Transcriptome & Networks Analysis Core

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Project Summary – Core B: TRANSCRIPTOME AND NETWORK ANALYSIS CORE The advent of high-throughput omics technologies enables powerful analyses of cellular transcriptional programs, gene-function relationships and genome-wide surveys at unprecedented detail. Individual investigators face many hurdles in implementing these new technologies and effectively translating these large datasets into mechanistic understanding of molecular pathways. The goal of the Transcriptome and Network Analysis Core (TNAC) is to facilitate the effective use of omics technologists and the downstream bioinformatics analyses. This core leverages the expertise of Dr. Gonzalez Hernandez, Director of the SDSU Genomics Sequencing Facility, with expertise in genetics and genomics analysis, and Dr. Xijin Ge, experienced bioinformatician and biomedical researcher. Specifically, this core will enable the project leads to use the following technology to study inflammation: RNA sequencing (RNA-seq), CRISPR whole genome screening, spatially resolved RNA-seq, and proteomics. The TNAC has 3 specific aims: 1) Transcriptomic analyses by conventional RNA-Seq and deep sequencing for analysis of CRISPR insertions; 2) The use of spatially resolved and single cell RNA-seq technology and associated bioinformatics workflows; and 3) Data integration and extensive pathway analysis using and adapting bioinformatics tools and resources, including those developed by Dr. Xijin Ge, to construct gene regulatory networks underlying inflammation, integrate proteomics data, and conduct meta-analysis of data generated by the three projects alongside data in the public domain. This core is innovative in that it brings together cutting-edge experimental technology with the latest bioinformatics tools and approaches. Working closely with the four project leads, this core will exemplify interdisciplinary collaboration, and significantly promote the adoption of cutting-edge technologies among biomedical researchers in the region.