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Single cell RNA sequencing (scRNA-seq) of embryonic zebrafish and human aortic endothelial cells following flow modulation

GSE275308 Danio rerio (zebrafish) Single-cell RNA-seq 9 samples Submitted 2026/04/20 Platform GPL20828Platform GPL18573
At a glance

Single-cell RNA-seq · zebrafish · 9 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Danio rerio (zebrafish)
Samples
9 samples: 9 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.
Paper
Flow-mediated endothelial remodeling and inflammation drive developmental vascular susceptibility in ldlr loss of functionNature communications · 2026
Summary (written by the submitters)
The earliest vascular manifestations during atherosclerosis development are incompletely understood. We utilize low density lipoprotein receptor knockout (ldlr-/-) zebrafish and human aortic endothelial cells (HAECs) to discern developmental and flow-dependent features underlying atherosclerosis. ScRNA-seq was used to analyze the transcripitional heterogeneity of endothelial cells from embryonic ldlr-/- zebrafish and HAECs following flow modulation.
Published in
Flow-mediated endothelial remodeling and inflammation drive developmental vascular susceptibility in ldlr loss of function
Kaveh A, Salazar-Martin AG, Dai W et al. · Nature communications 2026 · PMID 42168212 · doi:10.1038/s41467-026-72756-3
This dataset
Open GSE275308 in finder → Find more 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 GSE275308_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 PRJNA1150234 and SRA study SRP527611. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42168212) ↗
Study design
9 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 9 sample titles: 9 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
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Share this dataset

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