GEO series

Single-Cell Multiomic Atlas of Human Cortical Development in Down Syndrome - Fetal Cortex Bulk RNA-seq Dataset

GSE305139 Homo sapiens (human) Single-cell RNA-seq 12 samples Submitted 2025/12/23 Platform GPL30173

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: 3 × fetal brain, disomic, Library B12C vs 2 × fetal brain, trisomy 21, Library B12D vs 2 × fetal brain, trisomy 21, Library B13DGroups 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: Single-cell atlas of the developing Down syndrome brain cortexNature medicine · 2026

Summary (written by the submitters)

Down syndrome, caused by an extra copy of chromosome 21, is the most common genetic form of intellectual disability, which affects up to 1 in 700 live births. Yet, how increased dosage of the ~200 protein-coding genes on human chromosome 21 affects cortical development and function remains unclear. Here we generated a single-cell transcriptome and chromatin accessibility atlas of the human foetal cortex at mid gestation (11-20 weeks after conception), a critical period of cortical development.

Read the full summary ↓

We uncovered an early global transcriptional network disruption, subtly altering ~1000 genes involved in neural development and function primarily in excitatory neurons. These changes reflected clinical phenotypes like intellectual disability and epilepsy, were accompanied by a significant reduction in layer 4 neurons, and were driven by a network of transcription factors including chromosome 21 genes BACH1, PKNOX1, and GABPA. Finally, a xenograft model replicates key molecular features, offering an experimental platform for validating new therapeutic targets. This resource defines the gene-regulatory landscape of the developing human cortex in Down syndrome, revealing the earliest known molecular and cellular signatures of its neurological manifestations and novel candidate targets for therapeutic interventions.

Published in

Single-cell atlas of the developing Down syndrome brain cortex

Lattke M, Tan WL, Sukumaran SK et al. · Nature medicine 2026 · PMID 41545595 · doi:10.1038/s41591-026-04211-1

This dataset

Open GSE305139 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 GSE305139_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 PRJNA1304494 and SRA study SRP608243. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41545595) ↗

Study design

3 × fetal brain, disomic, Library B12C vs 2 × fetal brain, trisomy 21, Library B12D vs 2 × fetal brain, trisomy 21, Library B13D

Supports a between-group comparison across 7 samples.

How we read this: 3 replicated groups read from 12 sample titles; they account for 7 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

GSM9162694 fetal brain, disomic, Library B11C2
GSM9162695 fetal brain, trisomy 21, Library B11D2
GSM9162696 fetal brain, disomic, Library B12C1 fetal brain, disomic, L…
GSM9162697 fetal brain, disomic, Library B12C2 fetal brain, disomic, L…
GSM9162698 fetal brain, disomic, Library B12C4 fetal brain, disomic, L…
GSM9162699 fetal brain, trisomy 21, Library B12D1 fetal brain, trisomy 21…
GSM9162700 fetal brain, trisomy 21, Library B12D2, low quality/non-cortical, NOT IN FINAL ANALYSIS
GSM9162701 fetal brain, trisomy 21, Library B12D3 fetal brain, trisomy 21…
GSM9162702 fetal brain, disomic, Library B13C2
GSM9162703 fetal brain, trisomy 21, Library B13D1 fetal brain, trisomy 21…
GSM9162704 fetal brain, trisomy 21, Library B13D3 fetal brain, trisomy 21…
GSM9162705 fetal brain, disomic, Library B14C1

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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.