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Single-cell gene expression and TCR profiling reveal age-related differences in recent thymic emigrants

GSE288766 Mus musculus (mouse) Single-cell RNA-seq 16 samples Submitted 2026/04/27 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 16 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Mus musculus (mouse)
Samples
16 samples: 4 × scRNA-seq, Neonatal CD8+ Recent Thymic Emmigrant T cells, vs 4 × scTCR-seq, Neonatal CD8+ Recent Thymic Emmigrant T cells, vs 4 × scRNA-seq, Adult CD8+ Recent Thymic Emmigrant T cells, vs 4 × scTCR-seq, Adult CD8+ Recent Thymic Emmigrant T cells,Groups 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
Single-cell gene expression and TCR profiling reveal age-related differences in recent thymic emigrantsiScience · 2026
Summary (written by the submitters)
Following thymic egress, CD8+ T cells must undergo a post-thymic maturation process to transition from a recent thymic emigrant (RTE) to a mature naïve T cell. Since neonatal animals are comprised of significantly more RTEs, there is a prevailing notion that neonatal CD8+ T cells behave differently than their adult counterparts simply because they have undergone less post-thymic maturation.
Read the full summary ↓
To test this theory, we leveraged a fate mapping mouse model and single cell sequencing to compare neonatal and adult CD8+ RTEs that have undergone that same amount of post-thymic maturation. Interestingly, we found neonatal and adult CD8+ RTEs exhibit distinct phenotypes, gene expression profiles, TCR usage and functions. These data suggest that neonatal CD8+ T cells are not simply ‘young’ adult CD8+ T cells and that age-related changes in CD8+ T cell functions in early life cannot be solely attributed to differences in the amounts of post-thymic maturation.
Published in
Single-cell gene expression and TCR profiling reveal age-related differences in recent thymic emigrants
Tabilas C, Venturi V, Kean C et al. · iScience 2026 · PMID 42023153 · doi:10.1016/j.isci.2026.115582
This dataset
Open GSE288766 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 GSE288766_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 PRJNA1219217 and SRA study SRP561582. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42023153) ↗
Study design
4 × scRNA-seq, Neonatal CD8+ Recent Thymic Emmigrant T cells, vs 4 × scTCR-seq, Neonatal CD8+ Recent Thymic Emmigrant T cells, vs 4 × scRNA-seq, Adult CD8+ Recent Thymic Emmigrant T cells, vs 4 × scTCR-seq, Adult CD8+ Recent Thymic Emmigrant T cells,

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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
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