Core C Transcriptomics

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Project Summary/Abstract Transcriptomic Core (C) provides critical state-of-the-art services to support all of the Projects in this proposal. Core C will apply whole cell and nuclear single cell transcriptomics to evaluate molecular identity and activated gene networks in specific neural and non-neural human brain cells, and will use cutting-edge `Large area spatial transcriptomics (LaST)' to map gene expression across cell types and brain regions at key stages of human 3rd trimester-term neonatal brain development. The use of these technologies will advance our understanding of the mechanisms of cell lineage development in preterm and term neonatal human brain and serve as a high-resolution molecular map against which to measure how perinatal injuries, such as hypoxic ischemic encephalopathy (HIE) impact the development of the brain. Additionally, Core C will work with project leaders to develop a battery of novel cell-specific markers for already defined cell types, such as neural progenitor cells, newly born neurons, microglia, and glial cell lineages, as well as novel markers that will serve as tools to identify and characterize the newly-described cell types of the neonatal human brain such as the migrating neuronal streams that have already been discovered during the initial tenure of this proposal. Core C will be directed jointly by Drs. Kriegstein and Rowitch who have expertise in human brain development and in single cell transcriptomics and spatial transcriptomics respectively. Dr. Kriegstein will provide oversight and guidance of day-to-day operations, scheduling and experimental design. Dr. Kriegstein's laboratory has developed and validated both single cell and single nuclei mRNA sequencing technology recently documented in two joint publications with the Rowitch laboratory (Velmeshev et al, Science, 2019; Schirmer et al, Nature 2019); the Rowitch laboratory has designed a unique pathway for Large-area spatial transcriptomic (LaST) mapping of mouse and human brain (Bayraktar et al., 2019, Nat Neurosci; Schirmer et al, Nature 2019);. The combined use of both of these technologies will enable Projects 1-3 to molecularly profile diverse cell types including interneurons, oligodendrocytes, and microglia, discover new cell type specific markers, and map the in situ expression patterns of genes identified through single cell mRNA sequencing. The Core Directors, assisted by Dr. Dmitry Velmeshev, a talented bio-informatician who will serve as Core Manager, have developed an organizational scheme for Core C that is designed to meet the complementary needs of all the projects. They will also assist project leaders and trainees in the PPG in order to optimize design and execution of their single cell sequencing and mapping projects. In addition, Core C will work with the Scientific Advisory Committee to maintain the highest standard of quality control and with the Administrative Core (Core A) to manage operational and budgetary issues. Core C will provide critical support to help achieve the goals of Projects 1-3 that will, together, provide new insights into human brain development at clinically important neonatal stages of development.