GEO series

Accelerated Reprogramming of hiPSCs into Functional Brain Endothelial Cells with Multiplexed CRISPR Activation

GSE299978 Homo sapiens (human) RNA-seq (gene expression) 11 samples Submitted 2026/04/21 Platform GPL18573

At a glance

RNA-seq (gene expression) · human · 11 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: 11 samples: 3 × iBEC,Control, vs 3 × iBEC-RA,Control, vs 2 × iBEC,TranscriptionFactor, vs 2 × iBEC,EndothelialGenes,Groups 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: Accelerated reprogramming of hiPSCs into functional brain endothelial-like cells using multiplexed CRISPR activationScientific reports · 2026

Summary (written by the submitters)

The blood-brain barrier (BBB) is comprised of brain endothelial cells, which are utilized in vitro to model the BBB under normal and disease conditions. Despite physiological shortcomings, in vitro BBB models derived from human induced pluripotent stem cells (hiPSC) are favored due to their species specificity and superior barrier qualities.

Read the full summary ↓

Here, we demonstrate the generation of hiPSCs-derived brain endothelial cells (iBEC) using transcriptional reprogramming with a multiplex CRISPR/dCas9 activation (CRISPRa) strategy that selectively activates essential BEC genes. Transcriptional reprogramming simplified the differentiation of iPSCs into mature iBECs and accelerated differentiation from 13 to only five days. Furthermore, CRISPRa reprogrammed iBECs exhibit robust barrier formation with TEER values > 230 Ω x cm2 and correspondingly low transcellular permeability values (< 0.015 x10-3 cm/min). The iBECs expressed a panel of key BBB markers (Claudin-5, ZO-1, CDH5, PECAM1, Occludin, GLUT-1) and transporters involved in receptor-mediated transcytosis (TFR1, IGF1R, TMEM30A). Importantly, the CRISPRa iBECs exhibited a robust angiogenesis phenotype that was absent in the non-engineered iPSCs. This novel CRISPRa-directed differentiation strategy not only accelerates differentiation to the BEC phenotype but also demonstrates the utility of CRISPR gene regulation in modifying the phenotype of iPSC-derived cells.

Published in

Accelerated reprogramming of hiPSCs into functional brain endothelial-like cells using multiplexed CRISPR activation

Hwang RW, Khalil Y, Baumann E et al. · Scientific reports 2026 · PMID 41957080 · doi:10.1038/s41598-026-46961-5

This dataset

Open GSE299978 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 GSE299978_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 PRJNA1277804 and SRA study SRP592571. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41957080) ↗

Study design

3 × iBEC,Control, vs 3 × iBEC-RA,Control, vs 2 × iBEC,TranscriptionFactor, vs 2 × iBEC,EndothelialGenes,

Supports a between-group comparison across 10 samples.

How we read this: 4 replicated groups read from 11 sample titles; they account for 10 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

GSM9051343 iBEC,TranscriptionFactor,Rep1 iBEC,TranscriptionFacto…
GSM9051344 iBEC,TranscriptionFactor,Rep2 iBEC,TranscriptionFacto…
GSM9051345 iBEC,EndothelialGenes,Rep1 iBEC,EndothelialGenes,
GSM9051346 iBEC,EndothelialGenes,Rep2 iBEC,EndothelialGenes,
GSM9051347 iPSC,EndothelialGenes,Rep1
GSM9520317 iBEC,Control,Rep1 iBEC,Control,
GSM9520318 iBEC,Control,Rep2 iBEC,Control,
GSM9520319 iBEC,Control,Rep3 iBEC,Control,
GSM9520320 iBEC-RA,Control,Rep1 iBEC-RA,Control,
GSM9520321 iBEC-RA,Control,Rep2 iBEC-RA,Control,
GSM9520322 iBEC-RA,Control,Rep3 iBEC-RA,Control,

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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.