A Curated Compendium of Transcriptomic Data for the Exploration of Neocortical Development

• DOI: 10.1101/2024.02.26.581612
• Publication Date: 2024-02-29T00:35:12Z
• Authors: Shreyash Sonthalia; Ricky S. Adkins; Joshua Orvis; Guangyan Li; Xoel Mato Blanco; Alex Casella; Jinrui Liu; Genevieve Stein-O...; 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

Abstract Vast quantities of multi-omic data have been produced to characterize the development and diversity cell types in cerebral cortex humans other mammals. To more fully harness collective discovery potential these data, we assembled gene-level transcriptomic from 188 published studies neocortical development, including transcriptomes ∼30 million single-cells, extensive spatial experiments RNA sequencing sorted cells bulk tissues: nemoanalytics.org/landing/neocortex . Applying joint matrix decomposition ( SJD ) mouse, macaque human this collection, defined transcriptome dynamics that are conserved across mammalian neurogenesis which elucidate evolution outer, or basal, radial glial cells. Decomposition adult identified layer-specific signatures mature neurons and, combination with transfer learning methods NeMO Analytics, enabled charting their early developmental emergence protracted maturation years postnatal life. Interrogation organoids demonstrated while broad molecular elements vivo recapitulated vitro , many programs neuronal absent. We invite computational biologists without coding expertise use Analytics research fuel it emerging carlocolantuoni.org ).