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Thalamic NRXN1-Mediated Input to Human Cortical Progenitors Drives Excitatory Neurogenesis

GSE325956 Homo sapiens (human) Single-nucleus RNA-seq 43 samples Submitted 2026/03/25 Platform GPL34281Platform GPL24676
At a glance

Single-nucleus RNA-seq · human · 43 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). 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
43 samples: 11 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.
Summary (written by the submitters)
According to the protocortex hypothesis, extrinsic thalamic signaling is necessary for refining cortical areas and cell types, but the mechanism by which these inputs shape human cortex development remains largely unexplored. We fuse cortical and thalamic organoids to study this process. Using single-nuclei RNA-sequencing and cellular imaging, we discover that thalamic signals during a progenitor-rich critical period drive developmental gene expression changes and shift cell fate toward increased excitatory neurogenesis.
Read the full summary ↓
We find NRXN1 mediates thalamic axon contact with primate-enriched outer radial glia; genetic perturbation of NRXN1 reduces these contacts and significantly attenuates upper-layer neurogenesis. These findings underscore the influence of thalamic input on human cortical radial glia specification, and suggest a novel mechanism for thalamic regulation of human outer radial glia cell fate.
This dataset
Open GSE325956 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 GSE325956_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 PRJNA1442709 and SRA study SRP686597. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
11 conditions, mostly in duplicate
Corticocortical Assembloid, UCLA6, Week ×2 Thalamocortical Assembloid, Cortex, UCLA6, We… ×2 Thalamocortical Assembloid, Thalamus, UCLA6, … ×2 Corticocortical Assembloid, CW20107, Week ×2 Thalamocortical Assembloid, CW20107, Week ×2 Corticocortical Assembloid, CW20324, Week ×2 Thalamocortical Assembloid, CW20324, Week ×2 Corticocortical Assembloid, UCLA2, Week ×2 +24 more

Supports a case/control comparison: 6 samples read as cases, 6 as controls.

How we read this: 11 replicated groups read from 43 sample titles; they account for 22 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

+ 3 more — browse all 43 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

Share this dataset

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.