Genome-wide base-resolution mapping of DNA methylation in single cells using single-cell bisulfite sequencing (scBS-seq) (original) (raw)

• Tang, F. et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nat. Methods 6, 377–382 (2009).
  Article CAS PubMed Google Scholar
• Islam, S. et al. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res. 21, 1160–1167 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Sasagawa, Y. et al. Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity. Genome Biol. 14, R31 (2013).
  Article PubMed PubMed Central Google Scholar
• Hashimshony, T., Wagner, F., Sher, N. & Yanai, I. CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Rep. 2, 666–673 (2012).
  Article CAS PubMed Google Scholar
• Picelli, S. et al. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat. Methods 10, 1096–1098 (2013).
  Article CAS PubMed Google Scholar
• Jaitin, D.A. et al. Massively parallel single cell RNA-Seq for marker-free decomposition of tissues into cell types. Science 343, 776–779 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Klein, A.M. et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 161, 1187–1201 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Macosko, E.Z. et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202–1214 (2015).
  CAS PubMed PubMed Central Google Scholar
• Clark, S.J., Lee, H.J., Smallwood, S.A., Kelsey, G. & Reik, W. Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity. Genome Biol. 17, 72 (2016).
  Article PubMed PubMed Central Google Scholar
• Smallwood, S.A. et al. Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity. Nat. Methods 11, 817–820 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Farlik, M. et al. Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics. Cell Rep. 10, 1386–1397 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Gravina, S., Dong, X., Yu, B. & Vijg, J. Single-cell genome-wide bisulfite sequencing uncovers extensive heterogeneity in the mouse liver methylome. Genome Biol. 17, 150 (2016).
  Article PubMed PubMed Central Google Scholar
• Nashun, B. et al. Continuous histone replacement by Hira is essential for normal transcriptional regulation and de novo DNA methylation during mouse oogenesis. Mol. Cell 60, 611–625 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Macaulay, I.C. et al. G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nat. Methods 12, 519–522 (2015).
  Article CAS PubMed Google Scholar
• Angermueller, C. et al. Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity. Nat. Methods 13, 229–232 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Miura, F., Enomoto, Y., Dairiki, R. & Ito, T. Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging. Nucleic Acids Res. 40, e136 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Cokus, S.J. et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215–219 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Shirane, K. et al. Mouse oocyte methylomes at base resolution reveal genome-wide accumulation of non-CpG methylation and role of DNA methyltransferases. PLoS Genet. 9, e1003439 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Okae, H. et al. Genome-wide analysis of DNA methylation dynamics during early human development. PLoS Genet. 10, e1004868 (2014).
  Article PubMed PubMed Central Google Scholar
• Fisher, S. et al. A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol. 12, R1 (2011).
  Article PubMed PubMed Central Google Scholar
• Li, Y. et al. The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol. 8, e1000533 (2010).
  Article PubMed PubMed Central Google Scholar
• Bock, C. et al. DNA methylation dynamics during in vivo differentiation of blood and skin stem cells. Mol. Cell 47, 633–647 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Yu, M. et al. Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine. Nat. Protoc. 7, 2159–2170 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Mooijman, D., Dey, S.S., Boisset, J.-C., Crosetto, N. & van Oudenaarden, A. Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction. Nat. Biotechnol. 34, 852–856 (2016).
  Article CAS PubMed Google Scholar
• Booth, M.J. et al. Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine. Nat. Protoc. 8, 1841–1851 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Hu, Y. et al. Simultaneous profiling of transcriptome and DNA methylome from a single cell. Genome Biol. 17, 88 (2016).
  Article PubMed PubMed Central Google Scholar
• Hou, Y. et al. Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas. Cell Res. 26, 304–319 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Bronner, I.F., Quail, M.A., Turner, D.J. & Swerdlow, H. Improved protocols for Illumina sequencing. Curr. Protoc. Hum. Genet. 80 18.2.1 (2014).
• Habibi, E. et al. Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells. Cell Stem Cell 13, 360–369 (2013).
  Article CAS PubMed Google Scholar
• Macaulay, I.C. et al. Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq. Nat Protoc. 11, 2081–2103 (2016).
  Article CAS PubMed Google Scholar
• Guo, G. et al. Naive pluripotent stem cells derived directly from isolated cells of the human inner cell mass. Stem Cell Rep. 6, 437–446 (2016).
  Article CAS Google Scholar
• von Meyenn, F. et al. Comparative principles of DNA methylation reprogramming during human and mouse in vitro primordial germ cell specification. Dev. Cell 39, 104–115 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Eckersley-Maslin, M.A. et al. MERVL/Zscan4 network activation results in transient genome-wide DNA demethylation of mESCs. Cell Rep. 17, 179–192 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10–12 (2011).
  Article Google Scholar
• Krueger, F. & Andrews, S.R. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571–1572 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Langmead, B. & Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Guo, H. et al. Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing. Genome Res. 23, 2126–2135 (2013).
  Article CAS PubMed PubMed Central Google Scholar