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APOE Protects Against Severe Infection with Mycobacterium tuberculosis by Restraining Production of Neutrophil Extracellular Traps

GSE272446 Mus musculus (mouse) RNA-seq (gene expression) 41 samples Submitted 2025/06/05 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 41 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
41 samples: 14 conditions, mostly in triplicateGroups 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
APOE protects against severe infection with Mycobacterium tuberculosis by restraining production of neutrophil extracellular trapsPLoS pathogens · 2025
Summary (written by the submitters)
Mice lacking apolipoprotein E (APOE, Apoe-/- mice) are highly susceptible to infection with Mycobacterium tuberculosis (Mtb) but the underlying immune dysregulation has been unclear. We found that Mtb infected Apoe-/- mice have significantly elevated levels of neutrophils in their lungs compared to controls and demonstrated that depleting neutrophils, depleting pDCs, blocking type1 interferon signaling, and blocking LTB4 receptor signaling all improved the outcome of Mtb-infected Apoe-/- mice.
Read the full summary ↓
Neutrophils can undergo a specialized form of cell death termed NETosis in which activation of the enzyme PAD4 leads to extrusion of neutrophil extracellular traps (NETs). NETs have been associated with severe tuberculosis in other mouse models and in humans but a role of NETs in the pathology has not been directly established. We demonstrate that blocking PAD4 activation leads to a decrease in NETs in the lungs and, strikingly, completely reverses the hypersusceptiblity of Apoe-/- mice.
Published in
APOE protects against severe infection with Mycobacterium tuberculosis by restraining production of neutrophil extracellular traps
Liu D, Mai D, Jahn AN et al. · PLoS pathogens 2025 · PMID 40523023 · doi:10.1371/journal.ppat.1013267
This dataset
Open GSE272446 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 GSE272446_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 PRJNA1136892 and SRA study SRP520541. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40523023) ↗
Study design
14 conditions, mostly in triplicate
Alveolar macrophages,Apoe,Day10,bys, ×3 Alveolar macrophages,Apoe,Day10,inf, ×3 Monocyte-derived macrophages,Apoe,Day10,bys, ×3 Monocyte-derived macrophages,Apoe,Day28,bys, ×3 Monocyte-derived macrophages,Apoe,Day28,inf, ×3 Neutrophils,Apoe,Day28,bys, ×3 Neutrophils,Apoe,Day28,inf, ×3 Alveolar macrophages,C57BL/6,Day10,bys, ×3 +6 more

Supports a between-group comparison across 41 samples.

How we read this: 14 replicated groups read from 41 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

+ 1 more — browse all 41 samples with per-sample file links →

Datasets on a similar topic

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