GEO series

Gene expression profile at single cell level of OVA+ cells elicited by LTA1/OVA vaccine at different time points and CD4+T cells from naïve spleen as control

GSE280858 Mus musculus (mouse) Single-cell RNA-seq 10 samples Submitted 2025/02/01 Platform GPL30172

At a glance

Single-cell RNA-seq · mouse · 10 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: 10 samples: 10 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: Glycolysis maintains effector function of lung Th17 TRM cells in precision cut lung slicesiScience · 2025

Summary (written by the submitters)

Our previous work showed that vaccine elicited Klebsiella pneumoniae specific CD4+ tissue resident memory (TRM) cells in the lung provide serotype independent immunity against K. pneumoniae for up to 6 months. However, vaccine efficacy wanes in proportion to lung CD4+ TRM cell number. To study what controls TRM maintenance, apart from antigen, we developed an LTA/1Ovalbumin (OVA) model and tetramer pulldown method to enrich OVA+ lung CD4+ TRM cells over time.

Read the full summary ↓

We applied single-cell RNA-sequencing (scRNA-seq) of these cells, collected on days 30, 90 and 184 after prime immunization with OVA and our prior Th17 adjuvant, E. coli heat labile toxin A1 (LTA1). As control, we used splenic CD4+ T cells from naive mice

Published in

Glycolysis maintains effector function of lung Th17 TRM cells in precision cut lung slices

Yang H, Kumaran VR, Song K et al. · iScience 2025 · PMID 41399496 · doi:10.1016/j.isci.2025.114051

This dataset

Open GSE280858 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 GSE280858_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 PRJNA1180937 and SRA study SRP542616. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41399496) ↗

Study design

10 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 10 sample titles: 10 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

GSM8606608 day 30 OVA+ cells, replicate 1, scRNAseq [VDJ_GEX]
GSM8606609 day 30 OVA+ cells, replicate 2, scRNAseq [VDJ_GEX]
GSM8606610 day 90 OVA+ cells, replicate 1, scRNAseq [VDJ_GEX]
GSM8606611 day 90 OVA+ cells, replicate 2, scRNAseq [VDJ_GEX]
GSM8606612 day 184 OVA+ cells, replicate 1, scRNAseq [VDJ_GEX]
GSM8606613 day 184 OVA+ cells, replicate 2, scRNAseq [VDJ_GEX]
GSM8606614 Naïve spleen CD4 cells [VDJ_GEX]
GSM8606615 day 90 OVA+ cells, replicate 1, scRNAseq [VDJ_mTCR]
GSM8606616 day 90 OVA+ cells, replicate 2, scRNAseq [VDJ_mTCR]
GSM8606617 Naïve spleen CD4 cells [VDJ_mTCR]

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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.