GEO series

Stem cell derived spinal cord chips reproduce disease biomarkers in sporadic ALS patients [bulk RNAseq]

GSE255602 Homo sapiens (human) Single-nucleus RNA-seq 71 samples Submitted 2025/06/24 Platform GPL24676

At a glance

Single-nucleus RNA-seq · human · 71 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: 71 samples
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)

Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disorder with complex origins. Familial monogenetic causes of ALS make up a small percentage of patients overall, and the cause of the majority of idiopathic (sporadic) form remains unknown. Frequently utilized for disease modeling, human induced pluripotent stem cell (iPSC)-derived motor neuron cultures lack cellular maturity in vitro and rarely recapitulate clinically relevant phenotypes of ALS.

Read the full summary ↓

Microfluidic organ-on-chip systems enable co-culture of multiple disease-relevant cell types and enhance cellular maturity. Here, we describe the generation of spinal cord (SC)-chips from 8 sporadic ALS (sALS) patients and 10 non-diseased controls. Transcriptomic and proteomic analyses of SC-Chips revealed changes in expression of targets known to be disrupted in ALS patients. Particularly, intermediate filaments (IF) neurofilament heavy (NEFH), medium (NEFM), and light (NEFL) were upregulated in SC-Chips from sALS patients. Single nuclei RNAseq (sNucseq) of SC-Chips revealed two subpopulations of motor neurons and cell-specific changes related to ALS pathogenesis and mimicking conditions in vivo.

This dataset

Open GSE255602 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 GSE255602_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 PRJNA1075766 and SRA study SRP489681. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 71 more — browse all 71 samples with per-sample file links →

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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.