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Impaired cortical development and translational control in a missense mouse model of DDX3X syndrome

GSE296911 Mus musculus (mouse) RNA-seq (gene expression) 36 samples Submitted 2025/11/17 Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 36 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
36 samples: 12 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.
Summary (written by the submitters)
Heterozygous mutations in the X-linked RNA helicase DDX3X cause DDX3X syndrome, a rare neurodevelopmental disorder associated with cortical malformation and autism. Amongst the ~200 known de novo DDX3X variants, half are missense while the others are predicted loss-of-function (LoF). LoF mouse models reveal DDX3X loss impairs progenitors’ ability to generate excitatory neurons.
Read the full summary ↓
Yet, how missense mutations impact corticogenesis in vivo is unknown. Here, we generated a conditional mouse model of Ddx3xT532M, a clinically severe and recurrent DDX3X syndrome mutation found in females. Using Cre-mediated expression of Ddx3xT532M in cortical progenitors and their progeny, we show this mutation alters corticogenesis and translation. Ddx3xT532M conditional knock-in (KI) males have severe microcephaly and apoptosis. In contrast, Ddx3xT532M conditional heterozygous (cHet) females exhibit only mild reductions in cortical size and neurogenesis. Using polysome fractionation of Ddx3xT532M and Ddx3xLoF cHet female cortices, we discover that Ddx3xT532M affects translation of key targets, with qualitative differences from Ddx3xLoF cHet females. Collectively, these cellular and molecular findings suggest that, the clinically severe Ddx3xT532M variant in cHet females is phenotypically similar to, but molecularly distinct from, Ddx3x haploinsufficiency in corticogenesis. Our study establishes a new model for understanding how missense mutations may cause DDX3X syndrome.
This dataset
Open GSE296911 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 GSE296911_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 PRJNA1261923 and SRA study SRP584635. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
12 conditions, mostly in triplicate
CtrlF_LoF_input ×3 cHetF_LoF_input ×3 CtrlF_LoF_mono ×3 cHetF_LoF_mono ×3 CtrlF_LoF_poly ×3 cHetF_LoF_poly ×3 CtrlF_T532M_input ×3 cHetF_T532M_input ×3 +4 more

Supports a between-group comparison across 36 samples.

How we read this: 12 replicated groups read from 36 sample titles; they account for 36 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
Datasets on a similar topic

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