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Temporal single-cell profiling of distinct mesenchymal, epithelial, endothelial, and immune cell lineages in the lung after injury

GSE249931 Mus musculus (mouse) Single-cell RNA-seq 17 samples Submitted 2024/12/16 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 17 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
17 samples: 6 conditions, mostly in duplicateGroups 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
An injury-induced mesenchymal-epithelial cell niche coordinates regenerative responses in the lungScience (New York, N.Y.) · 2024
Summary (written by the submitters)
Upon severe injury to the lungs, a poorly understood multistep process results in either euplastic regeneration or dysplastic repair which leads to a loss of functional gas-exchanging alveolar tissue. We show that the dysplastic repair process consists of an injury-induced tissue niche (iTCH) containing Keratin 5+ epithelial cells and Pdgfra-derived Pdgfrb+ mesenchymal cells, which proliferate and transit across multiple cells states before localizing to dysplastic regions.
Read the full summary ↓
Temporal and spatial single cell analysis reveals that Pdgfra-derived Pdgfrb+ cells communicate via Notch signaling to dysplastic keratinized epithelium. Inactivation of proliferation and Notch signaling in these Pdgfra+ progenitor mesenchymal cells prevents the establishment of iTCHs. Mesenchymal Notch signaling in iTCHs suppresses Wnt and Fgf signaling, whereas loss of Notch rewires alveolar signaling patterns to promote euplastic regeneration and restore functional gas exchange in the lung. iTCH presence and signaling patterns can be used to differentially phenotype fibrotic from degenerative chronic lung disease, with associated apposing flows of FGF and WNT signaling discriminating these disease states. These data reveal the emergence of an injury and disease associated niche in the lung, its regulation by mesenchymal Notch signaling, and the impact these cellular decisions have on discriminating the choice between dysplastic repair or euplastic regeneration.
Published in
An injury-induced mesenchymal-epithelial cell niche coordinates regenerative responses in the lung
Jones DL, Morley MP, Li X et al. · Science (New York, N.Y.) 2024 · PMID 39666855 · doi:10.1126/science.ado5561
This dataset
Open GSE249931 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 GSE249931_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 PRJNA1051143 and SRA study SRP477413. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39666855) ↗
Study design
6 conditions, mostly in duplicate
Pdgfra-lineage - bleomycin day ×2 Epithelial, endothelial, and immune cells - b… ×2 Pdgfra-lineage - H1N1 influenza day ×2 Epithelial, endothelial, and immune cells - H… ×2 Pdgfrb-lineage - H1N1 influenza day ×2 Pdgfrb-lineage - bleomycin day ×2 Epithelial, endothelial, and immune cells - h… ×1 Pdgfrb-lineage - homeostasis ×1 +3 more

Supports a between-group comparison across 12 samples.

How we read this: 6 replicated groups read from 17 sample titles; they account for 12 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
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