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Developmental features and unique characteristics of peptide-specific PLZF+ innate-like T cells

GSE279513 Mus musculus (mouse) Single-cell RNA-seq 18 samples Submitted 2025/05/14 Platform GPL21626Platform GPL24247Platform GPL34328
At a glance

Single-cell RNA-seq · mouse · 18 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
18 samples: 18 samples, each with a distinct title — no replicated groupsGroups 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
Developmental features and unique characteristics of peptide-specific PLZF(+) innate-like T cells in miceNature communications · 2025
Summary (written by the submitters)
Innate-like T cells are considered a family of T lymphocytes capable of mounting quick responses, yet restricted to conserved antigens of non-peptide nature. Here, we performed single-cell transcriptomic analyses of peptide-specific PLZF+ innate-like T (PILT) cells and compared them to other members of the innate-like T cell family. Our data revealed that PILT cells share similar transcriptional profiles and overlapping developmental trajectories with invariant Natural Killer T (iNKT) cells as well as mucosal-associated invariant T (MAIT) cells.
Read the full summary ↓
Yet, in contrast to iNKT and MAIT cells, PILT cells displayed a polyclonal T cell receptor (TCR) repertoire closely resembling the one of conventional CD8 T cells, inferring MHC I restriction and a broader range of antigen specificity. We further show that artificial thymic organoid cultures (ATOC) support selection and development of PILT cells in vitro exhibiting similar transcriptional profiles to their counterparts maturing in the thymus. Lastly, using an “on-time” T-cell receptor retrogenic ATOC system, we demonstrate that PILT1 derived TCR clonotypes favour acquisition of PILT1 innate-like phenotype during T cell development in vitro suggesting an instructive role of TCR specificity in PILT cell lineage commitment and functional differentiation.
Published in
Developmental features and unique characteristics of peptide-specific PLZF(+) innate-like T cells in mice
Hassan A, Heise N, Schimrock A et al. · Nature communications 2025 · PMID 40480992 · doi:10.1038/s41467-025-60617-4
This dataset
Open GSE279513 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 GSE279513_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 PRJNA1173222 and SRA study SRP538744. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40480992) ↗
Study design
18 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 18 sample titles: 18 distinct titles with little repetition. 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
Datasets on a similar topic

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