GEO series

Pulmonary microvascular endothelial cells support alveolar epithelial growth via bone morphogenetic protein 6 secretion

GSE271971 Mus musculus (mouse) RNA-seq (gene expression) 72 samples Submitted 2025/02/01 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 72 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: 72 samples: 72 samples, each with a distinct title — no replicated groupsGroups 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)

Chronic obstructive pulmonary disease (COPD) is characterized by progressive airflow limitation and emphysema development, associated with enhanced tissue destruction and defective repair. Supporting cells in the alveolar niche play a crucial role in guiding the activation of alveolar epithelial progenitor cells during repair. Despite their close anatomical proximity, understanding of the supportive role of the pulmonary microvascular endothelium in adult alveolar epithelial repair remains limited.

Read the full summary ↓

We hypothesized that angiocrine factors secreted by pulmonary endothelial cells support alveolar epithelial cell growth. Here, we report that human pulmonary microvasculature endothelial cells (HPMECs) support murine and human alveolar organoid formation through paracrine signaling via the secretion of extracellular vesicles and soluble factors. Transcriptomic and proteomic analysis pinpointed HPMEC-derived bone morphogenetic protein 6 (BMP6) as a critical factor for alveolar organoid formation. BMP6 deficiency was associated with reduced Wnt signaling and augmented oxidative stress signaling in murine lung tissue. Furthermore, BMP6 promoted alveolar epithelial cell growth, whereas function-blocking antibodies targeting BMP6 inhibited the beneficial effect of endothelial cells on murine alveolar organoid formation. Taken together, our findings highlight BMP6 as a key regulator of adult epithelial repair and suggest its potential as a therapeutic target for lung repair, particularly in individuals with COPD.

This dataset

Open GSE271971 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 GSE271971_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 PRJNA1134224 and SRA study SRP519157. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

72 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 72 sample titles: 72 distinct titles with little repetition. 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

GSM8389879 105506-001-001, Lung, wild-type, Air, 4 weeks
GSM8389880 105506-001-002, Lung, wild-type, Air, 4 weeks
GSM8389881 105506-001-003, Lung, wild-type, Air, 4 weeks
GSM8389882 105506-001-004, Lung, wild-type, Air, 4 weeks
GSM8389883 105506-001-005, Lung, wild-type, Air, 4 weeks
GSM8389884 105506-001-006, Lung, wild-type, Air, 4 weeks
GSM8389885 105506-001-007, Lung, wild-type, Air, 4 weeks
GSM8389886 105506-001-008, Lung, wild-type, Air, 4 weeks
GSM8389887 105506-001-009, Lung, wild-type, CS, 4 weeks
GSM8389888 105506-001-010, Lung, wild-type, CS, 4 weeks
GSM8389889 105506-001-011, Lung, wild-type, CS, 4 weeks
GSM8389890 105506-001-012, Lung, wild-type, CS, 4 weeks
GSM8389891 105506-001-013, Lung, wild-type, CS, 4 weeks
GSM8389892 105506-001-014, Lung, wild-type, CS, 4 weeks
GSM8389893 105506-001-015, Lung, wild-type, CS, 4 weeks
GSM8389894 105506-001-016, Lung, wild-type, CS, 4 weeks
GSM8389895 105506-001-017, Lung, BMP6 KO, Air, 4 weeks
GSM8389896 105506-001-018, Lung, BMP6 KO, Air, 4 weeks
GSM8389897 105506-001-019, Lung, BMP6 KO, Air, 4 weeks
GSM8389898 105506-001-020, Lung, BMP6 KO, Air, 4 weeks
GSM8389899 105506-001-021, Lung, BMP6 KO, Air, 4 weeks
GSM8389900 105506-001-022, Lung, BMP6 KO, Air, 4 weeks
GSM8389901 105506-001-023, Lung, BMP6 KO, Air, 4 weeks
GSM8389902 105506-001-024, Lung, BMP6 KO, Air, 4 weeks
GSM8389903 105506-001-025, Lung, BMP6 KO, CS, 4 weeks
GSM8389904 105506-001-026, Lung, BMP6 KO, CS, 4 weeks
GSM8389905 105506-001-027, Lung, BMP6 KO, CS, 4 weeks
GSM8389906 105506-001-028, Lung, BMP6 KO, CS, 4 weeks
GSM8389907 105506-001-029, Lung, BMP6 KO, CS, 4 weeks
GSM8389908 105506-001-030, Lung, BMP6 KO, CS, 4 weeks
GSM8389909 105506-001-031, Lung, BMP6 KO, CS, 4 weeks
GSM8389910 105506-001-032, Lung, wild-type, Air, 24 weeks
GSM8389911 105506-001-033, Lung, wild-type, Air, 24 weeks
GSM8389912 105506-001-034, Lung, wild-type, Air, 24 weeks
GSM8389913 105506-001-035, Lung, wild-type, Air, 24 weeks
GSM8389914 105506-001-036, Lung, wild-type, Air, 24 weeks
GSM8389915 105506-001-037, Lung, wild-type, Air, 24 weeks
GSM8389916 105506-001-038, Lung, wild-type, Air, 24 weeks
GSM8389917 105506-001-039, Lung, wild-type, Air, 24 weeks
GSM8389918 105506-001-040, Lung, wild-type, Air, 24 weeks

+ 32 more — browse all 72 samples with per-sample file links →

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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.