GEO series

PTEN mutations impair CSF dynamics and cortical networks by dysregulating periventricular neural progenitors

GSE280368 Mus musculus (mouse) RNA-seq (gene expression) 14 samples Submitted 2025/04/01 Platform GPL19057

At a glance

RNA-seq (gene expression) · mouse · 14 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: 14 samples: 14 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: PTEN mutations impair CSF dynamics and cortical networks by dysregulating periventricular neural progenitorsNature neuroscience · 2025

Summary (written by the submitters)

Enlargement of the cerebrospinal fluid (CSF)-filled brain ventricles (ventriculomegaly) is a defining feature of congenital hydrocephalus (CH) and an underrecognized concomitant of autism. Here, we show that de novo mutations in the autism risk gene, PTEN, are among the most frequent monogenic causes of CH and primary ventriculomegaly.

Read the full summary ↓

Mouse Pten-mutant ventriculomegaly results from aqueductal stenosis due to hyperproliferation of periventricular Nkx2.1+ neuroprogenitor cells (NPCs) and increased CSF production from hyperplastic choroid plexus. Pten-mutant ventriculomegalic cortices exhibit network dysfunction from increased activity of Nkx2.1+ NPC-derived inhibitory interneurons. Raptor deletion or post-natal everolimus treatment corrects ventriculomegaly, rescues cortical deficits, and increases survival by antagonizing mTORC1-dependent Nkx2.1+ NPC pathology. Thus, PTEN mutations concurrently alter CSF dynamics and cortical networks by dysregulating Nkx2.1+ NPCs. These results implicate a non-surgical treatment for CH, demonstrate a genetic association of ventriculomegaly and ASD, and help explain neurodevelopmental phenotypes refractory to CSF shunting in select CH patients.

Published in

PTEN mutations impair CSF dynamics and cortical networks by dysregulating periventricular neural progenitors

DeSpenza T Jr, Kiziltug E, Allington G et al. · Nature neuroscience 2025 · PMID 39994410 · doi:10.1038/s41593-024-01865-3

This dataset

Open GSE280368 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 GSE280368_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 PRJNA1178102 and SRA study SRP540987. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39994410) ↗

Study design

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

Supports a case/control comparison: 7 samples read as cases, 7 as controls.

How we read this: Read from 14 sample titles: 14 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

GSM8595688 Control Choroid replica scRNAseq
GSM8595689 PTEN knockout Choroid replica scRNAseq
GSM8595690 Control Cortex replica 1 snRNAseq
GSM8595691 Control Cortex replica 2 snRNAseq
GSM8595692 Control Cortex replica 3 snRNAseq
GSM8595693 PTEN knockout Cortex replica 1 snRNAseq
GSM8595694 PTEN knockout Cortex replica 2 snRNAseq
GSM8595695 PTEN knockout Cortex replica 3 snRNAseq
GSM8595696 Control Svz replica 1 snRNAseq
GSM8595697 Control Svz replica 2 snRNAseq
GSM8595698 Control Svz replica 3 snRNAseq
GSM8595699 PTEN knockout Svz replica 1 snRNAseq
GSM8595700 PTEN knockout Svz replica 2 snRNAseq
GSM8595701 PTEN knockout Svz replica 3 snRNAseq

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.