Single Cell Analysis Core

University Of California-Irvine, Irvine CA

Investigators

Abstract

The overarching theme of this program project entitled “Tipping points in cancer” is to investigate the role of critical transitions, especially stochastic non-genetic transitions, in the initiation and progression of cancer. To support this goal, the program will develop a Single Cell Analysis Core (SCAC) to focus on the complex aspects of omics data originating from Project 1-3. This core will provide data analysis, modeling and training support for the program. High throughput multi-omics are a rich source of insights as to cell types, cell states, and cellular interactions. Because of its inherent heterogeneity and instability, cancer represents a uniquely complex community of cells in genetic, epigenetic, proteomic, metabolic and spatial and temporal dimensions. The goal of this core is to work closely with investigators and their laboratory staff to provide a high level of computational expertise for strategic planning of experiments, rigorous analysis of the data from experiments, feedback for refinement of experimental strategies, and integration of data within and across project areas into testable models of cancer development and metastasis. Insights from single cell experiments will incorporate multi-omic data documenting cell types, cell states, and transition dynamics. This will be accomplished through four specific aims: 1) provide computational guidance and integrated platforms for the analysis of state-of-the-art genomic technologies for genome, transcriptome, epi-genome profiling and spatial omics along with dedicated staff time and associated analytics to advance cancer research; 2) support for development of computational tools and promote innovation and facilitate development in multi omics and spatial omics analysis to foster understanding of cellular heterogeneities, cell-cell communication and cell state transition in cancer to address outstanding problems in single-cell data analysis; 3) robust training across all levels of research development to ensure basic skills, best practices and ability to interact effectively across biological and computational cultural divides; and 4) work with the Administrative core to support data sharing conventions and strategies for sharing across the cancer research community. This core will be directed by Dr. Jenny Wu, PhD, an accomplished computational biologist who has worked with the Genomics Research and Technology Hub (GRTH, formerly GHTF) for more than ten years and the UCI U54 Cancer Systems Biology Center for more than five years, and is knowledgeable about the key biological questions posed, as well as the multiple computational approaches demanded. Specifically, in her role as Director of the Single Cell Analysis Core (SCAC), she will continue to participate in the weekly project leader meetings, organize training in application of bioinformatics tools to multi-omics and modeling, and interface with UCI Center for Multiscale Cell Fate research (CMCF). She and staff will also participate in individual meetings with Project 1-3 and work with individual researchers through one-on-one consultation as needed.