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Effect of knocking down CERS2 or a double knockdown (KD) CERS5/6 in ventricular cardiomyocytes on gene expression under conditions of hypertrophy induced by phorbol 12-myristate 13-acetate (PMA) or controls.

GSE285142 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2025/08/27 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 24 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
24 samples: 8 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.
Paper
Selective Knockdown of Ceramide Synthases Reveals Opposite Roles of Different Ceramide Species in Cardiac HomeostasisMetabolites · 2025
Summary (written by the submitters)
Sphingolipids are an important class of lipids that play imperative structural and functional roles in the body. Ceramides constitute the central essential structural backbone of more complex sphingolipids, thus alterations in the genes that regulate their expression could dysregulate the entire cellular sphingolipid metabolic scheme.
Read the full summary ↓
The fatty acid acylated to the sphingosine backbones distinguishes ceramide species both structurally and functionally. Higher plasma concentrations of 16:0 ceramide are associated with an increased risk of heart failure, while higher concentrations of 22:0 plus 24:0 ceramide are associated with lower risk. Here, we silenced the ceramide synthase genes (CERS) responsible for the production of long-chain (LC) 16:0 ceramide (CERS5/6) or very long-chain (VLC) 22:0 and 24:0 ceramide (CERS2) in immortalized human ventricular cardiomyocytes and examined how these silenced genes altered the cardiomyocyte’s ability to maintain homeostasis in control conditions and under cardiac hypertrophy in response to PMA treatment. Taken together, our data provides support for the importance of the different ceramide species in maintaining cardiovascular homeostasis and in the development and progression of cardiac hypertrophy.
Published in
Selective Knockdown of Ceramide Synthases Reveals Opposite Roles of Different Ceramide Species in Cardiac Homeostasis
Wiley AM, Krueger MA, Becker JO et al. · Metabolites 2025 · PMID 41002968 · doi:10.3390/metabo15090584
This dataset
Open GSE285142 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 GSE285142_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 PRJNA1201240 and SRA study SRP553076. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41002968) ↗
Study design
8 conditions, mostly in triplicate
CERS2 KD, vehicle treatment, ×3 CERS2 KD, PMA treatment, ×3 Scramble control, vehicle treatment, ×3 Scramble control, PMA treatment, ×3 CERS5.6 KD, vehicle treatment, ×3 CERS5.6 KD, PMA treatment, ×3 Silencer negative control, vehicle treatment, ×3 Silencer negative control, PMA treatment, ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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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