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Mammary intraepithelial lymphocytes promote lactogenesis and offspring fitness

GSE279627 Mus musculus (mouse) Single-cell RNA-seq 24 samples Submitted 2025/02/14 Platform GPL32159
At a glance

Single-cell RNA-seq · mouse · 24 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
24 samples: 8 × scRNAseq GEX 10x vs 8 × scRNAseq HTO 10x vs 8 × scRNAseq VDJ 10xGroups 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
Mammary intraepithelial lymphocytes promote lactogenesis and offspring fitnessCell · 2025
Summary (written by the submitters)
T cells accumulate in the mammary gland during pregnancy and lactation. In order to understand the diversity, transcriptional states, TCR repertoire, and function of mammary gland T cells, and how these change during pregnancy and lactation compared to homeostasis, we performed single cell RNA sequencing on mammary gland T cells in mice.
Published in
Mammary intraepithelial lymphocytes promote lactogenesis and offspring fitness
Corral D, Ansaldo E, Delaleu J et al. · Cell 2025 · PMID 39954680 · doi:10.1016/j.cell.2025.01.028
This dataset
Open GSE279627 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 GSE279627_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 PRJNA1173726 and SRA study SRP538956. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39954680) ↗
Study design
8 × scRNAseq GEX 10x vs 8 × scRNAseq HTO 10x vs 8 × scRNAseq VDJ 10x

Supports a between-group comparison across 24 samples.

How we read this: 3 replicated groups read from 24 sample titles; they account for 24 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
Datasets on a similar topic

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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.