BICAN: Cell Census of Developing Brain
A Curated Compendium of Transcriptomic Data for the Exploration of Neocortical Development
companion
Authors
Shreyash Sonthalia, Ricky S. Adkins, Joshua Orvis, Guangyan Li, Xoel Mato Blanco, Alex Casella, Jinrui Liu, Genevieve Stein-O’Brien, Brian Caffo, Ronna Hertzano, Anup Mahurkar, Jesse Gillis, Jonathan Werner, Shaojie Ma, Nicola Micali, Nenad Sestan, Pasko Rakic, Gabriel Santpere, Seth A. Ament, Carlo Colantuoni
Citation
Sonthalia, S., et al. A curated compedium of transcriptomic data for the exploration of neocortical development. bioRxiv (2024).
Summary
We have assembled a curated compendium of public multi-omic data for the exploration of neocortical development in NeMO Analytics. Applying our joint matrix decomposition approaches, we perform an in silico transcriptomic dissection of neocortical excitatory neurogenesis, identifying conserved molecular dynamics in mammalian neurogenesis, as well as primate-specific programs. While the transcription factors that initiate laminar neuronal identities are expressed very early, we elucidate the prolonged maturational trajectories of layer-specific neurons in vivo and in pluripotent stem cell derived neural organoid models.
Data and Tools
Resource Name | Resource URL | Description |
|---|---|---|
NeMO Analytics | https://nemoanalytics.org/landing/neocortex/ | Data Exploration: Neocortex Devo Landing Page. Gene-level transcriptomic data from 188 published studies of neocortical development, including >33 million single cell transcriptomics, and spatial transcriptomic data. |