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Life long effects of radiation and high fat dieat on the mouse left ventricular tissue

GSE272168 Mus musculus (mouse) RNA-seq (gene expression) 80 samples Submitted 2024/07/17 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 80 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
80 samples: 40 × M vs 40 × FGroups 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
Evaluating sex-specific responses to western diet across the lifespan: impact on cardiac function and transcriptomic signatures in C57BL/6J mice at 530 and 640/750 days of ageCardiovascular diabetology · 2024
Summary (written by the submitters)
We studied the long-term effects of single whole-body gamma and simulated GCR irradiation (IR) and consumption of a Western Diet (WD) on the heart's left ventricle (LV). Three-month-old C57Bl/6J wild-type male and female mice were assigned to the following groups: 1) Gamma-irradiated with follow-up at 440(males and females) and 660(males)/550(females) days post-IR; 2) simGCRsim-irradiated with follow-up at 440(males and females) and 660(males)/550(females) days post-IR; 3) 270-days WD-fed animals with followup at 530 (males and females) and 750(males)/640(females).
Read the full summary ↓
Control groups consisted of non-irradiated (non-IR) mice and normal diet-fed mice. Control groups were followed up similarly to the treatment groups. LV tissues were collected at follow-up and subjected to bulk RNA sequencing analysis. Total RNA was extracted from LV tissues using the RNeasy Mini Kit (Qiagen, USA) according to the manufacturer’s protocol and stored at -80°C until further use. A poly-A selected mRNA library was prepared using the NEBNextUltra™II RNA Library Prep Kit. The sequencing was performed on the Illumina NovaSeq-6000 platform to collect an average of 48 million 2x150bp paired-end reads per sample.FastQC (version 0.11.9) was used for the quality assessment of raw sequencing reads (Q30% was greater than 94%). Next, we aligned the reads to the mouse reference genome (mm39) with STAR aligner (version 2.7.8a) with gene count quantification mode and obtained raw gene counts. Differential gene expression analysis and functional annotation were performed using DeSeq2 and fgsea R packages. The results of the studies provide insight into the long-term transcriptome disturbance in response to irradiation and the Western diet, their association with structural and functional changes in LV, and implications in the development of cardiovascular disease (CVD). Furthermore, the study results pointed to the strong sex-biased pathophysiological and transcriptomic changes in LV.
Published in
Evaluating sex-specific responses to western diet across the lifespan: impact on cardiac function and transcriptomic signatures in C57BL/6J mice at 530 and 640/750 days of age
Stepanyan A, Brojakowska A, Zakharyan R et al. · Cardiovascular diabetology 2024 · PMID 39732652 · doi:10.1186/s12933-024-02565-9
This dataset
Open GSE272168 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 GSE272168_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 PRJNA1135248 and SRA study SRP519621. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39732652) ↗
Study design
40 × M vs 40 × F

Supports a between-group comparison across 80 samples.

How we read this: 2 replicated groups read from 80 sample titles; they account for 80 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

+ 40 more — browse all 80 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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