Patent ID: 11939622
Assignee: BECTON, DICKINSON AND COMPANY
Field: Biotechnology (Chemistry)
Classification: CPC C | IPC C

Claim 9:
10. A method comprising:
permeabilizing a cell comprising a nuclear target associated with double-stranded deoxyribonucleic acid (dsDNA), wherein the dsDNA is a genomic DNA (gDNA), and wherein the nuclear target is a protein, wherein the nuclear target comprises a chromatin-associated protein and is attached to the dsDNA;
generating a plurality of nuclear target-associated dsDNA fragments by contacting the nuclear target associated with dsDNA with a conjugate comprising a transposome and a binding reagent capable of specifically binding to the nuclear target such that each of the plurality of nuclear target-associated dsDNA fragments comprising a first 5′ overhang and a 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, wherein the transposome comprises a domain that specifically binds the binding reagent and the transposase adds the first adaptor and the second adaptor to the dsDNA of the nuclear target associated with dsDNA, wherein the first adaptor comprises a first barcode sequence and the second adaptor comprises a second barcode sequence, and wherein the first barcode sequence and/or the second barcode sequence identify the nuclear target;
adding a synthetic particle comprising a first plurality of oligonucleotide barcodes to the permeabilized cell after the contacting step;
lysing the permeabilized cell after the adding step; and
generating a plurality of barcoded nuclear target-associated DNA fragments by barcoding the plurality of nuclear target-associated dsDNA fragments using the first plurality of oligonucleotide barcodes after the lysing step, wherein each oligonucleotide barcode of the first plurality of oligonucleotide barcodes comprises a first target-binding region capable of hybridizing to the plurality of nuclear target-associated dsDNA fragments, wherein said barcoding the plurality of nuclear target-associated dsDNA fragments comprises:
hybridizing the first plurality of oligonucleotide barcodes to the plurality of nuclear target-associated dsDNA fragments,
extending the first plurality of oligonucleotide barcodes hybridized to the plurality of nuclear target-associated dsDNA fragments, and/or
ligating the nuclear target-associated dsDNA fragments to the first plurality of oligonucleotide barcodes hybridized to the plurality of nuclear target-associated dsDNA fragments.