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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 (bulk RNA-seq)

GSE270727 Mus musculus (mouse) RNA-seq (gene expression) 233 samples Submitted 2024/07/01 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 233 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
233 samples: 30 conditions, mostly with about 8 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.
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 GSE270727 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 GSE270727_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 PRJNA1124926 and SRA study SRP514353. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
30 conditions, mostly with about 8 replicates each
zQ175_DBD_6M_8M_STR ×8 zQ175_Estop_6M_8M_STR ×8 WT_DBD_6M_8M_STR ×8 WT_Estop_6M_8M_STR ×8 WT_nZFP_6M_8M_STR ×8 zQ175_nZFP_6M_8M_STR ×8 WT_DBD_2M_6M_STR ×8 zQ175_Estop_2M_6M_STR ×8 +22 more

Supports a between-group comparison across 233 samples.

How we read this: 30 replicated groups read from 233 sample titles; they account for 233 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

+ 193 more — browse all 233 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.