Research Progress in Area 1 方向 ( 一 ) 課題進展 85 Abstract Single-cell genomics and transcriptomics have become an essential and powerful tool for biological research in recent years. One of the key advantages of single-cell studies is being able to obtain unbiased global measurements of important biomolecules such as DNA and RNA, rather than a few targeted ones, while preserving information about the sample or population heterogeneity. Despite having made immense impact in mammalian biology discovery, there is currently little effort to develop singlecell genomics platform tools for discovery in marine organisms. Prof. Wu proposes to develop a versatile microfluidic platform along with the necessary molecular biology tools that can be used to profile diverse marine microbes. In addition, her research aims are to implement methods for microfluidic high-throughput singlecell RNA-seq of cells from deep sea organisms. Research Activities and Progress • Successfully isolated single nuclei from frozen deep sea clam A. marissinica specimen and performed high-throughput single-nuclei RNA-sequencing (over 10,000 cells) to assess the heterogeneity of cell types in the gill and foot of the organism; • We also successfully isolated fixed whole cells from several other deep sea specimens that were preserved in-situ, and were able to obtain intact transcriptomes from these cells for single-cell sequencing; • Performed single embryo RNA-sequencing on a unique local sea urchin species ( H. crassispina) to investigate individual-wise differences in transcriptomic response to pH stress during embryonic development; • De novo assembly of H. crassispina genome and transcriptome. Key Findings • We are able to use frozen samples of A. marissinica collected from the deep sea to generate an atlas of the cell types in the gill and foot of the clam, and are able to identify cell clusters that express genes associated with the host-endosymbiont metabolic process. Work is on-going to further analyze this data and investigate the cellular heterogeneity; • We identified paternal lineage-specific gene expression programs in H. crassispina embryos subject to pH stress. On-going analysis is being done to further define these programs; • High quality assembly of H. crassispina genome and transcriptomes were generated for the first time. Research Output Publication 3 Trained personnel 5 Novel Genomics and Transcriptomics Technologies for Single Cell Manipulation and Analysis of Marine Organisms Prof. Angela Ruohao Wu The Hong Kong University of Science and Technology Fig 1. Workflow of deep sea organism cell isolation and sequencing. Smart-Seq2 bulk ands inglec ell 10Xg enomics Dounce homogenization Nuclei extract FACS sorting
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