GEO series

Early Developmental Origins of Cortical Disorders Modeled in Human Neural Stem Cells [scRNA-seq]

GSE271968 Homo sapiens (human) Single-cell RNA-seq 12 samples Submitted 2025/04/25 Platform GPL16791

At a glance

Single-cell RNA-seq · human · 12 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Samples: 12 samples: 6 conditions, mostly in duplicateGroups 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: Early developmental origins of cortical disorders modeled in human neural stem cellsNature communications · 2025

Summary (written by the submitters)

The implications of the early phases of human telencephalic development, involving neural stem cells (NSCs), in the etiology of cortical disorders remain elusive. Here, we explored the expression dynamics of cortical and neuropsychiatric disorder-associated genes in datasets generated from human NSCs across telencephalic fate transitions in vitro and in vivo.

Read the full summary ↓

We identified risk genes expressed in brain organizers and sequential gene regulatory networks across corticogenesis revealing disease-specific critical phases, when NSCs are more vulnerable to gene dysfunctions, and converging signaling across multiple diseases. Moreover, we simulated the impact of risk transcription factor (TF) depletions on different neural cell types spanning the developing human neocortex and observed a spatiotemporal-dependent effect for each perturbation. Finally, single-cell transcriptomics of newly generated autism-affected patient-derived NSCs in vitro revealed recurrent alterations of TFs orchestrating brain patterning and NSC lineage commitment. This work opens new perspectives to explore human brain dysfunctions at the early phases of development.

Published in

Early developmental origins of cortical disorders modeled in human neural stem cells

Mato-Blanco X, Kim SK, Jourdon A et al. · Nature communications 2025 · PMID 40634286 · doi:10.1038/s41467-025-61316-w

This dataset

Open GSE271968 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 GSE271968_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1134219 and SRA study SRP519218. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40634286) ↗

Study design

6 conditions, mostly in duplicate

iPSC, control, donor 1, ×2 iPSC, control, donor 2, ×2 iPSC, control, donor 3, ×2 iPSC, ASD, donor 4, ×2 iPSC, ASD, donor 5, ×2 iPSC, ASD, donor 6, ×2

Supports a between-group comparison across 12 samples.

How we read this: 6 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

GSM8389847 iPSC, control, donor 1, rep 1 iPSC, control, donor 1,
GSM8389848 iPSC, control, donor 2, rep 1 iPSC, control, donor 2,
GSM8389849 iPSC, control, donor 3, rep 1 iPSC, control, donor 3,
GSM8389850 iPSC, ASD, donor 4, rep 1 iPSC, ASD, donor 4,
GSM8389851 iPSC, ASD, donor 5, rep 1 iPSC, ASD, donor 5,
GSM8389852 iPSC, ASD, donor 6, rep 1 iPSC, ASD, donor 6,
GSM8389853 iPSC, control, donor 1, rep 2 iPSC, control, donor 1,
GSM8389854 iPSC, control, donor 2, rep 2 iPSC, control, donor 2,
GSM8389855 iPSC, control, donor 3, rep 2 iPSC, control, donor 3,
GSM8389856 iPSC, ASD, donor 4, rep 2 iPSC, ASD, donor 4,
GSM8389857 iPSC, ASD, donor 5, rep 2 iPSC, ASD, donor 5,
GSM8389858 iPSC, ASD, donor 6, rep 2 iPSC, ASD, donor 6,

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