GEO series

Neurofilament accumulations in Amyotrophic Lateral Sclerosis patients’ motor neurons impair structural axonal initial segment integrity

GSE200474 Homo sapiens (human) RNA-seq (gene expression) 65 samples Submitted 2024/07/03 Platform GPL11154

At a glance

RNA-seq (gene expression) · human · 65 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: 65 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.
Paper: Neurofilament accumulations in amyotrophic lateral sclerosis patients' motor neurons impair axonal initial segment integrityCellular and molecular life sciences : CMLS · 2023

Summary (written by the submitters)

Neurofilament (NF) accumulation is a pathological hallmark observed in motor neurons (MNs) of patients with Amyotrophic Lateral Sclerosis (ALS) and levels of NF in fluids is becoming the prime biomarker of ALS progression. However, the underlying mechanisms linking NF accumulations and MN degeneration are not elucidated. Here, we show that integrity of the axonal initial segment (AIS), the region of action potential initiation and of polarized trafficking, is impaired by NF accumulations in human MNs carrying mutations in the two main causal ALS genes: C9ORF72 and SOD1.

Read the full summary ↓

We show that in mutant MNs derived from induced pluripotent stem cells, both light (NF-L) and phosphorylated heavy chains (pNF-H) accumulated progressively with MN aging and that pNF-H accumulation in the AIS region led to significant structural and molecular alterations. In parallel, ALS MNs acquired altered excitability with aging. Focusing on axonal organization appears as an effective readout for MN cell death and preserving AIS integrity could have important therapeutic implications.

Published in

Neurofilament accumulations in amyotrophic lateral sclerosis patients' motor neurons impair axonal initial segment integrity

Lefebvre-Omar C, Liu E, Dalle C et al. · Cellular and molecular life sciences : CMLS 2023 · PMID 37184603 · doi:10.1007/s00018-023-04797-6

This dataset

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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 GSE200474_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 PRJNA824791 and SRA study SRP368264. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37184603) ↗

Samples in this study

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+ 65 more — browse all 65 samples with per-sample file links →

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