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Endothelial FOXQ1 is required for CNS angiogenesis and blood brain barrier formation

GSE332948 Mus musculus (mouse) Single-cell RNA-seq 2 samples Submitted 2026/06/01 Platform GPL28330

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)

The transcriptional mechanisms coordinating angiogenic sprouting with the acquisition of barrier properties in the developing central nervous system (CNS) remain incompletely defined. Here, we demonstrate that the forkhead box transcription factor Foxq1 is essential for CNS angiogenesis and blood-brain barrier (BBB) formation. Endothelial-specific deletion of Foxq1 in mice resulted in defective angiogenesis in the brain and retina, characterized by impaired tip cell identity, reduced vascular coverage, and diminished proliferation.

Read the full summary ↓

Moreover, mutant embryos exhibited compromised BBB integrity, evidenced by enhanced leakage of molecular tracers. Single-cell transcriptomics revealed that Foxq1 is enriched in tip cells and barrier-competent capillary populations, and its loss disrupts the transcriptional programs governing both endothelial sprouting and barrier maturation. Mechanistically, Foxq1 couples angiogenic morphogenesis with BBB acquisition by regulating tip cell-enriched transcripts such as Esm1, alongside core barrier determinants including Cdh5 and Mfsd2a.These findings establish Foxq1 as a critical transcriptional link between CNS vascular growth and functional barrier establishment, with implications for understanding neurovascular developmental disorders.

This dataset

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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 GSE332948_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 PRJNA1455264 and SRA study SRP692983. 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 →

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