Details and protocols of the technologies supported by YAP were described in our papers. Please find the corresponding references below.
snmC-seq2 / 3
The first publication of snmC-seq:
Luo, Chongyuan, Christopher L. Keown, Laurie Kurihara, Jingtian Zhou, Yupeng He, Junhao Li, Rosa Castanon, et al. 2017. “Single-Cell Methylomes Identify Neuronal Subtypes and Regulatory Elements in Mammalian Cortex.” Science 357 (6351): 600–604.
The improved version called snmC-seq2 (using V1 barcoding):
Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.
The protocol of snmC-seq3 (using V2 barcoding) is under preparation.
snmCT-seq
The snmCT-seq (and snmC2T-seq, which has NOMe treatment) preprint:
Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv.
snm3C-seq
The snm3C-seq paper
Lee, Dong-Sung, Chongyuan Luo, Jingtian Zhou, Sahaana Chandran, Angeline Rivkin, Anna Bartlett, Joseph R. Nery, et al. 2019. “Simultaneous Profiling of 3D Genome Structure and DNA Methylation in Single Human Cells.” Nature Methods 16 (10): 999–1006.
Another method developed in Ren Lab called Methyl-HiC that also profiles mC and chromatin contacts in the same cell
Li, Guoqiang, Yaping Liu, Yanxiao Zhang, Naoki Kubo, Miao Yu, Rongxin Fang, Manolis Kellis, and Bing Ren. 2019. “Joint Profiling of DNA Methylation and Chromatin Architecture in Single Cells.” Nature Methods 16 (10): 991–93.