csv

Donor & Dataset Metadata

Dataset manifests, donor-level clinical annotations and biomarker tables for the human immune atlas.

File	Size	Download
china_donor_manifest.tsv	5.5 MB	⇩ tsv
aging_atlas.tsv	3.3 KB	⇩ tsv
aging_biomarkers.tsv	4.3 KB	⇩ tsv
blood_omics_dataset_detail.tsv	6.5 KB	⇩ tsv
bulk_rnaseq_donor_expression_summary.tsv	198.5 KB	⇩ tsv
bulk_rnaseq_marker_expression.tsv	1.1 MB	⇩ tsv
bulk_rnaseq_top_genes.tsv	441.7 KB	⇩ tsv

Knowledge & Literature Tables

Manually verified longevity literature records and cohort evidence files backing the knowledge modules.

File	Size	Download
longevity_literature_verified.json	159.7 KB	⇩ json
gse213516_donors.json	6.7 KB	⇩ json
paper_evidence.json	19.9 KB	⇩ json

Notes on formats & provenance. Atlas packages: umap.bin.gz = per-cell float32 x, float32 y, uint16 cell-type index (10 bytes/cell); celltype_legend.json = category/cell-type names, colors and counts; config.json = dataset stats. Count matrices are gzipped TSV (genes × cells). h5ad files open with scanpy.read_h5ad. Cell-level CSV exports are generated on first request and cached; large species can take a few seconds. Site versions are archived on the Versions page. For questions or bulk requests contact the team via About. How each package was processed — ingestion track, QC, batch correction and annotation source — is documented on the Data Processing page and itemised per dataset in the Dataset Processing Table.