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Generation of hiPSC-derived brain microvascular endothelial cells using a combination of directed differentiation and transcriptional reprogramming strategies

GSE267498 Homo sapiens (human) RNA-seq (gene expression) 37 samples Submitted 2025/12/31 Platform GPL24676Platform GPL16791
At a glance

RNA-seq (gene expression) · human · 37 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
37 samples: 8 conditions, mostly with about 5 replicates eachGroups 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
Generation of hiPSC-Derived Brain Microvascular Endothelial Cells Using Directed Differentiation and Transcriptional ReprogrammingArteriosclerosis, thrombosis, and vascular biology · 2026
Summary (written by the submitters)
The blood-brain barrier (BBB), formed by specialized brain microvascular endothelial cells (BMECs), regulates brain function in health and disease. In vitro modeling of the human BBB is limited by the lack of robust protocols to generate BMECs from iPSCs. Here, we report generation of reprogrammed BMECs (rBMECs) through a combination of hiPSC differentiation into BBB-primed endothelial cells (bpECs) and subsequent reprogramming with two BBB transcription factors, FOXF2 and ZIC3.
Read the full summary ↓
rBMECs express a subset of the BBB gene repertoire including tight junctions and transporters, exhibit higher paracellular barrier properties, and have lower tracer diffusion and transcellular transport compared to primary hBMECs, and can be activated by oligomeric Ab42 . We then generated an hiPSC 3D microfluidic system that incorporates rBMECs, pericytes and astrocytes using the MIMETAS platform. This novel 3D system closely resembles the in vivo BBB at structural, functional and transcriptome levels, and can be used to study pathogenic mechanisms of neurological diseases.
Published in
Generation of hiPSC-Derived Brain Microvascular Endothelial Cells Using Directed Differentiation and Transcriptional Reprogramming
Cui A, Patel R, Bosco P et al. · Arteriosclerosis, thrombosis, and vascular biology 2026 · PMID 41287966 · doi:10.1161/ATVBAHA.125.323397
This dataset
Open GSE267498 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 GSE267498_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 PRJNA1111599 and SRA study SRP507689. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41287966) ↗
Study design
8 conditions, mostly with about 5 replicates each
rBMEC ×6 pEC ×5 HBMEC ×5 rBMEC_3D ×5 HBMEC_3D ×5 APPLondon ×5 HUVEC ×3 APPctrl ×3

Supports a between-group comparison across 37 samples.

How we read this: 8 replicated groups read from 37 sample titles; they account for 37 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
Datasets on a similar topic

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