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Single-cell RNA sequencing of human forebrain organoids from typical and autism subjects

GSE197887 Homo sapiens (human) Single-cell RNA-seq 25 samples Submitted 2026/03/30 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 25 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
25 samples: 13 × 8-week forebrain organoid XHI vs 12 × 8-week forebrain organoid, XHIGroups 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
Spatial architecture of autism pathogenesis reveals mosaic structural disarray during early developmentNature communications · 2026
Summary (written by the submitters)
The goal of this experiment is to define cellular phenotypes in human brain organoid models of autism.
Published in
Spatial architecture of autism pathogenesis reveals mosaic structural disarray during early development
Lin L, Saw TY, Chou N et al. · Nature communications 2026 · PMID 42288509 · doi:10.1038/s41467-026-74320-5
This dataset
Open GSE197887 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 GSE197887_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 PRJNA812590 and SRA study SRP362358. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42288509) ↗
Study design
13 × 8-week forebrain organoid XHI vs 12 × 8-week forebrain organoid, XHI

Supports a between-group comparison across 25 samples.

How we read this: 2 replicated groups read from 25 sample titles; they account for 25 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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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.