a) contacting a population of cells with a plurality of antibodies under conditions that promote specific binding of the antibodies to target antigens of the cells, wherein each antibody in the plurality is capable of binding to a unique target antigen in one or more cells, wherein each antibody is conjugated to an oligonucleotide via thiol/maleimide conjugation, and wherein the oligonucleotide comprises a unique molecular identifier sequence and an antibody identifier sequence corresponding to the unique target antigen;

b) separating single cells of the population into individual compartments, wherein each compartment further comprises an oligonucleotide comprising a unique cellular identifier sequence that corresponds to the single cell in each compartment;

c) lysing the single cells with an agent that extracts proteins and nucleic acids from the cells, wherein the nucleic acids comprise RNA and/or DNA;

d) amplifying the unique molecular identifier sequences and antibody identifier sequences in each individual compartment, using the oligonucleotide comprising the unique cellular identifier sequence;

e) analyzing the amplified unique molecular identifier sequences and antibody identifier sequences to identify the expression profile of each single cell, wherein the unique molecular identifier sequences reduce bias in the analysis; and

f) analyzing the RNA extracted from the cells to identify a transcriptomic profile of each single cell and/or the DNA extracted from the cells to obtain genomic information of each single cell.