Transposase-based genomic analysis

A method of barcoding DNA, the method comprising

• introducing oligonucleotide adaptors randomly into DNA comprising DNA-bound proteins by contacting the DNA with a transposase loaded with the oligonucleotide adaptors,
• wherein the oligonucleotide adaptors comprise a single stranded portion and a double stranded portion, and
• wherein the transposase introduces double-stranded breaks into the DNA, wherein each double-stranded break forms two DNA ends and the transposase ligates the first oligonucleotide to one strand of each DNA end, to form DNA fragments comprising the oligonucleotide adaptors at both ends;
• forming partitions, wherein the partitions contain the DNA fragments and a first oligonucleotide primer having a bead-specific barcode sequence, wherein the first oligonucleotide primer is linked to a bead and comprises a free 3′ end;
• in the partitions, gap filling 5′ overhangs with a polymerase that has strand displacing activity or 5′ to 3′ exonuclease activity to create a double-stranded sequence by extending 3′ ends;
• hybridizing the 3′ end of the first oligonucleotide primer to a 3′ single stranded portion of the oligonucleotide adaptor, thereby forming barcoded DNA fragments;
• combining contents of the partitions to form a reaction mixture.