GEO series

Downregulation of Scd1 promotes cardiac reprogramming by enhancing mitochondrial metabolism through PGC1α [RNA-seq]

GSE285211 Mus musculus (mouse) Single-cell RNA-seq 10 samples Submitted 2025/04/23 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 10 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
Samples: 10 samples: 10 samples, each with a distinct title — no replicated groupsGroups 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: Enhanced fatty acid oxidation via SCD1 downregulation fuels cardiac reprogrammingMolecular therapy : the journal of the American Society of Gene Therapy · 2025

Summary (written by the submitters)

Direct cardiac reprogramming of fibroblasts into induced cardiac-like myocytes (iCMs) has emerged as a promising therapeutic strategy to remuscularize injured myocardium. However, the intrinsic metabolic demands that drive the iCM program and maturity remain unclear. Here, we induce efficient iCM production and maturation through metabolic pathway modulations.

Read the full summary ↓

To explore the metabolic heterogeneity of iCMs, we performed single cell RNA sequencing (scRNA-seq) at reprograming day 14. Using single-cell metabolic flux estimation and flux balance analysis on day 14 iCM, we characterized the metabolic heterogeneity of iCMs and identified fatty acid oxidation (FAO) as a critical factor in iCM conversion. Mechanistically, we proved that Scd1 knockdown activates PGC1α/PPARβ transcription signal, which further promotes cardiac reprogramming, and induced cardiomyocytes demonstrated more frequent beating, calcium oscillation, and higher energy metabolism as evidenced by increased mitochondrial respiration and gene expression associated with FAO, which provides a new strategy and theoretical basis for cardiac regeneration and repair. Our findings collectively highlight FAO as a key determinant of iCM fate and offer new therapeutic avenues for advancing reprogramming strategies.

Published in

Enhanced fatty acid oxidation via SCD1 downregulation fuels cardiac reprogramming

Jia Z, Xiang L, Yu Z et al. · Molecular therapy : the journal of the American Society of Gene Therapy 2025 · PMID 40007118 · doi:10.1016/j.ymthe.2025.02.034

This dataset

Open GSE285211 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 GSE285211_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1201855 and SRA study SRP553287. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40007118) ↗

Study design

10 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 10 sample titles: 10 distinct titles with little repetition. 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

GSM8698418 Neo_CF, replicate 1, Day14
GSM8698419 Neo_CF, replicate 2, Day14
GSM8698420 Neo_iCM, MGT+DMSO replicate 1, Day14
GSM8698421 Neo_iCM, MGT+DMSO replicate 2, Day14
GSM8698422 Neo_iCM, MGT+ZLN005 replicate 1, Day14
GSM8698423 Neo_iCM, MGT+ZLN005 replicate 2, Day14
GSM8698424 Neo_iCM, MGT+GW501516 replicate 1, Day14
GSM8698425 Neo_iCM, MGT+GW501516 replicate 2, Day14
GSM8698426 Neo_CM, replicate 1, Day3
GSM8698427 Neo_CM, replicate 2, Day3

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