GEO series

DDX3X-Mediated Translation of Structured Cardiac mRNAs is Essential for Female Heart Development [Ribo-Seq]

GSE318098 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/04/27 Platform GPL30172

At a glance

RNA-seq (gene expression) · mouse · 12 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: 12 samples: 3 × WT E10.5 Female RNA-Seq vs 3 × Ddx3x CM-KO E10.5 Female RNA-Seq vs 3 × WT E10.5 Female RPF-Seq vs 3 × Ddx3x CM-KO E10.5 Female RPF-SeqGroups 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.

Summary (written by the submitters)

Sex differences influence congenital heart disease (CHD) development, yet underlying molecular mechanisms remain largely unclear. We demonstrate that the X-linked RNA helicase DDX3X associates in the heart with ribosomal subunit proteins, and eCLIP mapping reveals its preferential binding to cardiac mRNAs with long, structured 5′ untranslated regions (5′UTRs) that can hinder translation.

Read the full summary ↓

Using a cardiomyocyte-specific mouse Ddx3x knockout model, we show that female embryos lacking Ddx3x die at mid-gestation from heart failure due to impaired translation of key cardiac regulators, whereas male littermates survive. Ribosome profiling and proteomics demonstrate that DDX3X is required for efficient translation of female-differential cardiac mRNAs. Reporter assays confirm that translation of essential cardiac genes such as Srf and Rcor2 depends on their 5′ UTRs and requires DDX3X. These findings uncover a sex-specific post-transcriptional mechanism by which DDX3X safeguards female heart development through selective mRNA translation, providing insight into how X-linked dosage-sensitive regulators contribute to CHD.

This dataset

Open GSE318098 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 GSE318098_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 PRJNA1416463 and SRA study SRP670914. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

3 × WT E10.5 Female RNA-Seq vs 3 × Ddx3x CM-KO E10.5 Female RNA-Seq vs 3 × WT E10.5 Female RPF-Seq vs 3 × Ddx3x CM-KO E10.5 Female RPF-Seq

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM9486151 WT E10.5 Female RNA-Seq Rep 1 WT E10.5 Female RNA-Seq
GSM9486152 WT E10.5 Female RNA-Seq Rep 2 WT E10.5 Female RNA-Seq
GSM9486153 WT E10.5 Female RNA-Seq Rep 3 WT E10.5 Female RNA-Seq
GSM9486154 Ddx3x CM-KO E10.5 Female RNA-Seq Rep 1 Ddx3x CM-KO E10.5 Femal…
GSM9486155 Ddx3x CM-KO E10.5 Female RNA-Seq Rep 2 Ddx3x CM-KO E10.5 Femal…
GSM9486156 Ddx3x CM-KO E10.5 Female RNA-Seq Rep 3 Ddx3x CM-KO E10.5 Femal…
GSM9486157 WT E10.5 Female RPF-Seq Rep 1 WT E10.5 Female RPF-Seq
GSM9486158 WT E10.5 Female RPF-Seq Rep 2 WT E10.5 Female RPF-Seq
GSM9486159 WT E10.5 Female RPF-Seq Rep 3 WT E10.5 Female RPF-Seq
GSM9486160 Ddx3x CM-KO E10.5 Female RPF-Seq Rep 1 Ddx3x CM-KO E10.5 Femal…
GSM9486161 Ddx3x CM-KO E10.5 Female RPF-Seq Rep 2 Ddx3x CM-KO E10.5 Femal…
GSM9486162 Ddx3x CM-KO E10.5 Female RPF-Seq Rep 3 Ddx3x CM-KO E10.5 Femal…

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