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CLIPPER Regulates LPIN1-Mediated Mitochondrial Biogenesis and Heart Regeneration

GSE317535 Homo sapiens (human) RNA-seq (gene expression) 10 samples Submitted 2026/02/27 Platform GPL30173
At a glance

RNA-seq (gene expression) · human · 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
Homo sapiens (human)
Samples
10 samples: 5 × H1-hESC-CM, Clipper GapmeR Knockdown, vs 5 × H1-hESC-CM, Control GapmeR,Groups 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
CLIPPER Regulates LPIN1-Mediated Mitochondrial Biogenesis and Heart RegenerationCirculation research · 2026
Summary (written by the submitters)
The adult mammalian heart lacks the significant regenerative potential needed to cope with the massive loss of cardiomyocytes following myocardial infarction. Ultimately, irreversible cardiac damage leads to heart failure, which is associated with a very poor prognosis. Given this, reactivating dormant regenerative processes in the injured heart represents an attractive therapeutic approach.
Read the full summary ↓
When regeneration does occur, newly formed cardiomyocytes are derived from preexisting ones. We aimed to identify novel regulators of cardiomyocyte proliferation. In this context, the genome is transcribed for a large part into RNAs with little or no protein-coding potential. Among noncoding RNAs, long noncoding (lnc)RNAs represent the most diverse class of molecules, and are implicated in numerous epigenetic mechanisms, making them ideal targets for controlling cell identity and behavior. In this project, we developed a high-throughput screening assay to identify lncRNAs that promote cardiomyocyte proliferation upon knockdown. Using a stringent selection pipeline, we identified Clipper, an enhancer-associated lncRNA regulating the expression of its cognate protein-coding gene Lpin1 in cis. Clipper was found to control mitochondrial biogenesis via LPIN1. Specifically, productive mitochondrial division, characterized by fission site positioning at the midzone of the mitochondrion, was stimulated by Clipper or Lpin1 silencing. The process was associated with a change in mitochondrial bioenergetics, particularly decreased oxidative metabolism, reduced production of reactive oxygen species, and dampened DNA damage, creating favorable conditions for cardiomyocyte proliferation. Importantly, Clipper knockdown in vivo following myocardial infarction stimulated cardiac regeneration in the damaged myocardium leading to the restoration of heart function. Importantly, CLIPPER is positionally and functionally conserved in humans. Our data identify CLIPPER as a promising therapeutic target for heart regeneration, acting through control of LPIN1-dependent mitochondrial biogenesis and cardiomyocyte proliferation.
Published in
CLIPPER Regulates LPIN1-Mediated Mitochondrial Biogenesis and Heart Regeneration
Ruberto FP, Maric D, Kleele T et al. · Circulation research 2026 · PMID 41641546 · doi:10.1161/CIRCRESAHA.125.326739
This dataset
Open GSE317535 in finder → Find more human 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 GSE317535_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 PRJNA1414429 and SRA study SRP666387. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41641546) ↗
Study design
5 × H1-hESC-CM, Clipper GapmeR Knockdown, vs 5 × H1-hESC-CM, Control GapmeR,

Supports a case/control comparison: 5 samples read as cases, 5 as controls.

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
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