Welcome to CoDex (Cortical Development Expression) viewer! This resource comprises a single-cell expression dataset of the developing human neocortex. Here you can explore the dataset using heatmaps, tSNE’s, distribution graphs and statistical summary tables. In addition, you can explore which genes are differentially expressed for a given cell type during cortical development.
|Schematic of the developing human neocortex. VZ: ventricular zone; iSVZ: inner subventricular zone; oSVZ: outer subventricular zone; IZ: intermediate zone; SP: subplate; CPi: inner cortical plate; CPo: outer cortical plate; RG: radial glia; IP: intermediate progenitor; MN: newborn migrating excitatory neuron; EN: excitatory neuron; IN: interneuron; O: oligodendrocyte precursor; E: endothelial cell; P: pericyte; M: microglia.||Scatter plot visualization of cells after t-stochastic neighbor embedding (tSNE), colored by cell type annotation.|
This dataset was generated by Geschwind Lab. This webtool was built using R Shiny by Andrew Elkins. To view our associated publication:A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation
Damon Polioudakis†, Luis de la Torre-Ubieta†, Justin Langerman, Andrew G. Elkins, Xu Shi, Jason L. Stein, Celine K. Vuong, Susanne Nichterwitz, Melinda Gevorgian, Carli K. Opland, Daning Lu, William Connell, Elizabeth K. Ruzzo, Jennifer K. Lowe, Tarik Hadzic, Flora I. Hinz, Shan Sabri, William E. Lowry, Mark B. Gerstein, Kathrin Plath, Daniel H. Geschwind
We performed RNA sequencing on 40,000 cells to create a high-resolution single-cell gene expression atlas of developing human cortex, providing the first single-cell characterization of previously uncharacterized cell types, including human sub-plate neurons, comparisons with bulk tissue, and systematic analyses of technical factors. These data permit deconvolution of regulatory networks connecting regulatory elements and transcriptional drivers to single-cell gene expression programs, significantly extending our understanding of human neurogenesis, cortical evolution, and the cellular basis of neuropsychiatric disease. We tie cell-cycle progression with early cell fate decisions during neurogenesis, demonstrating that differentiation occurs on a transcriptomic continuum; rather than only expressing a few transcription factors that drive cell fates, differentiating cells express broad, mixed cell-type transcriptomes before telophase.By mapping neuropsychiatric disease genes to cell types, we implicate dysregulation of specific cell types in ASD, ID, and epilepsy. We developed CoDEx, an online portal to facilitate data access and browsing.
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