GEO series

Engineering perfusable vascular networks in organoids-on-chip [bulk RNA-seq]

GSE295400 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2026/04/22 Platform GPL30173

At a glance

RNA-seq (gene expression) · human · 12 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: Homo sapiens (human)
Samples: 12 samples: 3 × VNO chip static vs 3 × VNO chip LF vs 3 × VNO chip HF vs 3 × HUVECGroups 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)

Vascular networks are critical for the development and maintenance of human tissues, as they support metabolism and regulate tissue growth and function. In vitro models such as organoids and organs-on-chip often have a limited capacity to recapitulate in vivo functional vascular networks and their integration within tissues. Most existing systems fail to mimic the structural and functional complexity of native capillary beds, lack physiological flow dynamics, and do not support vascular circulation.

Read the full summary ↓

Here, we present a fully stem cell-derived microfluidic platform capable of generating perfusable vascular network organoids-on-chip with capillary-scale vessels, endothelial responses to biophysical forces, and physiologically accurate gene expression. Using this platform, we generate vascularized heart organoids-on-chip that replicate the dense capillary architecture of the heart and exhibit organ-specific vascular features and gene expression. These results establish a scalable and physiologically relevant approach for engineering and studying vascularized organoids under dynamic flow, with broad applications in developmental biology, disease modeling, and multi-organ in vitro systems.

This dataset

Open GSE295400 in finder → Find more human 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 GSE295400_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 PRJNA1254601 and SRA study SRP580737. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

3 × VNO chip static vs 3 × VNO chip LF vs 3 × VNO chip HF vs 3 × HUVEC

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM8947387 VNO chip static 1 VNO chip static
GSM8947388 VNO chip static 2 VNO chip static
GSM8947389 VNO chip static 3 VNO chip static
GSM8947390 VNO chip LF 1 VNO chip LF
GSM8947391 VNO chip LF 2 VNO chip LF
GSM8947392 VNO chip LF 3 VNO chip LF
GSM8947393 VNO chip HF 1 VNO chip HF
GSM8947394 VNO chip HF 2 VNO chip HF
GSM8947395 VNO chip HF 3 VNO chip HF
GSM8947396 HUVEC 1 HUVEC
GSM8947397 HUVEC 2 HUVEC
GSM8947398 HUVEC 3 HUVEC

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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.