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BrainSTEM: A multi-resolution fetal brain atlas to assess the fidelity of human midbrain cultures

GSE281535 Homo sapiens (human) Single-cell RNA-seq 48 samples Submitted 2025/09/25 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 48 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
48 samples: 6 conditions, mostly with about 8 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
BrainSTEM: A single-cell multiresolution fetal brain atlas reveals transcriptomic fidelity of human midbrain culturesScience advances · 2025
Summary (written by the submitters)
Midbrain dopaminergic neuron (mDA) differentiation protocols for Parkinson's disease (PD) modeling and cell replacement therapy lack comprehensive transcriptomic evaluations against in vivo references. To address this, we constructed an integrated human fetal whole brain atlas and a midbrain subatlas to use as standards of comparison.
Read the full summary ↓
From the whole brain atlas, we observed distinct brain-region-specific gene expression in most neural cell types, emphasizing the need to first evaluate protocols at the whole brain level to identify midbrain cells. These cells are then mapped to the midbrain subatlas for more refined neuronal subtype annotation. Using this biologically-driven multi-resolution mapping strategy which we termed BrainSTEM (Brain Single-cell Two tiEr Mapping), we extensively surveyed publicly available single-cell datasets of human midbrain culture models. We confirmed the presence of multiple midbrain cell types (‘on-target’), but also a substantial proportion of cells associated with non-midbrain regions (‘off-target’). This leads to an overall 'inflation' of mDA presence across all published protocols. BrainSTEM offers a systematic and unbiased framework for understanding the current state of midbrain models, providing a foundation for guiding future improvement of midbrain differentiation protocols for PD studies.
Published in
BrainSTEM: A single-cell multiresolution fetal brain atlas reveals transcriptomic fidelity of human midbrain cultures
Toh HSY, Xu L, Chen C et al. · Science advances 2025 · PMID 41171913 · doi:10.1126/sciadv.adu7944
This dataset
Open GSE281535 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 GSE281535_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 PRJNA1184341 and SRA study SRP544328. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41171913) ↗
Study design
6 conditions, mostly with about 8 replicates each
Day 20, sublibrary ×8 Day 25, sublibrary ×8 Day 30, sublibrary ×8 Day 40, sublibrary ×8 Day 50, sublibrary ×8 Day 60, sublibrary ×8

Supports a between-group comparison across 48 samples.

How we read this: 6 replicated groups read from 48 sample titles; they account for 48 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

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

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