GEO series

AT2-Derived GM-CSF Promotes CD301b⁺ cDC2 Generation and Type 2 Inflammation in the Lung

GSE295575 Mus musculus (mouse) Single-cell RNA-seq 2 samples Submitted 2025/08/04 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. 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: 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.

Summary (written by the submitters)

Pulmonary conventional dendritic cells (cDCs) are functionally and phenotypically heterogeneous antigen-presenting cells essential for orchestrating adaptive immune responses in the lung. Here, we define a critical role for granulocyte-macrophage colony-stimulating factor (GM-CSF) in generating a CD301b+ subset of terminally differentiated cDC2s.

Read the full summary ↓

GM-CSF signaling is intrinsically required for their development, independent of GM-CSF-dependent alveolar macrophages. Absence of GM-CSF results in a defect similar to that seen in CD103+XCR1+ cDC1s. Unbiased single-cell transcriptomic profiling of CD11c+ cells identified both immature and differentiated cDC populations. GM-CSF deficiency disrupted anti-apoptotic Bcl2a1 upregulation and impaired progression to the CD301b+ transcriptional state. Despite their positioning in lymphoid cell-rich adventitial cuff areas, hematopoietic GM-CSF was dispensable. Instead, genetic GM-CSF gain- and loss-of-function studies showed that alveolar epithelial type 2 cell-derived GM-CSF is required for CD301b+ cDC2 formation and pulmonary type 2 immune responses, highlighting the central role of GM-CSF signaling in shaping the pulmonary myeloid landscape.

This dataset

Open GSE295575 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 GSE295575_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 PRJNA1255205 and SRA study SRP581075. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

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

Datasets on a similar topic

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GSE261034 Single-cell transcriptomic analysis of mouse lung cDC2s at various times post allergic sensitization 6 samples shares cdc2, lung
GSE304646 Cytokine–ontogeny interaction shapes macrophage transcriptional states (combined GM-CSF– and M-CSF–derived macrophages) 47 samples shares gm-csf
GSE312134 Gene expression profiles of GM-CSF cultured bone marrow cells treated with HCQ or cGAMP. 42 samples shares gm-csf
GSE276029 Transcriptional profiling of cDC2 subsets in IFNAR∆CD11c mice treated with allergens 24 samples shares cdc2
GSE304645 Cytokine–ontogeny interaction shapes macrophage transcriptional states (GM-CSF–derived macrophages) 22 samples shares gm-csf
GSE304117 GM-CSF-derived DCs from BM and BM progenitors and Spleen(SP) in vitro 18 samples shares gm-csf

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