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Principal Investigator: Michael Gale
Organization: OREGON HEALTH & SCIENCE UNIVERSITY
Fiscal Year: 2024
Award: $1,164,339
Funding agency: National Institute of Allergy and Infectious Diseases
CORE D PROJECT SUMMARY
The `Omics, Bioinformatics, and Data Management Core (Core D) serves this Program by providing high
resolution functional genomics and bioinformatics computation analyses with statistical integration. The main
objective of the Core is to define the gene expression signatures and their functional output that program the
immune response for 68-1 RhCMV/SIV vaccine mediated SIV replication arrest in pre-clinical rhesus macaque
(RM) vaccine studies. The Core will interrogate single CD8+ T cells in blood and tissues, their linkage of specific
T cell receptor usage (to identify SIV-specific clonotypes), single non-CD8+ T cells in blood and tissues, and
whole immune tissues including whole blood, lymph node (LN), spleen, bone marrow (BM) and gut-associated
lymphoid tissues (GALT), and will link data sets with spatial transcriptomic data sets, to define gene expression
signatures and networks, and will apply cutting edge bioinformatics approaches to model their functional output
and inform the mechanisms of action by which RhCMV/SIV vaccination programs the immune response for
replication arrest-type protection against SIV infection. To meet these goals, Core D will address the following
Specific Aims: 1) provide specialized CITE-seq and/or TCR sequence identification using the 10X Genomics
platform, 2) conduct Nanostring and bulk RNAseq analysis of whole blood and tissues, 3) provide bioinformatic
and biostatistical analyses, and computational modeling, to define immune response gene expression signatures
linked with vaccine actions and virus control, and 4) develop and manage a comprehensive database for all
Program data to facilitate integrated data analysis. Core D is directed by Dr. Michael Gale, Jr., working closely
with Drs. Ben Bimber and Paul Edlefsen, to provide consistent, high-quality functional genomics data generation,
integrated data analysis, biostatistical analyses and computational modeling, with big data management, for all
aspects of the scientific program.
Terms: <Assay><Bar Codes><Big Data><BigData><Bio-Informatics><Bioassay><Bioinformatics><Biological><Biological Assay><Biometrics><Biometry><Biostatistics><Blood><Blood Reticuloendothelial System><Body Tissues><Bone Marrow><Bone Marrow Reticuloendothelial System><CD8 Cell><CD8 T cells><CD8 lymphocyte><CD8+ T cell><CD8+ T-Lymphocyte><CD8-Positive Lymphocytes><CD8-Positive T-Lymphocytes><CITE sequencing><CITE-seq><CITEseq><Cell Body><Cell Function><Cell Physiology><Cell Process><Cells><Cellular Function><Cellular Indexing of Transcriptomes and Epitopes by Sequencing><Cellular Physiology><Cellular Process><Computer Analysis><Computer Models><Computerized Models><Data><Data Analyses><Data Analysis><Data Bases><Data Management Resources><Data Management System><Data Set><Databases><Experimental Designs><Expression Signature><Gene Expression><Gene Expression Profile><Generations><Genes><Goals><Gut associated lymphoid tissue><Immune><Immune Response Genes><Immune response><Immunes><Immunization Programs><Immunochemical Immunologic><Immunologic><Immunological><Immunological response><Immunologically><Immunologics><Infection><Ir Gene><Laboratories><Link><Lymph Node Reticuloendothelial System><Lymph node proper><Lymphatic nodes><M mulatta><M. mulatta><MHC Receptor><Macaca mulatta><Major Histocompatibility Complex Receptor><Measurement><Mediating><Membrane Protein Gene><Membrane Proteins><Membrane-Associated Proteins><Messenger RNA><Methods><Modeling><Monitor><Output><Peptides><RNA Seq><RNA sequencing><RNAseq><Resolution><Rhesus Macaque><Rhesus Monkey><SIV><SIV Vaccines><Secure><Simian Immunodeficiency Viruses><Spleen><Spleen Reticuloendothelial System><Study Subject><Subcellular Process><Surface Proteins><T cell differentiation><T cell response><T-Cell Antigen Receptors><T-Cell Receptor><T-cell receptor repertoire><T8 Cells><T8 Lymphocytes><TCR repertoire><Tissues><Vaccinated><Vaccination><Vaccination Programs><Vaccines><Virus><Whole Blood><Work><antigen-specific T cells><barcode><big data management><biologic><cellular indexing of transcriptomes and epitopes by single cell sequencing><cohort><computational analyses><computational analysis><computational modeling><computational models><computer analyses><computer based models><computerized modeling><curating data><data base><data curation><data handling><data integration><data interpretation><data management><functional genomics><gene expression pattern><gene expression signature><gene function><genomic data><genomic data-set><genomic dataset><genomic platform><high dimensional data><host response><immune system response><immunoresponse><lymph gland><lymph nodes><lymphnodes><mRNA><multidimensional data><multidimensional datasets><multiomics><multiple omics><nano-string><nanostring><panomics><pre-clinical><pre-clinical study><preclinical><preclinical study><predictive signature><programs><resolutions><response><simian immunodeficiency virus vaccines><transcriptional profile><transcriptional signature><transcriptome sequencing><transcriptomic sequencing><transcriptomics><vaccination study><vaccination trial><vaccine efficacy><vaccine study><vaccine trial><web server><web-accessible>