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mRNA expression profiles in hearts from sepsis-induced myocardial dysfunction mouse modles and controls

GSE267388 Mus musculus (mouse) RNA-seq (gene expression) 10 samples Submitted 2024/08/09 Platform GPL28330
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 × Heart_PBS vs 5 × Heart_LPSGroups 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
Screening of novel disease genes of sepsis-induced myocardial Disfunction by RNA sequencing and bioinformatics analysisGenomics · 2024
Summary (written by the submitters)
In order to explore the genes and molecular mechanisms involved in the development and progression of sepsis-induced myocardial dysfunction, RNA sequencing was used to examine the total RNA in heart tissues of disease model mice and control individuals, and to generate this transcriptome dataset to compare gene expression differences between the two groups of tissues at the transcriptional level.
Published in
Screening of novel disease genes of sepsis-induced myocardial Disfunction by RNA sequencing and bioinformatics analysis
Yao H, Xiao Z, Liu S et al. · Genomics 2024 · PMID 39111545 · doi:10.1016/j.ygeno.2024.110911
This dataset
Open GSE267388 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 GSE267388_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 PRJNA1111387 and SRA study SRP507523. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39111545) ↗
Study design
5 × Heart_PBS vs 5 × Heart_LPS

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

Search all mouse RNA-seq datasets in GEO →

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