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Erroneous efferocytosis of live neutrophils during infection prevents the resolution of inflammation [RNAseq_dual_species]

GSE264523 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2025/08/25 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 24 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
24 samples: 6 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
The trapping of live neutrophils by macrophages during infectionCell death & disease · 2025
Summary (written by the submitters)
Here, we show that neutrophils infected with the bacterial pathogenPorphyromonas gingivalis (Pg) are internalized alive by macrophages in a manner that bypasses all known efferocytic receptor-ligand interactions. Live cell uptake was mediated by the proteolysis of neutrophil granule proteins by the Pg protease RgpB. Subsequent translocation and recognition of these RgpB-generated efferocytic ligands by macrophage complement receptor 3 (CR3) receptors led to the internalization of live neutrophils by macrophages.
Read the full summary ↓
Contrary to the immunosuppression induced by apoptotic cells, efferocytosis of live neutrophils was highly inflammatory. Thus, our data show a novel immune subversion strategy employed by a bacterial pathogen that utilizes a previously unknown receptor-ligand interaction for the efferocytosis of live cells and consequently dysregulates the resolution of inflammation.
Published in
The trapping of live neutrophils by macrophages during infection
Cooper KN, Terekhova M, Potempa B et al. · Cell death & disease 2025 · PMID 40610431 · doi:10.1038/s41419-025-07808-5
This dataset
Open GSE264523 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 GSE264523_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1103070 and SRA study SRP503248. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40610431) ↗
Study design
6 conditions, mostly with about 4 replicates each
AN_24h ×4 AN_4h ×4 gLN_24h ×4 gLN_4h ×4 isoctrl ×4 PEM ×4

Supports a between-group comparison across 24 samples.

How we read this: 6 replicated groups read from 24 sample titles; they account for 24 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
Datasets on a similar topic

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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.