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Neuronal Deficiency of Cytochrome c Oxidase Engineered by Mitochondrial DNA Editing Recapitulates Amyotrophic Lateral Sclerosis [snRNA-seq]

GSE275999 Rattus norvegicus (rat) Single-nucleus RNA-seq 6 samples Submitted 2024/12/18 Platform GPL34316
At a glance

Single-nucleus RNA-seq · rat · 6 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).
Organism
Rattus norvegicus (rat)
Samples
6 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 categorized into 10% familial and 90% sporadic cases. While the space of 10% familial ALS is crowded with mutations in many genes of diverse functions, most ALS-associated mutations could not faithfully recapitulate the disease phenotype in animal models. Remarkably, nearly half of sporadic ALS patients exhibit defective mitochondrial respiratory complex Ⅳ (CⅣ).
Read the full summary ↓
To establish the causal role of defective CⅣ in inducing ALS, we employed TALE-based mtDNA editing to mimic ALS-linked mutations in CⅣ compared to other respiratory complexes in rat neurons and demonstrated that mutations exclusively introduced to mtDNA-encoded CⅣ subunits are sufficient to cause a full spectrum of ALS-like phenotypes, including selective motor neuron loss, SOD1 overexpression and cytosolic TDP-43 aggregation. These findings reveal a broad basis for sporadic ALS, provide critical insights into the selective motor neuron vulnerability, and present a faithful animal model for advancing ALS therapy.
This dataset
Open GSE275999 in finder → Find more rat 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 GSE275999_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 PRJNA1154247 and SRA study SRP529478. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40069360) ↗
Samples in this study

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+ 6 more — browse all 6 samples with per-sample file links →

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