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A new mouse mutant with a discrete mutation in Pcdhgc5 reveals that the Protocadherin gC5 isoform is not essential for dendrite arborization in the cerebral cortex

GSE310953 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/01/28 Platform GPL24247
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: 5 × cerebral cortex 4-week wild-type male vs 3 × cerebral cortex 4-week mutant female vs 3 × cerebral cortex 4-week mutant maleGroups 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
A new mouse mutant with a discrete mutation in Pcdhgc5 reveals that the Protocadherin γC5 isoform is not essential for dendrite arborization in the cerebral cortexPloS one · 2026
Summary (written by the submitters)
There are ~60 clustered protocadherin (cPcdh) isoforms expressed from three gene clusters (Pcdha, Pcdhb, Pcdhg) arrayed in tandem across nearly 1 Mb in mammals. cPcdhs are homophilic cell adhesion molecules (CAMs) critical for a host of neural developmental functions consistent with a role in cell-cell recognition. Indeed, isoforms make recognition modules in combination to generate recognition diversity far exceeding the ~60 individual CAMs.
Read the full summary ↓
However, there is also growing evidence for specialized functions for specific isoforms, particularly the C-type isoforms found at the 3’ ends of the Pcdha cluster (aC1 and aC2) and at the 3’ end of the Pcdhg cluster (gC3, gC4, and gC5). We have previously described unique roles for gC3 in dendrite arborization in the cerebral cortex and neural circuit formation in the spinal cord, as well as for gC4 in neuronal survival. Here we report a new mouse mutant specifically targeting the Pcdhgc5 exon encoding gC5. Unlike the rest of the Pcdhg cluster, expression of this isoform does not begin until postnatal stages of mouse development, increasing in the second week of life, suggesting specialized roles. We found significant expression changes in gene pathways involved in synaptic activity, learning and memory, and cognition. Despite this, we saw no major disruption in the cerebral cortex in neuronal organization, survival, dendritic arborization, or synaptic protein expression in these mutants. This new model will be an important tool for future studies delineating specific functions for gC5.
Published in
A new mouse mutant with a discrete mutation in Pcdhgc5 reveals that the Protocadherin γC5 isoform is not essential for dendrite arborization in the cerebral cortex
Hanes CM, Steffen DM, Murray GC et al. · PloS one 2026 · PMID 41818197 · doi:10.1371/journal.pone.0344863
This dataset
Open GSE310953 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 GSE310953_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 PRJNA1367595 and SRA study SRP648298. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41818197) ↗
Study design
5 × cerebral cortex 4-week wild-type male vs 3 × cerebral cortex 4-week mutant female vs 3 × cerebral cortex 4-week mutant male

Supports a case/control comparison: 6 samples read as cases, 6 as controls.

How we read this: 3 replicated groups read from 12 sample titles; they account for 11 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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