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ndufs2-/- zebrafish model Leigh syndrome with shortened lifespan, developmental anomalies, altered transcriptome and disrupted metabolism

GSE259251 Homo sapiens (human) RNA-seq (gene expression) 30 samples Submitted 2025/12/01 Platform GPL24676Platform GPL24995
At a glance

RNA-seq (gene expression) · human · 30 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
30 samples: 30 samples, each with a distinct title — no replicated groupsGroups 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.
Summary (written by the submitters)
Mitochondrial complex I (CI) deficiency, one genetic etiology of Leigh syndrome spectrum (LSS), manifests with complex multi-system dysfunction with lactic acidemia and early mortality. To facilitate screening of therapeutic candidates for CI diseases, we used CRISPR/Cas9 to generate a ndufs2-/- zebrafish line. Ndufs2 deficient larvae displayed reduced survival, neuromuscular dysfunction, and morphological malformations.
Read the full summary ↓
We performed transcriptomic sequencing of ndufs2-/- larvae at 6 vs 7 dpf, across and within clutches, and relative to sibling or WT controls. These results were compared to transcriptome data of ndufs2-/- missense mutant C. elegans (gas-1(fc21)) and CI disease patient fibroblasts. Transcriptome profiling revealed consistently dysregulated pathways in ndufs2-/- larvae, gas-1(fc21) worms, and human CI deficient cell lines with increased expression of the electron transport chain, TCA cycle, fatty acid beta oxidation, and one-carbon metabolism. Targeted biochemical analyses revealed a reduction in CI activity and unbiased metabolomic studies identified increased lactate, TCA cycle intermediates, and carnitine species. These changes suggest central metabolism has shunted glucose utilization towards lactate production. Additionally, we determined alterations in one-carbon metabolism associated pathways likely contribute to pathology. Our established, validated ndufs2-/- zebrafish model of CI deficiency recapitulates LSS phenotypes and will be useful for future studies of CI disease and therapeutics.
This dataset
Open GSE259251 in finder → Find more 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 GSE259251_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 PRJNA1080530 and SRA study SRP491762. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
30 samples, each with a distinct title — no replicated groups

Supports a case/control comparison: 2 samples read as cases, 7 as controls.

How we read this: Read from 30 sample titles: 30 distinct titles with little repetition. 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
Datasets on a similar topic

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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.