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Transcriptome Dynamics in Mouse Amygdala under Acute and Chronic Stress Revealed by Thiol-labeled RNA Sequencing

GSE274148 Mus musculus (mouse) RNA-seq (gene expression) 32 samples Submitted 2024/08/14 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 5 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
Transcriptome dynamics in mouse amygdala under acute and chronic stress revealed by thiol-labeled RNA sequencingNeurobiology of stress · 2024
Summary (written by the submitters)
Both acute and chronic stress have significant impact on brain functions. The amygdala is essential in mediating stress responses, but how its transcriptomic dynamics change under stress remains elusive. To overcome the difficulties in detecting subtle stress-induced changes by evaluating total RNA using classic RNA sequencing, we conducted thiol-labeled RNA sequencing (SLAM-seq).
Read the full summary ↓
We injected 4-thiouridine (4sU) into mouse amygdala followed by SLAM-seq to detect nascent mRNA induced by acute and chronic restraint stress, and found that SLAM-seq could label actively transcribed genes in the major neuronal and glial subtypes. Using SLAM-seq, we found that chronic stress led to higher turnover of a group of genes associated with myelination, and this finding is confirmed by immunostaining which showed increased myelination in the chronically stressed amygdala. Additionally, genes detected by SLAM-seq and RNA-seq only partially overlapped, with SLAM-seq particularly sensitive to transcriptional changes in genes with high basal transcription levels. Thus, by applying SLAM-seq in vivo, we obtained a rich dataset of nascently transcribed genes in the amygdala under stress, and revealed distinct transcriptional dynamics associated with acute and chronic stress.
Published in
Transcriptome dynamics in mouse amygdala under acute and chronic stress revealed by thiol-labeled RNA sequencing
Zhao D, Zhang L, Yang Y · Neurobiology of stress 2024 · PMID 39583745 · doi:10.1016/j.ynstr.2024.100688
This dataset
Open GSE274148 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 GSE274148_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 PRJNA1145279 and SRA study SRP524711. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39583745) ↗
Study design
8 conditions, mostly with about 5 replicates each
Mouse brain, baseline, 4sU, ×5 Mouse brain, acute stress, 4sU, ×5 Mouse brain, acute stress, DMSO, ×5 Mouse brain, baseline, DMSO, ×4 Mouse brain, chronic stress, 4sU, ×4 Mouse brain, chronic stress, DMSO, ×3 Mouse brain, 4sU, ×3 Mouse brain, 4sU-, ×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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