GEO series

Interleukin-6 is critical in the development of gcn2-mutation associated pulmonary veno-occlusive disease in mice

GSE294702 Mus musculus (mouse) Single-cell RNA-seq 16 samples Submitted 2026/06/10 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 16 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: 16 samples: 5 × GCN2KO lung, CD45+ vs 5 × WT lung, CD45+ vs 3 × WT lung, CD45 vs 3 × GCN2KO lung, CD45Groups 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.

Summary (written by the submitters)

Biallelic mutations in eukaryotic translation initiation factor 2 α kinase 4, EIF2AK4 (which encodes general control nonderepressible 2, GCN2) underpin heritable forms of pulmonary veno-occlusive disease (PVOD), a rare and fatal form of pulmonary hypertension. The mechanisms linking these remain uncharacterised. We demonstrate for the first time that homozygous loss of gcn2 is sufficient to cause mild pulmonary hypertension in mice.

Read the full summary ↓

Single-cell transcriptomics of mouse lungs identified adventitial fibroblasts as having the greatest GCN2-dependent transcriptional differences, implicating them as key players in this model of PVOD. The most significantly upregulated pathways in gcn2-/- adventitial fibroblasts were inflammatory, and therefore we went on to demonstrate a pro-inflammatory phenotype in gcn2-/- mouse embryonic fibroblasts and gcn2-/- mice. When chronically exposed to lipopolysaccharide, the pulmonary hypertensive phenotype of gcn2-/- mice is exaggerated. Genetic ablation of interleukin-6 completely rescues both baseline and LPS-exaggerated pulmonary hypertensive phenotype. In an orthogonal murine model of pulmonary hypertension induced by exposure to mitomycin-C, deletion of interleukin-6 again rescued the pulmonary vascular phenotype. Targeting Il6-dependent pathways may be useful in treating this deadly disease.

This dataset

Open GSE294702 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 GSE294702_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 PRJNA1251345 and SRA study SRP578953. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

5 × GCN2KO lung, CD45+ vs 5 × WT lung, CD45+ vs 3 × WT lung, CD45 vs 3 × GCN2KO lung, CD45

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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

GSM8917194 G1: GCN2KO lung, CD45+ GCN2KO lung, CD45+
GSM8917195 G2: WT lung, CD45+ WT lung, CD45+
GSM8917196 G3: GCN2KO lung, CD45+ GCN2KO lung, CD45+
GSM8917197 G4: WT lung, CD45+ WT lung, CD45+
GSM8917198 G5: WT lung, CD45+ WT lung, CD45+
GSM8917199 G6: WT lung, CD45- WT lung, CD45
GSM8917200 G7: GCN2KO lung, CD45+ GCN2KO lung, CD45+
GSM8917201 G8: GCN2KO lung, CD45- GCN2KO lung, CD45
GSM8917202 G9: WT lung, CD45+ WT lung, CD45+
GSM8917203 G10: WT lung, CD45- WT lung, CD45
GSM8917204 G11: GCN2KO lung, CD45+ GCN2KO lung, CD45+
GSM8917205 G12: GCN2KO lung, CD45- GCN2KO lung, CD45
GSM8917206 G13: WT lung, CD45+ WT lung, CD45+
GSM8917207 G14: WT lung, CD45- WT lung, CD45
GSM8917208 G15: GCN2KO lung, CD45+ GCN2KO lung, CD45+
GSM8917209 G16: GCN2KO lung, CD45- GCN2KO lung, CD45

Datasets on a similar topic

GSE287501 Aging and the pathophysiology of pulmonary Mycobacterium avium complex (MAC) disease 12 samples shares pulmonary
GSE314055 FOSL2 binding to enhancer elements regulates endothelial cell state in systemic sclerosis pulmonary vascular disease 12 samples shares pulmonary
GSE316502 Transcriptomic Profiling of the Sex-linked Biological Pathways of Severe Pulmonary Arterial Hypertension associated with Endothelial Cell Caveolin-1 Depletion and Chronic Hypoxia 35 samples shares pulmonary
GSE270802 Diabetes induces exacerbated SARS-CoV-2 replication partly associated with ineffective pulmonary interferon responses, delayed cell-mediated immunity, and disruption of leptin receptor signaling 24 samples shares pulmonary
GSE272904 Emergence of inflammatory fibroblasts with aging in Hermansky-Pudlak syndrome associated pulmonary fibrosis 23 samples shares pulmonary
GSE190762 Reversibility of long-term changes to pulmonary function post early life respiratory viral infection 144 samples shares pulmonary
GSE289897 Loss of Tbx4 Affects Postnatal Lung Development and Predisposes to Pulmonary Hypertension 12 samples shares pulmonary
GSE267778 Prenatal VEGF Nano-Delivery Reverses Congenital Diaphragmatic Hernia-Associated Pulmonary Abnormalities 12 samples shares pulmonary

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.