Cell

Bisulfite sequencing

Methylation

Biology

Gene

Gene expression

Molecular biology

DNA methylation

Bisulfite

Computational biology

Genetics

Nature Biotechnology

Methylation profiling of single cells in high throughput achieves read-alignment rates approaching bulk cell population studies. We present a highly scalable assay for whole-genome methylation profiling of single cells. We use our approach, single-cell combinatorial indexing for methylation analysis (sci-MET), to produce 3,282 single-cell bisulfite sequencing libraries and achieve read alignment rates of 68 ± 8%. We apply sci-MET to discriminate the cellular identity of a mixture of three human cell lines and to identify excitatory and inhibitory neuronal populations from mouse cortical tissue.

Highly scalable generation of DNA methylation profiles in single cells