Systems and methods for detecting analytes from captured single biological particles

Abstract

Disclosed are systems and methods for selecting biological particles (e.g., cells or nuclei) based on specific binding to a substrate and single-biological particle measurement of analytes from the substrate-bound biological particles (e.g., cells or nuclei). Single biological particles (e.g., cells or nuclei) from a population of biological particles are captured through their binding to biological particle- (e.g., cell- or nucleus-) and/or molecule-specific biological particle (e.g., cell or nucleus) capture moieties on a substrate. Analytes are released from the single captured biological particles (e.g., cells or nuclei) and bind to analyte-specific barcode molecules associated with the specific biological particle (e.g., cell or nucleus) capture moieties to which a biological particle (e.g., a cell or nucleus) has bound. Analysis of the barcode molecules identifies the bound analytes. The systems and methods are used to select and capture immune cells, such as T-cells that bind specific peptide epitopes through their T-cell receptors (TCRs) or B-cells that bind antigen through their B cell receptors (BCRs). Detection and analysis of barcode molecules that have bound cellular analytes comprising rearranged V(D)J-expressing RNAs from the T-cells or B-cells allows identification of the specific TCR sequences that recognize and bind the specific peptide epitopes or specific BCR sequences that recognize and bind specific antigens.