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Transcriptional profiling of striatum and cortex from a mouse model of Huntington's disease (Q140) crossed with Pms1 heterozygous and homozygous mice

GSE288739 Mus musculus (mouse) RNA-seq (gene expression) 96 samples Submitted 2025/02/10 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 96 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: 96 samples: 96 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.
Paper: Distinct mismatch-repair complex genes set neuronal CAG-repeat expansion rate to drive selective pathogenesis in HD miceCell · 2025

Summary (written by the submitters)

Cerebral cortex and striatum were isolated from 6-month old Pms1+/- and Pms1-/- mice crossed with the Q140 knock-in (KI) mice and their respective controls. Transcriptomic analysis (RNASeq) was performed on 6 genotypes: WT, Q140, Pms1+/-, Q140 X Pms1+/-, Pms1-/-, and Q140 X Pms1-/-, 8 replicates per genotype.

Published in

Distinct mismatch-repair complex genes set neuronal CAG-repeat expansion rate to drive selective pathogenesis in HD mice

Wang N, Zhang S, Langfelder P et al. · Cell 2025 · PMID 39938516 · doi:10.1016/j.cell.2025.01.031

This dataset

Open GSE288739 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 GSE288739_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 PRJNA1220058 and SRA study SRP562074. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39938516) ↗

Study design

96 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 96 sample titles: 96 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

GSM8779575 Het (Q140) KI X Pms1+/- Cortex female 5-2-C
GSM8779576 Pms1+/- Cortex female 5-3-C
GSM8779577 Pms1+/- Cortex male 6-1-C
GSM8779578 Pms1+/- Cortex male 6-2-C
GSM8779579 Het (Q140) KI Cortex female 7-1-C
GSM8779580 Het (Q140) KI Cortex female 7-3-C
GSM8779581 Het (Q140) KI X Pms1+/- Cortex male 8-1-C
GSM8779582 Het (Q140) KI Cortex male 8-2-C
GSM8779583 Het (Q140) KI X Pms1+/- Cortex male 8-3-C
GSM8779584 Wild type Cortex male 8-4-C
GSM8779585 Het (Q140) KI Cortex female 9-2-C
GSM8779586 Het (Q140) KI X Pms1+/- Cortex female 9-3-C
GSM8779587 Het (Q140) KI X Pms1+/- Cortex female 9-4-C
GSM8779588 Pms1+/- Cortex male 10-1-C
GSM8779589 Pms1+/- Cortex male 10-2-C
GSM8779590 Pms1+/- Cortex female 11-1-C
GSM8779591 Wild type Cortex female 11-2-C
GSM8779592 Wild type Cortex female 11-4-C
GSM8779593 Het (Q140) KI X Pms1+/- Cortex male 12-1-C
GSM8779594 Wild type Cortex male 12-4-C
GSM8779595 Het (Q140) KI X Pms1+/- Cortex female 13-1-C
GSM8779596 Pms1+/- Cortex female 13-2-C
GSM8779597 Pms1+/- Cortex female 13-4-C
GSM8779598 Wild type Cortex male 14-2-C
GSM8779599 Wild type Cortex male 14-4-C
GSM8779600 Het (Q140) KI Cortex female 15-1-C
GSM8779601 Pms1-/- Cortex male 16-4-C
GSM8779602 Het (Q140) KI X Pms1-/- Cortex female 17-2-C
GSM8779603 Het (Q140) KI X Pms1-/- Cortex male 18-1-C
GSM8779604 Het (Q140) KI Cortex male 18-2-C
GSM8779605 Het (Q140) KI Cortex male 18-4-C
GSM8779606 Het (Q140) KI X Pms1+/- Cortex male 20-2-C
GSM8779607 Het (Q140) KI X Pms1-/- Cortex male 21-4-C
GSM8779608 Pms1-/- Cortex female 22-1-C
GSM8779609 Pms1-/- Cortex female 22-2-C
GSM8779610 Pms1-/- Cortex female 22-3-C
GSM8779611 Het (Q140) KI Cortex male 23-4-C
GSM8779612 Pms1-/- Cortex male 26-5-C
GSM8779613 Wild type Cortex female 27-2-C
GSM8779614 Het (Q140) KI X Pms1-/- Cortex female 27-3-C

+ 56 more — browse all 96 samples with per-sample file links →

Datasets on a similar topic

GSE229815 Transcriptional profiling of 12 month striatum and cortex from a mouse model of Huntington's disease (Q140) crossed with Msh2 heterozygous or homozygous conditional knockout mice [Msh2_12mon] 138 samples shares q140, heterozygous, huntington, homozygous, striatum, crossed, cortex
GSE271022 Transcriptional profiling of cerebral cortex and striatum from a mouse model of Huntington's disease (Q140) crossed with Msh6 heterozygous and homozygous mice 96 samples shares q140, heterozygous, huntington, homozygous, striatum, crossed, cortex
GSE229829 Transcriptional profiling of striatum and cortex from a mouse model of Huntington's disease (Q140) crossed with Polq heterozygous mice [Polq] 64 samples shares q140, heterozygous, huntington, striatum, crossed, cortex
GSE229811 Transcriptional profiling of striatum and cortex from a mouse model of Huntington's disease (Q140) crossed with Mlh1 heterozygous mice [Mlh1] 64 samples shares q140, heterozygous, huntington, striatum, crossed, cortex
GSE229832 Transcriptional profiling of striatum and cortex from a mouse model of Huntington's disease (Q140) crossed with Tcerg1 heterozygous mice [Tcerg1] 64 samples shares q140, heterozygous, huntington, striatum, crossed, cortex
GSE229826 Transcriptional profiling of cerebral cortex from a mouse model of Huntington's disease (Q140) crossed with Msh3 heterozygous and homozygous mice [Msh3_cortex] 48 samples shares q140, heterozygous, huntington, homozygous, crossed, cortex
GSE237577 Transcriptional profiling of cortex from a mouse model of Huntington's disease (Q140) crossed with Pms2 heterozygous and homozygous mice [Pms2] 48 samples shares q140, heterozygous, huntington, homozygous, crossed, cortex
GSE237571 Transcriptional profiling of striatum from a mouse model of Huntington's disease (Q140) crossed with Msh3 heterozygous and homozygous mice [Msh3_striatum_6m] 48 samples shares q140, heterozygous, huntington, homozygous, striatum, crossed

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