GEO series

Single-cell RNA sequencing reveals how myeloid cell reprogramming by commensal Prevotella enhances defense against Streptococcus pneumoniae lung infection

GSE313404 Mus musculus (mouse) Single-cell RNA-seq 1 samples Submitted 2026/06/26 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 1 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: 1 samples
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: Myeloid cell reprogramming drives enhanced defense against Streptococcus pneumoniae lung infection following exposure to commensal PrevotellabioRxiv : the preprint server for biology · 2026

Summary (written by the submitters)

Streptococcus pneumoniae expresses a suite of virulence factors that modulate the innate immune response, delaying effective clearance. However, immune interactions with other bacteria influence this dynamic. Depletion of respiratory tract anaerobes including Prevotella is associated with increased mortality from pneumonia, an effect that can be replicated by pre-exposure to Prevotella melaninogenica in mice.

Read the full summary ↓

Here, we demonstrate using single-cell RNA sequencing that P. melaninogenica shifts myeloid cell transcriptional profiles during pneumococcal infection from interferon-dominant to pro-phagocytic, correlating with increased S. pneumoniae phagocytosis and clearance from the lung. In neutrophils, improved antibacterial defense was dependent on TNF signaling through TNFR2. Prevotella-enhanced defense also required the recruitment of monocyte-derived macrophages, with selective enrichment of a Cxcl3+ population which differed from the C1qa+ population dominant during S. pneumoniae infection in unprimed mice. This work reveals an optimized innate immune defense program which may contribute to natural infection resistance mediated by respiratory tract commensal-host interactions.

Published in

Myeloid cell reprogramming drives enhanced defense against Streptococcus pneumoniae lung infection following exposure to commensal Prevotella

Stoner SN, Larson ED, Fulte S et al. · bioRxiv : the preprint server for biology 2026 · PMID 42395429 · doi:10.64898/2026.06.25.734552

This dataset

Open GSE313404 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 GSE313404_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 PRJNA1379440 and SRA study SRP654398. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42395429) ↗

Samples in this study

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+ 1 more — browse all 1 samples with per-sample file links →

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