GEO series

Temporal co-regulation of microRNA arms among cell types after myocardial infarction [RNA-Seq]

GSE252027 Mus musculus (mouse) RNA-seq (gene expression) 96 samples Submitted 2025/02/26 Platform GPL17021

At a glance

RNA-seq (gene expression) · mouse · 96 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: 96 samples: 24 conditions, mostly with about 4 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: A cell type-specific expression atlas of small and total RNA in the heart after myocardial infarctionScientific data · 2025

Summary (written by the submitters)

Acute myocardial infarction (AMI) is one of the leading causes of mortality worldwide. MicroRNAs (miRNAs) shape the transcript repertoire and control cellular functions. Imprecise cleavage of miRNA hairpins during biogenesis and downstream enzymatic processing alters mature miRNA arm abundance. Using small and total RNA sequencing, miRNA temporal dynamics and regulatory effects were studied in four cell types of the heart upon myocardial infarction.

Read the full summary ↓

We define differentially processed miRNAs, which have changes in their arm ratios and have effects on target gene regulation. The identified miRNA subsets are enriched in templated isomiR modifications and show associations with RNA binding proteins, biogenesis and other processing factors. Our analysis reveals antagonistic functions co-regulated by the processed miRNA arms, beyond known pathways involved in cardiac regeneration. This study highlights novel insights into disease mechanisms controlled by dysregulated microRNA processing concerning acute damage response as well as long-time adaptation after AMI.

Published in

A cell type-specific expression atlas of small and total RNA in the heart after myocardial infarction

Kumar Maji R, Fischer A, Rogg EM et al. · Scientific data 2025 · PMID 40389446 · doi:10.1038/s41597-025-05061-1

This dataset

Open GSE252027 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 GSE252027_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 PRJNA1057142 and SRA study SRP480120. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40389446) ↗

Study design

24 conditions, mostly with about 4 replicates each

CM, Day 0, RNA-Seq, ×4 CM, Day 1, RNA-Seq, ×4 CM, Day 3, RNA-Seq, ×4 CM, Day 7, RNA-Seq, ×4 CM, Day 14, RNA-Seq, ×4 CM, Day 28, RNA-Seq, ×4 EC, Day 0, RNA-Seq, ×4 EC, Day 1, RNA-Seq, ×4 +16 more

Supports a between-group comparison across 96 samples.

How we read this: 24 replicated groups read from 96 sample titles; they account for 96 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

GSM7992278 CM, Day 0, RNA-Seq, Replicate 1 CM, Day 0, RNA-Seq,
GSM7992279 CM, Day 0, RNA-Seq, Replicate 2 CM, Day 0, RNA-Seq,
GSM7992280 CM, Day 0, RNA-Seq, Replicate 3 CM, Day 0, RNA-Seq,
GSM7992281 CM, Day 0, RNA-Seq, Replicate 4 CM, Day 0, RNA-Seq,
GSM7992282 CM, Day 1, RNA-Seq, Replicate 1 CM, Day 1, RNA-Seq,
GSM7992283 CM, Day 1, RNA-Seq, Replicate 2 CM, Day 1, RNA-Seq,
GSM7992284 CM, Day 1, RNA-Seq, Replicate 3 CM, Day 1, RNA-Seq,
GSM7992285 CM, Day 1, RNA-Seq, Replicate 4 CM, Day 1, RNA-Seq,
GSM7992286 CM, Day 3, RNA-Seq, Replicate 1 CM, Day 3, RNA-Seq,
GSM7992287 CM, Day 3, RNA-Seq, Replicate 2 CM, Day 3, RNA-Seq,
GSM7992288 CM, Day 3, RNA-Seq, Replicate 3 CM, Day 3, RNA-Seq,
GSM7992289 CM, Day 3, RNA-Seq, Replicate 4 CM, Day 3, RNA-Seq,
GSM7992290 CM, Day 7, RNA-Seq, Replicate 1 CM, Day 7, RNA-Seq,
GSM7992291 CM, Day 7, RNA-Seq, Replicate 2 CM, Day 7, RNA-Seq,
GSM7992292 CM, Day 7, RNA-Seq, Replicate 3 CM, Day 7, RNA-Seq,
GSM7992293 CM, Day 7, RNA-Seq, Replicate 4 CM, Day 7, RNA-Seq,
GSM7992294 CM, Day 14, RNA-Seq, Replicate 1 CM, Day 14, RNA-Seq,
GSM7992295 CM, Day 14, RNA-Seq, Replicate 2 CM, Day 14, RNA-Seq,
GSM7992296 CM, Day 14, RNA-Seq, Replicate 3 CM, Day 14, RNA-Seq,
GSM7992297 CM, Day 14, RNA-Seq, Replicate 4 CM, Day 14, RNA-Seq,
GSM7992298 CM, Day 28, RNA-Seq, Replicate 1 CM, Day 28, RNA-Seq,
GSM7992299 CM, Day 28, RNA-Seq, Replicate 2 CM, Day 28, RNA-Seq,
GSM7992300 CM, Day 28, RNA-Seq, Replicate 3 CM, Day 28, RNA-Seq,
GSM7992301 CM, Day 28, RNA-Seq, Replicate 4 CM, Day 28, RNA-Seq,
GSM7992302 EC, Day 0, RNA-Seq, Replicate 1 EC, Day 0, RNA-Seq,
GSM7992303 EC, Day 0, RNA-Seq, Replicate 2 EC, Day 0, RNA-Seq,
GSM7992304 EC, Day 0, RNA-Seq, Replicate 3 EC, Day 0, RNA-Seq,
GSM7992305 EC, Day 0, RNA-Seq, Replicate 4 EC, Day 0, RNA-Seq,
GSM7992306 EC, Day 1, RNA-Seq, Replicate 1 EC, Day 1, RNA-Seq,
GSM7992307 EC, Day 1, RNA-Seq, Replicate 2 EC, Day 1, RNA-Seq,
GSM7992308 EC, Day 1, RNA-Seq, Replicate 3 EC, Day 1, RNA-Seq,
GSM7992309 EC, Day 1, RNA-Seq, Replicate 4 EC, Day 1, RNA-Seq,
GSM7992310 EC, Day 3, RNA-Seq, Replicate 1 EC, Day 3, RNA-Seq,
GSM7992311 EC, Day 3, RNA-Seq, Replicate 2 EC, Day 3, RNA-Seq,
GSM7992312 EC, Day 3, RNA-Seq, Replicate 3 EC, Day 3, RNA-Seq,
GSM7992313 EC, Day 3, RNA-Seq, Replicate 4 EC, Day 3, RNA-Seq,
GSM7992314 EC, Day 7, RNA-Seq, Replicate 1 EC, Day 7, RNA-Seq,
GSM7992315 EC, Day 7, RNA-Seq, Replicate 2 EC, Day 7, RNA-Seq,
GSM7992316 EC, Day 7, RNA-Seq, Replicate 3 EC, Day 7, RNA-Seq,
GSM7992317 EC, Day 7, RNA-Seq, Replicate 4 EC, Day 7, RNA-Seq,

+ 56 more — browse all 96 samples with per-sample file links →

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Search all mouse RNA-seq datasets in GEO →

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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.