GEO series

Dysregulation of synaptic transcripts underlies network abnormalities in ALS patient-derived motor neurons

GSE268090 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2025/01/07 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 18 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Samples: 18 samples: 6 conditions, mostly in triplicateGroups 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: Dysregulation of synaptic transcripts underlies network abnormalities in ALS patient-derived motor neuronsAmerican journal of physiology. Cell physiology · 2025

Summary (written by the submitters)

Amyotrophic lateral sclerosis (ALS) is characterized by dysfunction and loss of upper and lower motor neurons. Several studies have identified structural and functional alterations in the motor neurons before the manifestation of symptoms, yet the underlying cause of such alterations and how they contribute to the progressive degeneration of affected motor neuron networks remain unclear.

Read the full summary ↓

Importantly, the short and long-term spatiotemporal dynamics of neuronal network activity make it challenging to discern how ALS-related network reconfigurations emerge and evolve. To address this, we systematically monitored the structural and functional dynamics of motor neuron networks with a confirmed endogenous C9orf72 mutation. We show that ALS patient-derived motor neurons display time-dependent neural network dysfunction, specifically reduced firing rate and spike amplitude, impaired bursting, but higher overall synchrony in network activity. These changes coincided with altered neurite outgrowth and branching within the networks. Moreover, transcriptional analyses revealed dysregulation of molecular pathways involved in synaptic development and maintenance, neurite outgrowth and cell adhesion, suggesting impaired synaptic stabilization. This study identifies early synaptic dysfunction as a contributing mechanism resulting in network-wide structural and functional compensation, which may over time render the networks vulnerable to neurodegeneration.

Published in

Dysregulation of synaptic transcripts underlies network abnormalities in ALS patient-derived motor neurons

Kollstrøm AM, Christiansen N, Sandvig A et al. · American journal of physiology. Cell physiology 2025 · PMID 39726289 · doi:10.1152/ajpcell.00725.2024

This dataset

Open GSE268090 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 GSE268090_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1114643 and SRA study SRP509161. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39726289) ↗

Study design

6 conditions, mostly in triplicate

Motor neurons, ALS, Day 18, ×3 Motor neurons, ALS, Day 38, ×3 Motor neurons, ALS, Day 52, ×3 Motor neurons, healthy control, Day 18, ×3 Motor neurons, healthy control, Day 38, ×3 Motor neurons, healthy control, Day 52, ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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

GSM8285682 Motor neurons, ALS, Day 18, rep 1 Motor neurons, ALS, Da…
GSM8285683 Motor neurons, ALS, Day 18, rep 2 Motor neurons, ALS, Da…
GSM8285684 Motor neurons, ALS, Day 18, rep 3 Motor neurons, ALS, Da…
GSM8285685 Motor neurons, ALS, Day 38, rep 1 Motor neurons, ALS, Da…
GSM8285686 Motor neurons, ALS, Day 38, rep 2 Motor neurons, ALS, Da…
GSM8285687 Motor neurons, ALS, Day 38, rep 3 Motor neurons, ALS, Da…
GSM8285688 Motor neurons, ALS, Day 52, rep 1 Motor neurons, ALS, Da…
GSM8285689 Motor neurons, ALS, Day 52, rep 2 Motor neurons, ALS, Da…
GSM8285690 Motor neurons, ALS, Day 52, rep 3 Motor neurons, ALS, Da…
GSM8285691 Motor neurons, healthy control, Day 18, rep 1 Motor neurons, healthy …
GSM8285692 Motor neurons, healthy control, Day 18, rep 2 Motor neurons, healthy …
GSM8285693 Motor neurons, healthy control, Day 18, rep 3 Motor neurons, healthy …
GSM8285694 Motor neurons, healthy control, Day 38, rep 1 Motor neurons, healthy …
GSM8285695 Motor neurons, healthy control, Day 38, rep 2 Motor neurons, healthy …
GSM8285696 Motor neurons, healthy control, Day 38, rep 3 Motor neurons, healthy …
GSM8285697 Motor neurons, healthy control, Day 52, rep 1 Motor neurons, healthy …
GSM8285698 Motor neurons, healthy control, Day 52, rep 2 Motor neurons, healthy …
GSM8285699 Motor neurons, healthy control, Day 52, rep 3 Motor neurons, healthy …

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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.