-BIOINFORMATICS AND COMPUTATIONAL BIOLOGY CORE: The Bioinformatics and Computational Biology Core will support all three Projects and the Single-Cell Transcriptomics and Epigenetics Core (SCTE) in a range of activities related to data processing, storage, distribution and integrative analysis. A key role of the Core is to provide a centralized portal for integrative analysis of the different omics data (RNA-seq, ChIP-seq and ATAC-seq) to be generated by the Projects and SCTE Core. The goal is to illuminate the transcriptomic and epigenomic landscape of T cells in response to acute and chronic viral infection, and uncover the critical regulators that determine the state or fate of T cells. The Core will utilize advanced bioinformatics tools for the high-dimensional data matrices generated at different stages of the immune response and in distinct tissues by the Program Project and will apply innovative techniques to discover core regulators. The Core will assist the three Projects and SCTE Core for experimental design, and work closely with the other Investigators to analyze individual data sets and also the combined data set. In particular, the Core will establish a data deposit, tracking, storage and distribution system to allow data sharing and sample tracking among all the participating laboratories. The Core will also establish three bioinformatics pipelines to process RNA-seq, ChIP-seq and ATAC-seq data respectively, including sequencing read mapping, quality control and peak calling. Advanced analyses such as enhancer prediction, motif analysis and genetic network analysis will also be conducted to reveal the key regulators critical for defining particular T cell states.
