Single cell assay for transposase-accessible chromatin

A method of labeling DNA, the method comprising:

• contacting double-stranded deoxyribonucleic acid (dsDNA) with a transposome to generate a plurality of dsDNA fragments each comprising a first 5′ overhang and a second 5′ overhang, wherein each dsDNA fragment of the plurality of dsDNA fragments comprises a first strand comprising the first 5′ overhang and a second strand comprising the second 5′ overhang, wherein the transposome comprises a transposase, a first adaptor having the first 5′ overhang, and a second adaptor having the second 5′ overhang, and wherein the first 5′ overhang comprises a coupling sequence;
• providing a coupling oligonucleotide comprising a 5′ complement of the coupling sequence and a 3′ complement of a second target-binding region;
• and
• barcoding the plurality of dsDNA fragments, or products thereof, using a second plurality of oligonucleotide barcodes to generate a plurality of barcoded DNA fragments, wherein each oligonucleotide barcode of the second plurality of oligonucleotide barcodes comprises the second target-binding region.

A kit comprising:

• (i) a transposome comprising a transposase, a first adaptor having a first 5′ overhang, and a second adaptor having a second 5′ overhang;
• and
• a first plurality of oligonucleotide barcodes, wherein the 3′ end of each oligonucleotide barcode of the first plurality of oligonucleotide barcodes is associated with a solid support, wherein the 5′ end of each oligonucleotide barcode of the first plurality of oligonucleotide barcodes comprises a first target-binding region capable of hybridizing to the first 5′ overhang;
• or
• (ii) a transposome comprising a transposase, a first adaptor having a first 5′ overhang, and a second adaptor having a second 5′ overhang, wherein the first 5′ overhang comprises a coupling sequence;
• and
• a coupling oligonucleotide comprising a 5′ complement of the coupling sequence and a 3′ complement of a second target-binding region.