PFC develop

Author

Hu Zheng

Published

2025-12-01

PFC develop

A single-cell spatiotemporal transcriptomic atlas of mouse prefrontal cortex maps dynamics of intratelencephalic neurons during postnatal development

Abstract

In early postnatal brain, the prefrontal cortex (PFC) remains immature and highly plastic, particularly for the intratelencephalic (IT) neurons. However, the spatiotemporal molecular and cellular dynamics of PFC during this period remain poorly characterized. Here, we performed spatiotemporal single-cell RNA analysis on mouse PFC during different postnatal time points and systematically delineated the molecular and cellular dynamics of mouse PFC during early postnatal development, among which IT neurons exhibit most dramatic alterations. Based on these comprehensive spatiotemporal atlases of PFC, we deciphered the time-specific molecular and cellular characteristics during the maturation process of IT neurons in PFC, particularly the dynamic expression programs of genes regulating axon development and synaptic formation, and the risk genes of neurological developmental diseases. Furthermore, we revealed the dynamic neuron-glia interaction patterns and the underlying signaling pathways during early postnatal period. Our study provided a comprehensive resource and important insights for PFC development and PFC-associated neurological diseases.

Data Visualization

We developed is a shiny application PFCdev-web that allows users to interactively access our data. You can access our online website at https://huggingface.co/spaces/TigerZheng/PFCdev-web

Users can browse the following content through the scRNAseq page:

Select dataset: Select datasets containing different cell types
Select celltype: Select different resolutions to view cell clusters on UMAP
Select gene: Select different genes to view their expression

Users can browse the following content through the spatial page:

Spatial Clustering: Select different cell subtypes to view their spatial distribution
Spatial Gene Expression: Select different genes to view their spatial expression

Code View

We compiled the code for this study using Quarto documentation, which contains the code for all the figures in this study. You can access the documents at https://zhengtiger.github.io/PFC_develop.

Citation

Our project has been released in the following publication:

Zheng H, Yan K, et al. A single-cell spatiotemporal transcriptomic atlas of mouse prefrontal cortex maps dynamics of intratelencephalic neurons during postnatal development. PLOS Biology.

# PFC develop {.unnumbered} A single-cell spatiotemporal transcriptomic atlas of mouse prefrontal cortex maps dynamics of intratelencephalic neurons during postnatal development <img src="https://github.com/ZhengTiger/picx-images-hosting/raw/master/PFCdev/Figure1A.3yer620cdm.webp" width="100%" /> ## Abstract In early postnatal brain, the prefrontal cortex (PFC) remains immature and highly plastic, particularly for the intratelencephalic (IT) neurons. However, the spatiotemporal molecular and cellular dynamics of PFC during this period remain poorly characterized. Here, we performed spatiotemporal single-cell RNA analysis on mouse PFC during different postnatal time points and systematically delineated the molecular and cellular dynamics of mouse PFC during early postnatal development, among which IT neurons exhibit most dramatic alterations. Based on these comprehensive spatiotemporal atlases of PFC, we deciphered the time-specific molecular and cellular characteristics during the maturation process of IT neurons in PFC, particularly the dynamic expression programs of genes regulating axon development and synaptic formation, and the risk genes of neurological developmental diseases. Furthermore, we revealed the dynamic neuron-glia interaction patterns and the underlying signaling pathways during early postnatal period. Our study provided a comprehensive resource and important insights for PFC development and PFC-associated neurological diseases. ## Data Visualization We developed is a shiny application **PFCdev-web** that allows users to interactively access our data. You can access our online website at <https://huggingface.co/spaces/TigerZheng/PFCdev-web> ![movie](images/PFCdev-demo.gif) Users can browse the following content through the scRNAseq page: - Select dataset: Select datasets containing different cell types - Select celltype: Select different resolutions to view cell clusters on UMAP - Select gene: Select different genes to view their expression Users can browse the following content through the spatial page: - Spatial Clustering: Select different cell subtypes to view their spatial distribution - Spatial Gene Expression: Select different genes to view their spatial expression ## Code View We compiled the code for this study using Quarto documentation, which contains the code for all the figures in this study. You can access the documents at <https://zhengtiger.github.io/PFC_develop>. ## Citation Our project has been released in the following publication: ``` Zheng H, Yan K, et al. A single-cell spatiotemporal transcriptomic atlas of mouse prefrontal cortex maps dynamics of intratelencephalic neurons during postnatal development. PLOS Biology. ```