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Principal Investigator: Peter Alan Sims
Organization: COLUMBIA UNIVERSITY HEALTH SCIENCES
Fiscal Year: 2024
Award: $359,953
Funding agency: National Institute of Allergy and Infectious Diseases
SINGLE CELL CORE: PROJECT SUMMARY
The Single Cell Core will provide state-of-the-art experimental technology for single-cell multi-omic profiling. Two
major limitations of conventional scRNA-seq for immunophenotyping include the lack of correlation between
mRNA levels and surface protein expression and the lack of clonal identity from immune receptor sequence.
The Core will provide access to technologies for simultaneous profiling of mRNA, immune receptor sequence,
and surface protein expression from individual cells at scale. For experiments with limited cell numbers, we will
also provide scPLATE-seq, a fully automated platform for index sorting and scRNA-seq that is cost-effective for
low cell numbers. Given the focus on analyzing virus-specific immune responses longitudinally and across
tissues, the ability to associate immunophenotypes such as surface protein expression, the transcriptome, and
TCR sequence with antigen specificity is also highly desirable. This information will allow us to determine the
phenotypic subset and clonal identity of each cell in a virus-specific T cell population, to anchor virus-specific T
cells from different individuals, ages, and tissue sites to our reference map, and to investigate their functional
capacities with single-cell resolution. The Core will provide scalable technology for associating antigen specificity
and T cell receptor sequence with targeted mRNA and surface protein profiles of individual cells (TetTCR-
seqHD). We will develop and optimize barcoded tetramer pools for a broad range of viruses and vaccines
including CMV, influenza, and SARS-CoV-2 for joint analysis T cell receptor antigen recognition, clonotype,
and immunophenotype in individual T cells.
Terms: <2019 novel corona virus><2019 novel coronavirus><2019-nCoV><21+ years old><Activities of Daily Living><Activities of everyday life><Address><Adult><Adult Human><Age><Antibodies><Antigenic Determinants><Antigens><B cell receptor><B-Cell Antigen Receptor><Bar Codes><Binding Determinants><Body Tissues><CITE sequencing><CITE-seq><CITEseq><CMV><COVID-19 antigen><COVID-19 virus><COVID19 virus><Cell Body><Cell Count><Cell Isolation><Cell Number><Cell Segregation><Cell Separation><Cell Separation Technology><Cells><Cellular Indexing of Transcriptomes and Epitopes by Sequencing><Circulation><CoV-2><CoV2><Cytomegalovirus><DNA><Deoxyribonucleic Acid><Epitopes><Flow Cytofluorometries><Flow Cytofluorometry><Flow Cytometry><Flow Microfluorimetry><Flow Microfluorometry><Funding><Genome Library><Genomic Library><Genomics><Grippe><HCMV><Human><Immune><Immune response><Immunes><Immunologic Receptors><Immunologic Subtyping><Immunological Receptors><Immunological response><Immunology><Immunophenotyping><Individual><Infant><Influenza><Investigators><Joints><Libraries><Link><MHC Receptor><Major Histocompatibility Complex Receptor><Maps><Membrane Protein Gene><Membrane Proteins><Membrane-Associated Proteins><Messenger RNA><Microfluidics><Modern Man><Organ Donor><Phenotype><Population><Preparation><Proteome><Protocol><Protocols documentation><Quality Control><Reporting><Research Personnel><Research Resources><Researchers><Resolution><Resources><Rest><SARS corona virus 2><SARS-CO-V2><SARS-COVID-2><SARS-CoV-2><SARS-CoV-2 antigen><SARS-CoV2><SARS-associated corona virus 2><SARS-associated coronavirus 2><SARS-coronavirus-2><SARS-related corona virus 2><SARS-related coronavirus 2><SARSCoV2><Salivary Gland Viruses><Sampling><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 related corona virus 2><Site><Sorting><Specificity><Staining method><Stains><Surface><Surface Proteins><T cell receptor repertoire sequencing><T cell receptor sequencing><T-Cell Activation><T-Cell Antigen Receptor Specificity><T-Cell Antigen Receptors><T-Cell Receptor><T-Cell Receptor Specificity><T-Cells><T-Lymphocyte><TCR repertoire sequencing><TCR sequencing><TCR-seq><TCRseq><Technology><Tissue Donors><Tissues><Vaccines><Viral><Virus><Wuhan coronavirus><activate T cells><adulthood><ages><antigen-specific T cells><barcode><cell sorting><cellular indexing of transcriptomes and epitopes by single cell sequencing><comparative><coronavirus disease 2019 antigen><coronavirus disease 2019 virus><coronavirus disease-19 virus><cost effective><cytomegalovirus group><daily living function><daily living functionality><experiment><experimental research><experimental study><experiments><flow cytophotometry><functional ability><functional capacity><global gene expression><global transcription profile><hCoV19><host response><immune receptor><immune system response><immunogen><immunophenotype><immunoresponse><indexing><mRNA><multiomics><multiple omics><nCoV2><panomics><preparations><protein expression><protein profiling><resolutions><scRNA-seq><severe acute respiratory syndrome coronavirus 2 antigen><single cell RNA-seq><single cell RNAseq><single cell analysis><single cell expression profiling><single cell genomics><single cell technology><single cell transcriptomic profiling><single-cell RNA sequencing><thymus derived lymphocyte><tool><transcriptome><µfluidic>