Human Lung Cell Atlas Human Lung Cell Atlas Dr. Shepherds focus on this project will be to develop molecular and optical methods to image multiple RNA and protein within intact human lung tissue. This task will involve the integration of optical tissue clearing, cell maker selection from single cell RNA-Seq data, whole tissue fluorescent labeling of selected markers, development of 3D optical methods (specifically light sheet microscopy), performing 3D/4D microscopy of fixed lung tissue, volumetric image analysis, and interpretation. These experiments will assist other team members on generating a spatial cell atlas in the human lung. Dr. Shepherd will commit approximately 0.6 academic months per year to the project, and he will directly supervise a lab manager at Arizona State University in years 2 and 3 of the project. Human Lung Cell Atlas - Revision - 1 Dr. Shepherds focus on this project will be to develop and apply the computational, biochemical, optical imaging, and data analysis tools necessary for iterative multiplexed in situ hybridization in human lung tissue. This task will involve the integration of optical tissue clearing, target gene selection from single cell RNA-Seq data, custom encoding probe panel design, custom amplified readout probe design, custom encoding probe panel amplification and purification, gel embedding, digestion, clearing, and cross linking of human lung tissue, modification of unique 3D optical methods (specifically high numerical aperture single objective light sheet microscopy), performing iterative multiplexed 3D microscopy of human lung tissue, data analysis pipeline for approaching petabyte level data, and distributing data to members of the Human Lung Cell Atlas v1.0 consortium. Initial trial in Y1 showed sufficient progress to justify expanded work at the ASU performance site. We will purchase all needed supplies for iterative multiplexed labeling of RNA in human lung tissue. Salaries are increased to design, perform, and analyze experiments.
|Effective start/end date||7/1/19 → 6/30/22|
- Chan Zuckerberg Initiative (CZI): $327,519.00
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