GEO series

Protocadherin 8 and transcription factor Dbx1 regulate the formation of developing cerebral cortex

GSE229603 Mus musculus (mouse) RNA-seq (gene expression) 2 samples Submitted 2024/10/13 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 2 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: 2 samples
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: Bidirectional interaction between protocadherin 8 and the transcription factor Dbx1 regulates cerebral cortex developmentDevelopment (Cambridge, England) · 2026

Summary (written by the submitters)

Normal development of the mammalian central nervous system requires correct tissue patterning, production of the appropriate cell types and establishment of functional neuronal circuits. Transcription factors (TFs) play essential roles in these processes, regulating the expression of target genes responsible for neuronal subtypes specific features.

Read the full summary ↓

Cell adhesion molecules are key components of neuronal identities that control cell sorting, migration, neurite outgrowth/guidance and synaptogenesis. So far, the link between cell adhesion and cell fate is not known TFs are known to control neuronal adhesion but not the opposite. Here, using acute gain- and loss-of-function experiments by in utero electroporation in the developing mouse telencephalon we demonstrate that ectopic expression of Dbx1, a homeodomain TF acting as a cell fate determinant, leads to increased expression of Protocadherin 8 (Pcdh8) and cell aggregation, together with the induction of neuronal fate markers Nr4a2 (Nurr1) and Pax6. These effects were are modulated depending on the region and timing of electroporation. Furthermore, we found that Pcdh8 expression is required for Dbx1-induced fate specification. Surprisingly, Pcdh8 overexpression also proved sufficient to induce Dbx1 expression as well as a complete reorganisation of the apico-basal polarity and dorso-ventral patterning. Finally, we present evidence that these effects are mediated through regulation of the expression of Notch ligands and promotion of cell cycle exit. Altogether, our work therefore points to cell adhesion molecules as unexpectedimportant, yet unexpected important, players in the regulation of cell identity and, in particular, Pcdh8 through its bidirectional action crossregulation with the Dbx1 transcription factor.

Published in

Bidirectional interaction between protocadherin 8 and the transcription factor Dbx1 regulates cerebral cortex development

Cwetsch AW, Ferreira S, Delberghe E et al. · Development (Cambridge, England) 2026 · PMID 41493231 · doi:10.1242/dev.205011

This dataset

Open GSE229603 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 GSE229603_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 PRJNA955124 and SRA study SRP432431. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41493231) ↗

Samples in this study

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+ 2 more — browse all 2 samples with per-sample file links →

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