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An in vivo and in vitro spatiotemporal atlas of human fetal midbrain development

GSE277032 Homo sapiens (human) Single-cell RNA-seq 29 samples Submitted 2025/11/11 Platform GPL20301Platform GPL24676
At a glance

Single-cell RNA-seq · human · 29 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
29 samples: 6 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
An in vivo and in vitro spatiotemporal profile of human midbrain developmentNature communications · 2026
Summary (written by the submitters)
The dopaminergic system has key roles in human physiology and is implicated in a broad range of neurological and neuropsychiatric conditions that are increasingly investigated using induced pluripotent stem cell-derived midbrain models. To determine the similarity of such models to human systems, we undertook single cell and spatial profiling of first and second trimester fetal midbrain and compared it to in vitro midbrain models.
Read the full summary ↓
Our initial histological analysis of second trimester fetal midbrain revealed structural complexity already similar to that of adult tissue, although this similarity did not fully extend to transcriptional activity. Moreover, we show that in vitro models recapitulate the transcriptional activity of late first trimester fetal midbrain, while 3D models replicate the spatial organization and cellular microenvironments of first and second trimester fetal midbrain. Understanding the extent of human tissue recapitulation in midbrain laboratory models is essential to justify their use as biological proxies.
Published in
An in vivo and in vitro spatiotemporal profile of human midbrain development
Budinger D, Puigdevall P, Hall GT et al. · Nature communications 2026 · PMID 41633979 · doi:10.1038/s41467-025-67779-1
This dataset
Open GSE277032 in finder → Find more human 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 GSE277032_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 PRJNA1160261 and SRA study SRP532348. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41633979) ↗
Study design
6 conditions, mostly in triplicate
mid_organoids ×9 OCT_BLOCK ×4 PC_AGE_1 ×3 PC_AGE_2 ×3 PC_AGE_3 ×3 PC_AGE_4 ×3 F10121620_A ×1 F10121620_B ×1 +2 more

Supports a between-group comparison across 25 samples.

How we read this: 6 replicated groups read from 29 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
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