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BMP, MEK and WNT modulation with NGN2 expression for rapid generation of hiPSC-derived neurons amenable to regional patterning [bulk RNA-seq]

GSE279590 Homo sapiens (human) RNA-seq (gene expression) 61 samples Submitted 2025/06/19 Platform GPL21697
At a glance

RNA-seq (gene expression) · human · 61 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
61 samples: 17 conditions, mostly with about 4 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
BMP, MEK, and WNT inhibition with NGN2 expression for rapid generation of hiPSC-derived neurons amenable to regional patterningStem cell reports · 2025
Summary (written by the submitters)
hiPSC are a promising tool for studying neurological diseases and developing therapies for neurodegenerative diseases. Differentiation of hiPSC into neurons can be achieved by dual SMAD inhibition (dSMADi) or induced NGN2 overexpression (“iNGN2”). Starting directly from hiPSC, iNGN2 shortens the time to a neuronal stage but leads to neurons partially resembling peripheral or posterior fates while dSMADi more faithfully recapitulates forebrain development.
Read the full summary ↓
To modify the iNGN2 paradigm, we applied an accelerated induction paradigm that is dependent on inhibition of BMP, MEK and WNT pathways (“BMWi”), to commit hiPSC into a rostral neuroectoderm fate before iNGN2. The resulting neurons showed strong expression of telencephalic and cortical markers, with decreased levels of peripheral and posterior marker genes compared to iNGN2 alone. The resulting cortical neurons are suitable for a tau aggregation assay. Furthermore, we could demonstrate that during BMWi treatment, the cells are amenable to additional regional patterning cues. This allowed the generation of neurons from different regions of the CNS and PNS, which will significantly facilitate in vitro modeling of a range of neurodevelopmental and neurodegenerative disorders.
Published in
BMP, MEK, and WNT inhibition with NGN2 expression for rapid generation of hiPSC-derived neurons amenable to regional patterning
Habich C, Kowalski A, Wachter A et al. · Stem cell reports 2025 · PMID 40541177 · doi:10.1016/j.stemcr.2025.102539
This dataset
Open GSE279590 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 GSE279590_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 PRJNA1173557 and SRA study SRP538908. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40541177) ↗
Study design
17 conditions, mostly with about 4 replicates each
hiPSC_1 cell line, BMWi protocol, 14d differe… ×4 hiPSC_1 cell line, dSMAD protocol, 14d differ… ×4 hiPSC_1 cell line, dSMAD protocol, 28d differ… ×4 hiPSC_5 cell line, BMWi protocol, 14d differe… ×4 hiPSC_5 cell line, dSMAD protocol, 14d differ… ×4 hiPSC_5 cell line, dSMAD protocol, 28d differ… ×4 hiPSC_3 cell line, dSMAD protocol, 14d differ… ×4 hiPSC_3 cell line, dSMAD protocol, 28d differ… ×4 +9 more

Supports a between-group comparison across 61 samples.

How we read this: 17 replicated groups read from 61 sample titles; they account for 61 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

+ 21 more — browse all 61 samples with per-sample file links →

Datasets on a similar topic

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