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Analysis of striatal zinc finger protein (ZFP) repression of mutant Huntingtin (HTT) in the zQ175DN knock-in mouse model of Huntington's disease (snRNA-seq)

GSE270728 Mus musculus (mouse) Single-nucleus RNA-seq 120 samples Submitted 2024/07/01 Platform GPL24247
At a glance

Single-nucleus RNA-seq · mouse · 120 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
Mus musculus (mouse)
Samples
120 samples: 120 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)
We assessed the relative efficacy of selectively lowering mHTT in the striatum at different intervention times in a human HTT exon 1 knock-in mouse model of Huntington’s disease, zQ175DN KI, using a virally delivered zinc finger protein transcriptional repressor directed against the expanded CAG repeat of the mutant HTT gene (Zeitler et al. Nat Med. 2019 Jul;25(7):1131-1142).
This dataset
Open GSE270728 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 GSE270728_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 PRJNA1124937 and SRA study SRP514381. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
120 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 120 sample titles: 120 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

+ 80 more — browse all 120 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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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.