← BioTransfer GEO Dataset Finder
GEO series

Type I IFN impedes early bacterial control in TB-resistant and -susceptible mice and activates neutrophils to restrict lung macrophage-T cell interactions [RNA-seq]

GSE298786 Mus musculus (mouse) Single-cell RNA-seq 70 samples Submitted 2025/09/12 Platform GPL34328Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 70 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
70 samples: 15 conditions, mostly with about 5 replicates eachGroups 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
Type I IFN drives neutrophil swarming, impeding lung T cell-macrophage interactions and TB controlThe Journal of experimental medicine · 2025
Summary (written by the submitters)
Only a minority of M. tuberculosis-infected individuals progress to tuberculosis, however the early immune mechanisms determining outcome are unclear. C3HeB/FeJ mice display high, partially type I IFN-dependent, tuberculosis susceptibility, compared to relatively tuberculosis-resistant C57BL/6 mice. Using bulk and scRNA-seq over the first weeks of M.
Read the full summary ↓
tuberculosis infection, we describe an unexpected, higher early pulmonary type I IFN response in C57BL/6 than C3HeB/FeJ mice, accompanying more pronounced early monocyte-derived macrophage (MDM) accumulation and lesion formation. The C57BL/6 type I IFN response plateaued with formation of extensive CD4+ T cell-MDM interactions in lesions, accompanied by high expression of T cell-attractant chemokines by MDMs. Conversely, delayed immune initiation in C3HeB/FeJ mice preceded rapid domination of lesions by inflammatory neutrophils, depletion of which enhanced CD4+ T cell-MDM interactions. Type I IFNs unexpectedly promoted early bacterial replication and limited lesion CD4+ T cell numbers in both C57BL/6 and C3HeB/FeJ mice, while pronounced later effects on inflammatory neutrophil activation were observed in C3HeB/FeJ, suggestive of context-dependent effects of type I IFNs during M. tuberculosis infection.
Published in
Type I IFN drives neutrophil swarming, impeding lung T cell-macrophage interactions and TB control
Branchett WJ, Stavropoulos E, Shields J et al. · The Journal of experimental medicine 2025 · PMID 40986319 · doi:10.1084/jem.20250466
This dataset
Open GSE298786 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 GSE298786_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 PRJNA1271108 and SRA study SRP589332. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40986319) ↗
Study design
15 conditions, mostly with about 5 replicates each
C57BL/6_uninfected_BAL ×5 C57BL/6_Mtb_HN878_d14_BAL ×5 C57BL/6_Mtb_HN878_d21_BAL ×5 C3HeB/FeJ_uninfected_BAL ×5 C3HeB/FeJ_Mtb_HN878_d14_BAL ×5 C3HeB/FeJ_Mtb_HN878_d21_BAL ×5 C57BL/6_uninfected_lung ×5 C57BL/6_Mtb_HN878_d14_lung ×5 +7 more

Supports a between-group comparison across 70 samples.

How we read this: 15 replicated groups read from 70 sample titles; they account for 70 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

+ 30 more — browse all 70 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.