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Transcriptomes across seven brain regions from mouse model of anxiety

GSE254448 Mus musculus (mouse) RNA-seq (gene expression) 10 samples Submitted 2025/02/25 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 10 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
10 samples: 5 × CA3 AAV-shRNA(scramble) vs 5 × CA3 AAV-shRNA(mef2c)Groups 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
Integrative analysis identifies region- and sex-specific gene networks and Mef2c as a mediator of anxiety-like behaviorCell reports · 2024
Summary (written by the submitters)
Anxiety disorders are highly heterogeneous diseases. The molecular mechanisms underlying multi-brain region origin and sex dimorphism remain largely unknown. Herein, by leveraging large-scale transcriptomes across seven brain regions from mouse model of anxiety and extensive experiments at the molecular, synapse activity, and behavior levels, we dissected brain region- and sex-specific gene networks and identified critical sex-specific mediators of anxiety susceptibility.
Published in
Integrative analysis identifies region- and sex-specific gene networks and Mef2c as a mediator of anxiety-like behavior
Hong Y, Hu J, Zhang S et al. · Cell reports 2024 · PMID 38990717 · doi:10.1016/j.celrep.2024.114455
This dataset
Open GSE254448 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 GSE254448_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 PRJNA1070600 and SRA study SRP486495. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38990717) ↗
Study design
5 × CA3 AAV-shRNA(scramble) vs 5 × CA3 AAV-shRNA(mef2c)

Supports a between-group comparison across 10 samples.

How we read this: 2 replicated groups read from 10 sample titles; they account for 10 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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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.