GEO series

scRNA-Seq of immune populations from nasal mucosa and lungs of C57BL/6 mice and BLT1 receptor deficient mice infected intranasally with MCMV K181 strain

GSE306035 Mus musculus (mouse) Single-cell RNA-seq 20 samples Submitted 2025/08/22 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 20 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: 20 samples: 20 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: Leukotriene B4 regulates T cell recognition and control of MCMV in mucosal tissuesMucosal immunology · 2025

Summary (written by the submitters)

We used a single cell sequencing approach using 10x Genomics scRNAseq to understand the transcriptional differences between immune populations from MCMV infected wildtype C57BL/6 mice and BLT1-/- mice. IFNy producing cells were similar between both experimental groups, however, BLT1-/- mice showed a reduced contribution of IFNy from CD8+T cells which was sublte in the nasal mucosa (NM) but obvious in the lungs.

Read the full summary ↓

Comparison of T cell clusters showed that WT T cells had increased gene signatures associated with proliferation, integrin signaling, cytoskeleton regulation by Rho GTPases, T cell activation, and cytokine/chemokine signaling compared to BLT1-/- T cells, with this being true in CD8 clusters in the NM and both Cd4 and CD8 in the lungs.

Published in

Leukotriene B4 regulates T cell recognition and control of MCMV in mucosal tissues

Springer LE, Rao HZ, Abinader O et al. · Mucosal immunology 2025 · PMID 40835209 · doi:10.1016/j.mucimm.2025.08.002

This dataset

Open GSE306035 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 GSE306035_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 PRJNA1308997 and SRA study SRP610629. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40835209) ↗

Study design

20 samples, each with a distinct title — no replicated groups

Supports a case/control comparison: 4 samples read as cases, 8 as controls.

How we read this: Read from 20 sample titles: 20 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

GSM9191939 Wild-type Mice (B6), infection day 0 (uninfected), nasal mucosa
GSM9191940 Wild-type Mice (B6), infection day 0 (uninfected), nasal mucosa, CITE-Seq
GSM9191941 Wild-type Mice (B6), infection day 0 (uninfected), lung
GSM9191942 Wild-type Mice (B6), infection day 0 (uninfected), lung, CITE-Seq
GSM9191943 Knockout mice (BLT) infection day 0 (uninfected), nasal mucosa
GSM9191944 Knockout mice (BLT), infection day 0 (uninfected), nasal mucosa, CITE-Seq
GSM9191945 Knockout mice (BLT) infection day 0 (uninfected), lung
GSM9191946 Knockout mice (BLT), infection day 0 (uninfected), lung, CITE-Seq
GSM9191947 Wild-type Mice (B6), infection day 3, nasal mucosa
GSM9191948 Wild-type Mice (B6), infection day 3, nasal mucosa, CITE-Seq
GSM9191949 Wild-type Mice (B6), infection day 3, lung
GSM9191950 Wild-type Mice (B6), infection day 3, lung, CITE-Seq
GSM9191951 Knockout mice (BLT) infection day 14, nasal mucosa
GSM9191952 Knockout mice (BLT), infection day 14, nasal mucosa, CITE-Seq
GSM9191953 Knockout mice (BLT) infection day 14, lung
GSM9191954 Knockout mice (BLT), infection day 14, lung, CITE-Seq
GSM9191955 Wild-type mice (B6), infection day 14, nasal mucosa
GSM9191956 Wild-type mice (B6), infection day 14, nasal mucosa, CITE-Seq
GSM9191957 Wild-type mice (B6), infection day 14, lung
GSM9191958 Wild-type mice (B6), infection day 14, lung, CITE-Seq

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