Platform for discovery and analysis of therapeutic agents

A method of characterizing a plurality of cells, comprising:

• (a) contacting a substrate with a plurality of cells to form an array of cells, wherein the substrate is a component of a flow cell;
• (b) contacting the array of cells with one or more reporter molecules;
• (c) detecting the one or more reporter molecules using a nucleic acid sequencing device comprising imaging optics;
• (d) identifying a phenotypic cellular characteristic of a cell within the array of cells based on the detecting of the one or more reporter molecules, wherein the phenotypic cellular characteristic is an optically detectable characteristic;
• (e) synthesizing at least one nucleic acid complementary to one or more nucleic acid tags associated with the cell within the array of cells, wherein the synthesizing comprises a plurality of cycles in which one or more types of nucleotides contact the one or more nucleic acid tags;
• (f) detecting, over the plurality of cycles, the one or more types of nucleotides contacting the one or more nucleic acid tags using the imaging optics of the nucleic acid sequencing device;
• (g) determining a nucleic acid sequence of the one or more nucleic acid tags based on the detecting of the one or more types of nucleotides;
• and
• (h) characterizing the cell within the array of cells based on the phenotypic cellular characteristic and the nucleic acid sequence of the one or more nucleic acid tags, wherein the characterizing comprises determining a cellular behavior.