Droplet-based bisulfite sequencing for high-throughput profiling of single-cell DNA methylomes

We present a high-throughput and droplet-based bisulfite sequencing library preparation platform. Our protocol allows production of BS library of 2,000-10,000 single cells within 2 days. In addition to validation using mixed cell lines, we also used the technology to profile various cell types in mouse and human brain samples. Overall design: We used our developed Drop-BS platform to profile single-cell methylomes on one human-mouse mixed sample, four cell line samples, one mouse brain PFC sample, and two human brain PFC samples. In the “Human_mouse_species_mixing”, we mixed equal amounts of GM12878 nuclei and mouse brain nuclei as the input nuclei to prepare a sequencing library using Drop-BS. We used GM12878 cell line, HEK293 cell line, MCF7 cell line separately to prepare three cell line Drop-BS samples. The Drop-BS library of “Three_cell_lines_mixing” was prepared using a mixture of the three with equal portions. We extracted nuclei from mouse, the first human brain PFC tissue, and the second human brain PFC tissue to prepare the “Mouse_brain” library, “Human_brain” library, and “Human_brain2” library respectively. >>> Submitter states that raw data for the Human_brain sample will be submitted to dbGaP due to patient privacy concerns.<<<