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BMP, MEK and WNT modulation with NGN2 expression for rapid neuron differentiation from hiPSC amenable to regional patterning

GSE279593 Homo sapiens (human) RNA-seq (gene expression) 158 samples Submitted 2025/06/19 Platform GPL21697
At a glance

RNA-seq (gene expression) · human · 158 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
158 samples: 38 conditions, mostly in triplicateGroups 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
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
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 GSE279593 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 GSE279593_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 PRJNA1173548 and SRA study SRP484277. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40541177) ↗
Study design
38 conditions, mostly in triplicate
BMWi_NMMmin_final_hiPSC_3 ×5 BMWi_NMMmin_final_hiPSC_2 ×4 iNGN2_NMMmin_final_hiPSC_3 ×4 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 +62 more

Supports a between-group comparison across 126 samples.

How we read this: 38 replicated groups read from 158 sample titles; they account for 126 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

+ 118 more — browse all 158 samples with per-sample file links →

Datasets on a similar topic

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Share this dataset

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.