GEO series

Cardiomayocyte specific translating RNA sequencing from mice in heart failure

GSE100532 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2017/10/04 Platform GPL18635

At a glance

RNA-seq (gene expression) · mouse · 18 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: 18 samples: 6 conditions, mostly in triplicateGroups 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)

Mammalian organs vary widely in regenerative capacity, and poorly regenerative organs, such as the heart are particularly vulnerable to organ failure. Once established, heart failure commonly results in in considerable mortality and early demise. The Hippo pathway, a kinase cascade that prevents adult cardiomyocyte proliferation and regeneration, is upregulated in human heart failure.

Read the full summary ↓

We show that deletion of the Hippo pathway component Salvador (Salv) in mouse hearts with established ischemic heart failure after myocardial infarction induced a reparative genetic program characterized by increased scar border vascularity, reduced fibrosis, and recovery of pumping function to that of sham-operated controls. To isolate cardiomyocyte specific translating mRNA we used TRAP (translating ribosomal affinity purification) followed by RNA sequencing. Hippo deficient cardiomyocytes had increased expression of proliferative, and stress response genes. Interestingly the mitochondrial quality control gene, Park2 was among the stress response genes. Further genetic studies indicated that Park2 was essential for heart repair in both the neonatal mouse and the adult Salv conditional knockout mouse. Thus, suggesting a requirement for mitochondrial quality control in the regenerating myocardium. Our findings indicate that the failing heart has a previously unrecognized capacity for repair involving more than cardiomyocyte renewal.

This dataset

Open GSE100532 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 GSE100532_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 PRJNA392044 and SRA study SRP110583. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 28976966) ↗

Study design

6 conditions, mostly in triplicate

total_MI_ctrl ×3 total_MI_mut ×3 trap_MI_ctrl ×3 trap_MI_mut ×3 trap_sham_ctrl ×3 trap_sham_mut ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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

GSM2686082 total_MI_ctrl1 total_MI_ctrl
GSM2686083 total_MI_ctrl2 total_MI_ctrl
GSM2686084 total_MI_ctrl3 total_MI_ctrl
GSM2686085 total_MI_mut1 total_MI_mut
GSM2686086 total_MI_mut2 total_MI_mut
GSM2686087 total_MI_mut3 total_MI_mut
GSM2686088 trap_MI_ctrl1 trap_MI_ctrl
GSM2686089 trap_MI_ctrl2 trap_MI_ctrl
GSM2686090 trap_MI_ctrl3 trap_MI_ctrl
GSM2686091 trap_MI_mut1 trap_MI_mut
GSM2686092 trap_MI_mut2 trap_MI_mut
GSM2686093 trap_MI_mut3 trap_MI_mut
GSM2686094 trap_sham_ctrl1 trap_sham_ctrl
GSM2686095 trap_sham_ctrl2 trap_sham_ctrl
GSM2686096 trap_sham_ctrl3 trap_sham_ctrl
GSM2686097 trap_sham_mut1 trap_sham_mut
GSM2686098 trap_sham_mut2 trap_sham_mut
GSM2686099 trap_sham_mut3 trap_sham_mut

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GSE267693 Pannexin 1 Channels Control Cardiomyocyte Metabolism and Neutrophil Recruitment During Non-Ischemic Heart Failure 23 samples shares failure, heart
GSE269053 Two-hit mouse model of heart failure with preserved ejection fraction combining diet-induced obesity and renin-mediated hypertension 21 samples shares failure, heart
GSE279007 Transcriptome of adult hearts with cardiomyocyte-specific deficiency of Aars2 20 samples shares specific, heart
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GSE252028 A cell type-specific expression atlas of small and total RNA in the heart after myocardial infarction 192 samples shares specific, heart
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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.