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in vivo human embryonic spinal cord atlas validates stem cell-derived human dorsal interneurons and reveals ASD spinal signatures [day43NMP_scRNAseq]

GSE326655 Homo sapiens (human) Single-cell RNA-seq 12 samples Submitted 2026/04/01 Platform GPL34284

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: 10 distinct titles, 2 of them repeatedGroups 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: In vivo human embryonic spinal cord atlas validates stem cell-derived human dorsal interneurons and reveals ASD spinal signaturesbioRxiv : the preprint server for biology · 2025

Summary (written by the submitters)

Spinal cord injuries (SCI) result in the loss of motor and sensory function. We are working towards restoring sensation by developing directed differentiation protocols to generate dorsal spinal interneurons (dIs; dI1-dI6) from human embryonic stem cells (hESCs). Here, we present an improved method that produces human dIs via a neuromesodermal progenitor state, the physiological intermediate for spinal cord development.

Read the full summary ↓

We show that retinoic acid (RA), bone morphogenetic protein 4 (BMP4) and growth differentiation factor (GDF) 11 direct dI identity, while GDF11 and extended time in culture promotes posterior spinal identities. Together, these protocols generate the full complement of dorsal subtypes along the entire anterior-posterior axis of the spinal cord. To benchmark in vitro-derived dIs, we constructed a single-cell RNA-Seq atlas of the human embryonic spinal cord and used it to show that hESC-derived dIs closely match their endogenous counterparts. The atlas also reveals that the dI4/dI5 populations dramatically expand in comparison with the other spinal lineages. Moreover, they have mechanosensory circuit signatures linked to autism spectrum disorder, implicating spinal circuits in autistic phenotypes.

Published in

In vivo human embryonic spinal cord atlas validates stem cell-derived human dorsal interneurons and reveals ASD spinal signatures

Gupta S, Heinrichs E, Rodriguez C et al. · bioRxiv : the preprint server for biology 2025 · PMID 41509229 · doi:10.64898/2025.12.22.696129

This dataset

Open GSE326655 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 GSE326655_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 PRJNA1446710 and SRA study SRP688464. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41509229) ↗

Study design

10 distinct titles, 2 of them repeated

day 43, 2D NMP, RA_BMP, ×2 day 43, 2D NMP, RA, ×2

How we read this: Read from 12 sample titles: 10 distinct titles with little repetition. 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

GSM9636665 day 43, 2D NMP, RA_BMP, rep 1
GSM9636666 day 43, 2D NMP, RA, rep 1
GSM9636667 day 43, 4D NMP, RA_BMP4
GSM9636668 day 43, 4D NMP, RA
GSM9636669 day 43, 10D NMP, RA_BMP4
GSM9636670 day 43, 10D NMP, RA
GSM9636671 day 43, 2D GDF(50) NMP, RA_BMP
GSM9636672 day 43, 2D GDF(100) NMP, RA_BMP
GSM9636673 day 43, 2D NMP, RA_BMP, rep 2
GSM9636674 day 43, 2D GDF(50) NMP, RA
GSM9636675 day 43, 2D GDF(100) NMP, RA
GSM9636676 day 43, 2D NMP, RA, rep 2

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