Core C - Functional Genomics and Computational Biology Core

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CORE SUMMARY The overall goal of this PPG application is to compare and contrast the mechanisms by which the inhibitory receptors PD1 and LAG3 operate on T cells in the context of tolerance and autoimmunity, cancer, and chronic infection. One major approach to be used throughout the studies is the application of genome-wide transcriptional profiling. The purpose of the Functional Genomics and Computational Biology Core (Core C) is to provide essential and centralized sequencing-based genomics services for all three Projects in this Program. In addition, this Core will operate provide the service of a retroviral (RV)-enforced expression and knockdown platform that can directly test in vivo individual genes and pathways identified from computational analyses. Thus, Core C will provide integrated bioinformatic and computational analytical platforms and data integration services coupled to downstream RV-enforced expression and knockdown as well as in vivo CRISPR/Cas9-focused genetic screening. The Aims are: AIM 1: To provide initial data hosting, normalization, preprocessing, and analysis as well as perform cross-Project data integration and computational network modeling for bulk and single-cell transcriptomic and epigenetic datasets. Core C will (i) provide raw data QC, data cleaning, pre-processing, and generation of files for downstream analyses as well as operate a web portal interface for user exploration of the data; (ii) perform primary and secondary genomics data analyses; and (iii) perform network and integrated analyses including. The Core also will support and/or develop new analytical tools as technologies become available (as for scRNA-seq in the last cycle). AIM 2: To enable in vivo CRISPR/Cas9 screening and provide an RV-enforced expression and knowckdown platform for downstream in vivo interrogation of genes and pathways regulated by PD-1 and/or LAG3. Core C will aid in design of CRISPR screening libraries for in vivo CRISPR screening platforms by the Projects as well as downstream data analysis. Core C will also provide an in vivo retroviral platform to enforce expression or shRNA knock-down of high-priority GOIs. By its nature, Core C is highly interactive with other components of this PPG. Samples from Projects 1, 2, and 3 will enter Core C, which will analyze samples with input from the Projects and integrate results among the three Projects. Core C will interact heavily with Cores A, B, and D for administrative support and to identify gene targets for novel mouse strains and immunostaining analysis.