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INNATE IMMUNE TRAINING IN THE NEONATAL RESPONSE TO SEPSIS

GSE276868 Mus musculus (mouse) Single-cell RNA-seq 43 samples Submitted 2025/05/07 Platform GPL34290
At a glance

Single-cell RNA-seq · mouse · 43 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
43 samples: 8 conditions, mostly with about 4 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
Innate immune training in the neonatal response to sepsisMolecular medicine (Cambridge, Mass.) · 2025
Summary (written by the submitters)
Neonates, especially those born prematurely, are highly vulnerable to infection-induced mortality. Numerous observational and immunological studies in newborns have shown that live attenuated vaccines have beneficial, non-specific effects (NSEs) against secondary infections to unrelated pathogens. These beneficial effects have been attributed to trained immunity, and emergency granulopoiesis plays an essential role.
Read the full summary ↓
However, trained immunity has been shown to affect multiple myeloid subsets and the diversity by which trained immunity influences the host protective response is still undefined. Here we show that Bacillus-Calmette-Guérin (BCG) vaccination improves mortality to polymicrobial sepsis by simultaneously reprogramming broad aspects of myelopoiesis. Specifically, BCG results in the expansion of multiple myeloid subsets, including LSKs and GMPs, and increases CD11b+GR1+ cell number, as well as their oxidative metabolism and capacity to stimulate T-cell proliferation in response to sepsis. Single-cell RNA sequencing (scRNA-seq) of cells contained in the neonatal spleen suggests that BCG-vaccination changes the broad transcriptional landscape of multiple myeloid subsets promoting the maturation of various neutrophil and monocyte subsets and stimulating antimicrobial processes, while suppressing inflammatory pathways and myeloid-derived suppressor cell (MDSC) transcription. These findings reveal that BCG administration early after birth fundamentally reorganizes the myeloid landscape to benefit the subsequent response to polymicrobial infection.
Published in
Innate immune training in the neonatal response to sepsis
Rincon JC, Wang D, Polcz VE et al. · Molecular medicine (Cambridge, Mass.) 2025 · PMID 40307728 · doi:10.1186/s10020-025-01179-5
This dataset
Open GSE276868 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 GSE276868_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 PRJNA1159313 and SRA study SRP531900. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40307728) ↗
Study design
8 conditions, mostly with about 4 replicates each
BCG neonatal ×7 Naive neonatal ×7 BCG CS18h neonatal ×6 CS18h neonatal ×5 Naive young adult female ×4 Naive young adult male ×4 Sepsis young adult female ×4 Sepsis young adult male ×4 +2 more

Supports a between-group comparison across 41 samples.

How we read this: 8 replicated groups read from 43 sample titles; they account for 41 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

+ 3 more — browse all 43 samples with per-sample file links →

Datasets on a similar topic

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