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A Panoramic View of Cell Population Dynamics in Mammalian Aging

GSE247719 Mus musculus (mouse) Single-cell RNA-seq 78 samples Submitted 2024/03/05 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 78 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
78 samples: 13 conditions, mostly with about 6 replicates eachGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
A panoramic view of cell population dynamics in mammalian agingScience (New York, N.Y.) · 2025
Summary (written by the submitters)
To elucidate the aging-associated cellular population dynamics throughout the body, here we present PanSci, a single-cell transcriptome atlas profiling over 20 million cells from 623 mouse tissue samples, encompassing a range of organs across different developmental stages, genders, and genotypes. This comprehensive dataset allowed us to identify more than 3,000 unique cellular states and catalog over 200 distinct aging-associated cell populations experiencing significant depletion or expansion.
Read the full summary ↓
Our panoramic analysis uncovered four distinct, temporally structured aging-related cell population dynamic waves that are organ- and lineage-specific. Moreover, we investigated aging-associated alterations in immune cell populations, revealing both widespread shifts and organ-specific changes. We further explored the regulatory roles of the immune system on aging and pinpointed specific age-related cell population expansions that are lymphocyte-dependent. The breadth and depth of our 'cell-omics' methodology not only enhance our comprehension of cellular aging but also lay the groundwork for exploring the complex regulatory networks among varied cell types in the context of aging and aging-associated diseases.
Published in
A panoramic view of cell population dynamics in mammalian aging
Zhang Z, Schaefer C, Jiang W et al. · Science (New York, N.Y.) 2025 · PMID 39607904 · doi:10.1126/science.adn3949
This dataset
Open GSE247719 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE247719_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1036289 and SRA study SRP470408. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39607904) ↗
Study design
13 conditions, mostly with about 6 replicates each
PanSci, mouse kidney, part ×9 PanSci, mouse lung, part ×9 PanSci, mouse jejunum, part ×9 PanSci, mouse liver, part ×8 PanSci, mouse colon, part ×8 PanSci, mouse heart, part ×6 PanSci, mouse perigonadal adipose tissue, part ×6 PanSci, mouse ileum, part ×6 +5 more

Supports a between-group comparison across 78 samples.

How we read this: 13 replicated groups read from 78 sample titles; they account for 78 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

+ 38 more — browse all 78 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.