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Principal Investigator: Peter Skene
Organization: SEATTLE CHILDREN'S HOSPITAL
Fiscal Year: 2023
Award: $815,639
Funding agency: National Institute of Allergy and Infectious Diseases
Abstract
The immune system is composed of many heterogeneous cell types that respond in a synergistic
manner to mount both immediate and long-lived immunity against pathogens. The complexity of
the immune system necessitates an integrated view of multiple biological modalities to understand
different roles of varying cell types of the immune system. Detailed transcriptomic and protein
analysis at the single cell level is essential to follow the immune system’s response to pathogens
in mounting an antigen specific response. With heavy emphasis on assays that facilitate the
analysis of antigen-specific cellular and humoral immune responses, the Integrative Multi-Omics
Core will serve as a resource to standardize, optimize, and perform multi-omic single cell research
to support the biological research objectives of Projects 1, 2 and 3. The implementation of highly
standardized and automated assays will enable longitudinal and cross-sectional analysis of the
human samples within and across the research projects. Specifically, the core will provide: i.
standardized high throughput flow cytometry, bulk transcriptomics and plasma proteomics; ii. well
established synergistic assays for the analysis of antigen-specific T cell and B cell responses,
including several orthogonal approaches for profiling antigen-specific T cells and a range of
systems serology assays; and iii. optimized cost-efficient single-cell sequencing multi-omics
methods for analysis of cellular protein-expression, gene-expression, adaptive receptor
sequences, antigen-specificity, and epigenomics based on the 10x Genomics platform.
Furthermore, we will use a collaborative cloud environment to support data ingest, processing
and provision to the DMAC for deposition into ImmPort in support of rapid public access and
innovation in data integration and visualization.
Terms: <2019 novel corona virus><2019 novel coronavirus><2019-nCoV><ACE2><AIDS Virus><Acquired Immune Deficiency Syndrome Virus><Acquired Immunodeficiency Syndrome Virus><Antibodies><Antibody Specificity><Antigens><Assay><Avidity><B blood cells><B cell><B cells><B-Cells><B-Lymphocytes><B-cell><B-cell receptor repertoire sequencing><B-cell receptor sequencing><BCR repertoire sequencing><BCR seq><BCR sequencing><BCRseq><Bioassay><Biologic Assays><Biological><Biological Assay><Blood Plasma><CITE sequencing><CITE-seq><CITEseq><COVID-19 infection><COVID-19 virus><COVID-19 virus infection><COVID19 infection><COVID19 virus><Cell Body><Cell Isolation><Cell Segregation><Cell Separation><Cell Separation Technology><Cells><Cellular Indexing of Transcriptomes and Epitopes by Sequencing><Characteristics><CoV-2><CoV2><Cross Sectional Analysis><Cross-Sectional Analyses><Cross-Sectional Studies><Cross-Sectional Survey><Cytometry><Deposit><Deposition><Disease Frequency Surveys><Environment><Evaluation><Flow Cytofluorometries><Flow Cytofluorometry><Flow Cytometry><Flow Microfluorimetry><Flow Microfluorometry><Gene Expression><Generations><HIV><HIV-1><HIV-I><HIV1><Human><Human Immunodeficiency Virus Type 1><Human Immunodeficiency Viruses><Human immunodeficiency virus 1><Immune><Immune response><Immune system><Immunes><Immunity><Immunization><Immunological response><LAV-HTLV-III><Label><Libraries><Lymphadenopathy-Associated Virus><MHC Receptor><Major Histocompatibility Complex Receptor><Malaria><Methods><Modality><Modern Man><Molecular><Myelogenous><Myeloid><PBMC><Paludism><Peptide-MHC><Peptide-Major Histocompatibility Protein Complex><Peptide/MHC Complex><Peptides><Peripheral Blood Mononuclear Cell><Phenotype><Plasma><Plasma Serum><Plasmodium Infections><Population><Protein Analysis><Proteomics><R-Series Research Projects><R01 Mechanism><R01 Program><Receptor Protein><Research><Research Grants><Research Project Grants><Research Projects><Research Resources><Resources><Reticuloendothelial System, Serum, Plasma><Role><SARS corona virus 2><SARS-CO-V2><SARS-COVID-2><SARS-CoV-2><SARS-CoV-2 infection><SARS-CoV2><SARS-CoV2 infection><SARS-associated corona virus 2><SARS-associated coronavirus 2><SARS-coronavirus-2><SARS-related corona virus 2><SARS-related coronavirus 2><SARSCoV2><Sampling><Serology><Serology test><Services><Severe Acute Respiratory Coronavirus 2><Severe Acute Respiratory Distress Syndrome CoV 2><Severe Acute Respiratory Distress Syndrome Corona Virus 2><Severe Acute Respiratory Distress Syndrome Coronavirus 2><Severe Acute Respiratory Syndrome CoV 2><Severe Acute Respiratory Syndrome-associated coronavirus 2><Severe Acute Respiratory Syndrome-related coronavirus 2><Severe acute respiratory syndrome associated corona virus 2><Severe acute respiratory syndrome coronavirus 2><Severe acute respiratory syndrome coronavirus 2 infection><Severe acute respiratory syndrome related corona virus 2><Sorting><Specificity><Staining method><Stains><Standardization><System><T cell receptor repertoire sequencing><T cell receptor sequencing><T-Cell Antigen Receptors><T-Cell Receptor><TCR repertoire sequencing><TCR sequencing><TCR-seq><TCRseq><Virus-HIV><Whole Blood><Wuhan coronavirus><analyzing longitudinal><angiotensin converting enzyme 2><angiotensin converting enzyme II><antigen-specific T cells><biologic><biological research><cell sorting><cell type><cellular indexing of transcriptomes and epitopes by single cell sequencing><coronavirus disease 2019 infection><coronavirus disease 2019 virus><coronavirus disease-19 virus><cost efficient><cytokine><data ingestion><data integration><data visualization><epigenomics><flow cytophotometry><genomic platform><hCoV19><host response><immune system response><immunogen><immunoresponse><infected with COVID-19><infected with COVID19><infected with SARS-CoV-2><infected with SARS-CoV2><infected with coronavirus disease 2019><infected with severe acute respiratory syndrome coronavirus 2><innovate><innovation><innovative><longitudinal analysis><multiomics><multiple omics><nCoV2><pMHC><pathogen><protein biomarkers><protein expression><protein markers><receptor><response><scRNA-seq><serology assay><single cell RNA-seq><single cell RNAseq><single cell expression profiling><single cell sequencing><single cell transcriptomic profiling><single-cell RNA sequencing><social role><transcriptomics>