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Enhancer Dynamics and Spatial Organization Drive Anatomically Restricted Cellular States in the Human Spinal Cord [scRNA-seq]

GSE300791 Homo sapiens (human) Single-cell RNA-seq 20 samples Submitted 2026/02/12 Platform GPL21697Platform GPL24676
At a glance

Single-cell RNA-seq · human · 20 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
20 samples: 8 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
Enhancer dynamics and cellular architecture in the human spinal cordNeuron · 2026
Summary (written by the submitters)
Here, we report the spatial organization of RNA transcription and associated enhancer dynamics in the human spinal cord at single-cell and single-molecule resolution. We expand traditional multiomic measurements to reveal epigenetically poised and bivalent active transcriptional enhancer states that define cell type specification. Simultaneous detection of chromatin accessibility and histone modifications in spinal cord nuclei reveals previously unobserved cell-type specific cryptic enhancer activity, in which transcriptional activation is uncoupled from chromatin accessibility.
Read the full summary ↓
Such cryptic enhancers define both stable cell type identity and transitions between cells undergoing differentiation. We also define glial cell gene regulatory networks that reorganize along the rostrocaudal axis, revealing anatomical differences in gene regulation. Finally, we identify the spatial organization of cells into distinct cellular organizations and address the functional significance of this observation in the context of paracrine signaling. We conclude that cellular diversity is best captured through the lens of enhancer state and intercellular interactions that drive transitions in cellular state. This study provides fundamental insights into the cellular organization of the healthy human spinal cord.
Published in
Enhancer dynamics and cellular architecture in the human spinal cord
Kandror EK, Carriere M, Peterson A et al. · Neuron 2026 · PMID 41687613 · doi:10.1016/j.neuron.2025.12.035
This dataset
Open GSE300791 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 GSE300791_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 PRJNA1267494 and SRA study SRP587473. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41687613) ↗
Study design
8 conditions, mostly in duplicate
Donor 2, Lumbar spinal cord, snRNA sample ×4 Donor 3, Thoracic spinal cord, snRNA sample ×4 Donor 4, Lumbar spinal cord, snRNA sample ×2 Donor 4, Thoracic spinal cord, snRNA sample ×2 Donor 5, Lumbar spinal cord, snRNA sample ×2 Donor 5, Thoracic spinal cord, snRNA sample ×2 Donor 6, Lumbar spinal cord, snRNA sample ×2 Donor 6, Thoracic spinal cord, snRNA sample ×2

Supports a between-group comparison across 20 samples.

How we read this: 8 replicated groups read from 20 sample titles; they account for 20 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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