A method of preparing a sequencing library for determining the methylation status of nucleic acids from a plurality of single cells, the method comprising: (a) providing isolated nuclei from a plurality of cells; (b) subjecting the isolated nuclei to a chemical treatment to generate nucleosome-depleted nuclei, while maintaining integrity of the isolated nuclei; (c) distributing subsets of the nucleosome-depleted nuclei into a first plurality of compartments comprising a transposome complex, wherein the transposome complex in each compartment comprises a first index sequence that is different from first index sequences in the other compartments; (d) fragmenting nucleic acids in the subsets of nucleosome-depleted nuclei into a plurality of nucleic acid fragments and incorporating the first index sequences into at least one strand of the nucleic acid fragments to generate indexed nuclei; (e) combining the indexed nuclei to generate pooled indexed nuclei; (f) distributing subsets of the pooled indexed nuclei into a second plurality of compartments and subjecting the indexed nuclei to bisulfite treatment to generate bisulfite-treated nucleic acid fragments; (g) amplifying the bisulfite-treated nucleic acid fragments in each compartment by linear amplification with a plurality of primers comprising a universal nucleotide sequence at the 5' end and a random nucleotide sequence at the 3' end to generate amplified fragment-adapter molecules; (h) incorporating a second index sequence into the amplified fragment-adapter molecules to generate dual-index fragment-adapter molecules, wherein the second index sequence in each compartment is different from second index sequences in the other compartments; and (i) combining the dual-index fragment-adapter molecules, thereby producing a sequencing library for determining the methylation status of nucleic acids from the plurality of single cells, optionally wherein the distributing in steps (c) and (f) is performed by fluorescenceactivated nuclei sorting. (a) providing isolated nuclei from a plurality of cells; (b) subjecting the isolated nuclei to a chemical treatment to generate nucleosome-depleted nuclei, while maintaining integrity of the isolated nuclei; (c) distributing subsets of the nucleosome-depleted nuclei into a first plurality of compartments comprising a transposome complex, wherein the transposome complex in each compartment comprises a first index sequence that is different from first index sequences in the other compartments; (d) fragmenting nucleic acids in the subsets of nucleosome-depleted nuclei into a plurality of nucleic acid fragments and incorporating the first index sequences into at least one strand of the nucleic acid fragments to generate indexed nuclei; (e) combining the indexed nuclei to generate pooled indexed nuclei; (f) distributing subsets of the pooled indexed nuclei into a second plurality of compartments and subjecting the indexed nuclei to bisulfite treatment to generate bisulfite-treated nucleic acid fragments; (g) amplifying the bisulfite-treated nucleic acid fragments in each compartment by linear amplification with a plurality of primers comprising a universal nucleotide sequence at the 5' end and a random nucleotide sequence at the 3' end to generate amplified fragment-adapter molecules; (h) incorporating a second index sequence into the amplified fragment-adapter molecules to generate dual-index fragment-adapter molecules, wherein the second index sequence in each compartment is different from second index sequences in the other compartments; and (i) combining the dual-index fragment-adapter molecules, thereby producing a sequencing library for determining the methylation status of nucleic acids from the plurality of single cells, optionally wherein the distributing in steps (c) and (f) is performed by fluorescenceactivated nuclei sorting.