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Single-Cell Multiomic Atlas of Human Cortical Development in Down Syndrome - Neural Progenitors in vitro - Treatment with Antisense Oligonucleotides for PKNOX1, BACH1 and GABPA (Bulk RNA-seq Dataset)

GSE305132 Homo sapiens (human) Single-cell RNA-seq 68 samples Submitted 2025/12/23 Platform GPL28038
At a glance

Single-cell RNA-seq · human · 68 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
68 samples: 29 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
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 GSE305132 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 GSE305132_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 PRJNA1304493 and SRA study SRP608119. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41545595) ↗
Study design
29 conditions, mostly in duplicate
iPSC-derived neural progenitors, trisomy 21, … ×4 iPSC-derived neural progenitors, trisomy 21, … ×4 iPSC-derived neural progenitors, trisomy 21, … ×3 iPSC-derived neural progenitors, trisomy 21, … ×3 iPSC-derived neural progenitors, disomic, non… ×3 iPSC-derived neural progenitors, disomic, unt… ×3 iPSC-derived neural progenitors, trisomy 21, … ×2 iPSC-derived neural progenitors, trisomy 21, … ×2 +23 more

Supports a between-group comparison across 66 samples.

How we read this: 29 replicated groups read from 68 sample titles; they account for 66 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

+ 28 more — browse all 68 samples with per-sample file links →

Datasets on a similar topic

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