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Transcriptional profiling of striatum from a zQ175 KI mouse model of Huntington's disease with or without homozygous knockout of the Msh3 gene

GSE245510 Mus musculus (mouse) RNA-seq (gene expression) 32 samples Submitted 2024/05/24 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 32 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
32 samples: 8 conditions, mostly with about 4 replicates eachGroups 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 CAG repeat threshold for therapeutics targeting somatic instability in Huntington's diseaseBrain : a journal of neurology · 2024
Summary (written by the submitters)
Previous studies have suggested a strong association between lower MSH3 expression, reduced somatic repeat expansion, and slower disease onset and progression. The effects of a homozygous knock-out in the Msh3 gene on transcriptome phenotypes in striatum in six-month-old WT and zQ175 mice were studied. Striatum was isolated from 6-month-old mice.
Read the full summary ↓
Transcriptomic analysis (RNASeq) was performed on four genotypes with 8 replicates per genotype: WT (WT for Htt and Msh3), zQ175 (zQ175 for Htt, WT for Msh3), WT.Msh3.HOM (WT for Htt, Homozygous for Msh3 KO), and zQ175.Msh3.HOM (zQ175 for Htt, Homozygous for Msh3 KO).
Published in
A CAG repeat threshold for therapeutics targeting somatic instability in Huntington's disease
Aldous SG, Smith EJ, Landles C et al. · Brain : a journal of neurology 2024 · PMID 38387080 · doi:10.1093/brain/awae063
This dataset
Open GSE245510 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 GSE245510_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 PRJNA1028632 and SRA study SRP466626. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38387080) ↗
Study design
8 conditions, mostly with about 4 replicates each
Striatum_6M_zQ175.Msh3.HOM_male ×5 Striatum_6M_WT.Msh3.HOM_male ×4 Striatum_6M_WT.Msh3.HOM_female ×4 Striatum_6M_WT_female ×4 Striatum_6M_WT_male ×4 Striatum_6M_zQ175_female ×4 Striatum_6M_zQ175_male ×4 Striatum_6M_zQ175.Msh3.HOM_female ×3

Supports a between-group comparison across 32 samples.

How we read this: 8 replicated groups read from 32 sample titles; they account for 32 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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