Xseq

A method for biochemical analysis of a cell-containing sample, comprising:

• a) contacting a cell-containing sample with a plurality of antigen-binding molecules under conditions that promote specific binding of the antigen-binding molecules to target antigens of the cells in the sample;
• wherein each antigen-binding molecule in the plurality binds to a unique target antigen in one or more cells of the sample, wherein each antigen-binding molecule is conjugated to an oligonucleotide, and wherein the oligonucleotide comprises (i) a unique molecular identifier sequence, (ii) an antigen-binding molecule identifier sequence corresponding to the unique target antigen, and (iii) an assay molecular identifier sequence;
• b) tagmenting genomic DNA in the cells to produce a plurality of double-stranded genomic DNA fragments comprising an oligonucleotide adaptor sequence at the 5′ end of each genomic DNA fragment;
• c) lysing the cells in the sample;
• d) isolating mRNA transcripts from the cell lysate to produce a first fraction comprising the mRNA transcripts and a second fraction comprising tagmented genomic DNA fragments and the antigen-binding molecule-bound antigens from the cell lysate;
• e) analyzing the tagmented genomic DNA fragments in the second fraction and/or the mRNA transcripts in the first fraction to identify the genomic profile of the sample;
• and
• f) analyzing the unique molecular identifier sequences, the assay molecular identifier sequences, and the antigen-binding molecule identifier sequences to identify at least one target antigen in the second fraction to identify the expression profile of the sample.