GEO series

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

GSE252028 Mus musculus (mouse) Non-coding RNA profiling 192 samples Submitted 2025/02/26 Platform GPL17021

At a glance

Non-coding RNA profiling · mouse · 192 samples

What it is: Non-coding RNA profilingLevels of RNAs that do not code for proteins, such as miRNA or lncRNA.
Organism: Mus musculus (mouse)
Samples: 192 samples: 48 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

SuperSeries — this record groups several sub-series.

Summary (written by the submitters)

This SuperSeries is composed of the SubSeries listed below. Each sample is annotated as the cell type viz. CM or cardiomyocytes, EC or endothelial cells, FB or fibroblasts and HC or hematopoietic cells. The day corresponds to time point post 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 GSE252028 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 GSE252028_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 ↗

Also filed as BioProject PRJNA1057136 and SRA study SRP480100. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40389446) ↗

Study design

48 conditions, mostly with about 4 replicates each

CM, Day 0, smallRNA-Seq, ×4 CM, Day 1, smallRNA-Seq, ×4 CM, Day 3, smallRNA-Seq, ×4 CM, Day 7, smallRNA-Seq, ×4 CM, Day 14, smallRNA-Seq, ×4 CM, Day 28, smallRNA-Seq, ×4 EC, Day 0, smallRNA-Seq, ×4 EC, Day 1, smallRNA-Seq, ×4 +40 more

Supports a between-group comparison across 192 samples.

How we read this: 48 replicated groups read from 192 sample titles; they account for 192 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

GSM7992182 CM, Day 0, smallRNA-Seq, Replicate 1 CM, Day 0, smallRNA-Seq,
GSM7992183 CM, Day 0, smallRNA-Seq, Replicate 2 CM, Day 0, smallRNA-Seq,
GSM7992184 CM, Day 0, smallRNA-Seq, Replicate 3 CM, Day 0, smallRNA-Seq,
GSM7992185 CM, Day 0, smallRNA-Seq, Replicate 4 CM, Day 0, smallRNA-Seq,
GSM7992186 CM, Day 1, smallRNA-Seq, Replicate 1 CM, Day 1, smallRNA-Seq,
GSM7992187 CM, Day 1, smallRNA-Seq, Replicate 2 CM, Day 1, smallRNA-Seq,
GSM7992188 CM, Day 1, smallRNA-Seq, Replicate 3 CM, Day 1, smallRNA-Seq,
GSM7992189 CM, Day 1, smallRNA-Seq, Replicate 4 CM, Day 1, smallRNA-Seq,
GSM7992190 CM, Day 3, smallRNA-Seq, Replicate 1 CM, Day 3, smallRNA-Seq,
GSM7992191 CM, Day 3, smallRNA-Seq, Replicate 2 CM, Day 3, smallRNA-Seq,
GSM7992192 CM, Day 3, smallRNA-Seq, Replicate 3 CM, Day 3, smallRNA-Seq,
GSM7992193 CM, Day 3, smallRNA-Seq, Replicate 4 CM, Day 3, smallRNA-Seq,
GSM7992194 CM, Day 7, smallRNA-Seq, Replicate 1 CM, Day 7, smallRNA-Seq,
GSM7992195 CM, Day 7, smallRNA-Seq, Replicate 2 CM, Day 7, smallRNA-Seq,
GSM7992196 CM, Day 7, smallRNA-Seq, Replicate 3 CM, Day 7, smallRNA-Seq,
GSM7992197 CM, Day 7, smallRNA-Seq, Replicate 4 CM, Day 7, smallRNA-Seq,
GSM7992198 CM, Day 14, smallRNA-Seq, Replicate 1 CM, Day 14, smallRNA-Se…
GSM7992199 CM, Day 14, smallRNA-Seq, Replicate 2 CM, Day 14, smallRNA-Se…
GSM7992200 CM, Day 14, smallRNA-Seq, Replicate 3 CM, Day 14, smallRNA-Se…
GSM7992201 CM, Day 14, smallRNA-Seq, Replicate 4 CM, Day 14, smallRNA-Se…
GSM7992202 CM, Day 28, smallRNA-Seq, Replicate 1 CM, Day 28, smallRNA-Se…
GSM7992203 CM, Day 28, smallRNA-Seq, Replicate 2 CM, Day 28, smallRNA-Se…
GSM7992204 CM, Day 28, smallRNA-Seq, Replicate 3 CM, Day 28, smallRNA-Se…
GSM7992205 CM, Day 28, smallRNA-Seq, Replicate 4 CM, Day 28, smallRNA-Se…
GSM7992206 EC, Day 0, smallRNA-Seq, Replicate 1 EC, Day 0, smallRNA-Seq,
GSM7992207 EC, Day 0, smallRNA-Seq, Replicate 2 EC, Day 0, smallRNA-Seq,
GSM7992208 EC, Day 0, smallRNA-Seq, Replicate 3 EC, Day 0, smallRNA-Seq,
GSM7992209 EC, Day 0, smallRNA-Seq, Replicate 4 EC, Day 0, smallRNA-Seq,
GSM7992210 EC, Day 1, smallRNA-Seq, Replicate 1 EC, Day 1, smallRNA-Seq,
GSM7992211 EC, Day 1, smallRNA-Seq, Replicate 2 EC, Day 1, smallRNA-Seq,
GSM7992212 EC, Day 1, smallRNA-Seq, Replicate 3 EC, Day 1, smallRNA-Seq,
GSM7992213 EC, Day 1, smallRNA-Seq, Replicate 4 EC, Day 1, smallRNA-Seq,
GSM7992214 EC, Day 3, smallRNA-Seq, Replicate 1 EC, Day 3, smallRNA-Seq,
GSM7992215 EC, Day 3, smallRNA-Seq, Replicate 2 EC, Day 3, smallRNA-Seq,
GSM7992216 EC, Day 3, smallRNA-Seq, Replicate 3 EC, Day 3, smallRNA-Seq,
GSM7992217 EC, Day 3, smallRNA-Seq, Replicate 4 EC, Day 3, smallRNA-Seq,
GSM7992218 EC, Day 7, smallRNA-Seq, Replicate 1 EC, Day 7, smallRNA-Seq,
GSM7992219 EC, Day 7, smallRNA-Seq, Replicate 2 EC, Day 7, smallRNA-Seq,
GSM7992220 EC, Day 7, smallRNA-Seq, Replicate 3 EC, Day 7, smallRNA-Seq,
GSM7992221 EC, Day 7, smallRNA-Seq, Replicate 4 EC, Day 7, smallRNA-Seq,

+ 152 more — browse all 192 samples with per-sample file links →

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