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A murine model lacking Lyst recapitulates Chediak-Higashi syndrome with an earlier-onset neurodegenerative phenotype

GSE266142 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2024/06/01 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 24 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
Mus musculus (mouse)
Samples
24 samples: 8 conditions, mostly in duplicateGroups 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
A murine model lacking Lyst recapitulates Chediak-Higashi syndrome with an earlier-onset neurodegenerative phenotypeCommunications biology · 2025
Summary (written by the submitters)
Chediak-Higashi Syndrome (CHS) is a rare autosomal recessive disorder caused by mutations in the lysosomal trafficking regulator (LYST) gene, characterized by partial oculocutaneous albinism, bleeding diathesis, immune deficiency, and progressive neurodegeneration. We generated a Lyst knockout model (ΔLYST-B6) in which to accurately study pathophysiology seen in patients.
Read the full summary ↓
Here we show the ΔLYST-B6 model faithfully recapitulates characteristic features of CHS, including neurological manifestations at 6 months of age with associated progressive loss of Purkinje cells. Transcriptomic and lipidomic analyses of ΔLYST-B6 brain tissue reveals numerous differentially expressed genes and lipids in the cerebellum of 18-month-old ΔLYST-B6 mice suggesting progressive cerebellar decline and microglial involvement. Immunofluorescence studies implicate a plausible role of Bergmann glia in the pathology of CHS. Our findings demonstrate that the ΔLYST-B6 model recapitulates key features of the human CHS phenotype, including CHS-associated neurodegeneration, and provides a reliable model in which to study the function of LYST and explore future therapies for CHS.
Published in
A murine model lacking Lyst recapitulates Chediak-Higashi syndrome with an earlier-onset neurodegenerative phenotype
Greene S, Talbert ML, Frost FG et al. · Communications biology 2025 · PMID 40681653 · doi:10.1038/s42003-025-08482-1
This dataset
Open GSE266142 in finder → Find more mouse 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 GSE266142_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 PRJNA1105982 and SRA study SRP504723. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40681653) ↗
Study design
8 conditions, mostly in duplicate
Lyst-Knockout mouse 19351, brain tissue (cor… ×3 Lyst-Knockout mouse 19351, brain tissue (cere… ×2 Lyst-Knockout mouse 390, brain tissue (cerebe… ×2 Lyst-Knockout mouse 390, brain tissue (cortex… ×2 Wildtype mouse 19352, brain tissue (cerebellu… ×2 Wildtype mouse 19352, brain tissue (cortex), ×2 Wildtype mouse 397, brain tissue (cerebellum), ×2 Wildtype mouse 397, brain tissue (cortex), ×2 +7 more

Supports a case/control comparison: 12 samples read as cases, 12 as controls.

How we read this: 8 replicated groups read from 24 sample titles; they account for 17 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
Datasets on a similar topic

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