GEO series

Single-cell RNA-sequence of the resolution phase of lung inflammation in LPS-induced ARDS model

GSE268245 Mus musculus (mouse) Single-cell RNA-seq 2 samples Submitted 2025/04/23 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 2 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: 2 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: Emerging roles of basophils in the resolution of acute respiratory distress syndromeThe European respiratory journal · 2025

Summary (written by the submitters)

Acute respiratory distress syndrome (ARDS) is a serious lung failure with a high mortality rate and no effective pharmacological therapies. While the cellular and molecular mechanisms underlying the induction of ARDS have been extensively studied, those controlling its resolution remain poorly understood. Recent human cohort studies have implied the correlation between the severity of ARDS and the paucity of blood basophils.

Read the full summary ↓

To examine the causative relationships between basophils and the pathogenesis of ARDS, we assessed the effect of basophil depletion in an LPS-induced mouse model of ARDS and explored the possible role for basophils in the induction and resolution of ARDS by using genetically engineered mice and single-cell RNA-sequencing (scRNA-seq) analyses. Intratracheal LPS administration induced severe lung inflammation with massive neutrophil accumulation, followed by the recovery to homeostatic conditions. Basophil depletion impaired the recovery but not induction of lung inflammation, demonstrating the crucial role for basophils in the resolution phase of ARDS. scRNA-seq analysis identified that basophils accumulating in the lung were predominant sources of cytokine IL-4. Mice with basophil-specific IL-4 deficiency failed to resolve the lung inflammation. This was also the case in mice with neutrophil-specific IL-4 receptor deficiency. scRNA-seq analysis suggested that basophil-derived IL-4 acts on neutrophils to suppress their expression of anti-apoptotic genes and pro-inflammatory mediators. Thus, the present study demonstrated that basophils play a crucial role in the resolution phase of a mouse model of ARDS through the production of IL-4 which in turn acts on neutrophils to restrict lung inflammation.

Published in

Emerging roles of basophils in the resolution of acute respiratory distress syndrome

Takasawa S, Tateishi T, Sugihara J et al. · The European respiratory journal 2025 · PMID 40744690 · doi:10.1183/13993003.01150-2024

This dataset

Open GSE268245 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 GSE268245_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 PRJNA1115717 and SRA study SRP509542. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40744690) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 2 more — browse all 2 samples with per-sample file links →

Datasets on a similar topic

GSE300288 Single-cell and spatial transcriptomics analysis of tobacco-associated lung adenocarcinoma development, and in response to targeting inflammation alone or in combination with immune checkpoint blockade in precancerous phase [scRNA-seq] 31 samples shares single-cell, phase, lung
GSE264278 TIme-cource single-cell RNA-seq analysis of bleomycin and LPS-induced lung injury and fibrosis 18 samples shares single-cell, lps-induced, lung
GSE276682 Single-cell transcriptome analysis revealed cellular reprogramming following Tetramethylpyrazine treatment in LPS-induced acute lung injury 12 samples shares single-cell, lps-induced, lung
GSE277789 Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution [Smart-seq3-RNA-seq-add] 830 samples shares single-cell, resolution
GSE309471 Single-cell RNA sequencing of lung cells from bleomycin-induced and doxycycline-inducible TGF-β transgenic mouse models of pulmonary fibrosis 46 samples shares single-cell, lung
GSE276180 Single-cell temporal landscape of tumor microenvironment of lung cancer and lung metastases 37 samples shares single-cell, lung
GSE150817 Transcriptional dynamics of the murine heart during perinatal development at single-cell resolution 30 samples shares single-cell, resolution
GSE225948 Brain and blood single-cell transcriptomic analysis in acute and subacute phases after experimental stroke 29 samples shares single-cell, phase

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.