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The intracellular domain of the epilepsy protein PCDH19 regulates spine density in cortical neurons in vivo via Xlr genes.

GSE333999 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/07/01 Platform GPL19057
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 × mESC-derived cortical neurons, day in vitro 8, WT, vs 3 × mESC-derived cortical neurons, day in vitro 8, PCDH19-ICD-OE, vs 3 × mESC-derived cortical neurons, day in vitro 12, WT, vs 3 × mESC-derived cortical neurons, day in vitro 12, PCDH19-ICD-OE,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
The intracellular domain of the epilepsy protein PCDH19 regulates spine density in cortical neurons in vivo via Xlr genesThe Journal of neuroscience : the official journal of the Society for Neuroscience · 2026
Summary (written by the submitters)
Mosaic mutations in the X-linked cell adhesion molecule Protocadherin 19 (PCDH19) lead to epilepsy with cognitive impairment, whereas complete absence of functional protein, although possibly linked to autistic features, does not elicit any seizures. It is believed that mosaic expression of PCDH19 leads to defective neuronal communication, but whether further roles beyond cell adhesion are critical for PCDH19 function in the cortex is currently unknown.
Read the full summary ↓
We confirm that the proteolytic processing of PCDH19, previously described in hippocampal neurons, also takes place in mouse cortical neurons in vivo and show that nuclear transport of its intracellular domain is mediated by importins. RNAseq analysis further indicates that the intracellular domain of PCDH19 leads to broad transcriptomic changes. Finally, we use in utero electroporation to provide the first in vivo data about the role of this cleaved intracellular domain in upper layer cortical neurons of male and female mice, where it reduces spine density through an increase in Xlr gene expression without affecting overall dendritic morphology. Our results suggest that PCDH19 could act as an activity sensor in a synapse to nucleus signalling pathway involved in synaptic homeostasis.
Published in
The intracellular domain of the epilepsy protein PCDH19 regulates spine density in cortical neurons in vivo via Xlr genes
Newbold SA, Becerra-Espinosa V, Fabra-Beser J et al. · The Journal of neuroscience : the official journal of the Society for Neuroscience 2026 · PMID 42303573 · doi:10.1523/JNEUROSCI.2030-23.2026
This dataset
Open GSE333999 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 GSE333999_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 PRJNA1473363 and SRA study SRP705893. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42303573) ↗
Study design
3 × mESC-derived cortical neurons, day in vitro 8, WT, vs 3 × mESC-derived cortical neurons, day in vitro 8, PCDH19-ICD-OE, vs 3 × mESC-derived cortical neurons, day in vitro 12, WT, vs 3 × mESC-derived cortical neurons, day in vitro 12, PCDH19-ICD-OE,

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
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