sequencing/scg-protocols-v1 · Datasets at Hugging Face

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468–481 (2011).
28. Smallwood, S.A. & Kelsey, G. Genome-wide analysis of DNA methylation in
Reprints and permissions information is available online at http://www.nature. low cell numbers by reduced representation bisulfite sequencing. Methods
com/reprints/index.html. Mol. Biol. 925, 187–197 (2012).
29. Smith, Z.D., Gu, H., Bock, C., Gnirke, A. & Meissner, A. High-throughput
1. Bird, A. DNA methylation patterns and epigenetic memory. Genes Dev. 16, bisulfite sequencing in mammalian genomes. Methods 48, 226–232
6–21 (2002). (2009).
2. Smith, Z.D. et al. A unique regulatory phase of DNA methylation in the 30. Gu, H. et al. Genome-scale DNA methylation mapping of clinical samples
early mammalian embryo. Nature 484, 339–344 (2012). at single-nucleotide resolution. Nat. Methods 7, 133–136 (2010).
3. Smallwood, S.A. et al. Dynamic CpG island methylation landscape in 31. Boyle, P. et al. Gel-free multiplexed reduced representation bisulfite
oocytes and preimplantation embryos. Nat. Genet. 43, 811–814 (2011). sequencing for large-scale DNA methylation profiling. Genome Biol. 13,
4. Gu, T.P. et al. The role of Tet3 DNA dioxygenase in epigenetic R92 (2012).
reprogramming by oocytes. Nature 477, 606–610 (2011). 32. Smallwood, S.A. et al. Single-cell genome-wide bisulfite sequencing for
5. Hackett, J.A. et al. Germline DNA demethylation dynamics and imprint assessing epigenetic heterogeneity. Nat. Methods 11, 817–820 (2014).
erasure through 5-hydroxymethylcytosine. Science 339, 448–452 (2013). 33. Miura, F., Enomoto, Y., Dairiki, R. & Ito, T. Amplification-free whole-
6. Iqbal, K., Jin, S.G., Pfeifer, G.P. & Szabo, P.E. Reprogramming of the genome bisulfite sequencing by post-bisulfite adaptor tagging.
paternal genome upon fertilization involves genome-wide oxidation of Nucleic Acids Res. 40, e136 (2012).
5-methylcytosine. Proc. Natl. Acad. Sci. USA 108, 3642–3647 (2011). 34. Guo, F. et al. Active and passive demethylation of male and female
7. Mayer, W., Niveleau, A., Walter, J., Fundele, R. & Haaf, T. Demethylation pronuclear DNA in the mammalian zygote. Cell Stem Cell 15, 447–458
of the zygotic paternal genome. Nature 403, 501–502 (2000). (2014).
8. Wossidlo, M. et al. 5-Hydroxymethylcytosine in the mammalian zygote is 35. Krueger, F. & Andrews, S.R. Bismark: a flexible aligner and methylation
linked with epigenetic reprogramming. Nat. Commun. 2, 241 (2011). caller for bisulfite-seq applications. Bioinformatics 27, 1571–1572
9. Okada, Y., Yamagata, K., Hong, K., Wakayama, T. & Zhang, Y. A role for (2011).
the elongator complex in zygotic paternal genome demethylation. Nature 36. Xi, Y. & Li, W. BSMAP: whole-genome bisulfite sequence mapping program.
463, 554–558 (2010). BMC Bioinformatics 10, 232 (2009).
10. Guo, H. et al. The DNA methylation landscape of human early embryos. 37. Chen, P.Y., Cokus, S.J. & Pellegrini, M. BS Seeker: precise mapping for
Nature 511, 606–610 (2014). bisulfite sequencing. BMC Bioinformatics 11, 203 (2010).
11. Smith, Z.D. et al. DNA methylation dynamics of the human 38. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-
preimplantation embryo. Nature 511, 611–615 (2014). efficient alignment of short DNA sequences to the human genome. Genome
12. Hackett, J.A. & Surani, M.A. DNA methylation dynamics during the Biol. 10, R25 (2009).
mammalian life cycle. Philos. Trans. R. Soc. Lond. B Biol. Sci. 368, 39. Li, H. et al. The Sequence Alignment/Map format and SAMtools.
20110328 (2013). Bioinformatics 25, 2078–2079 (2009).
13. Seisenberger, S. et al. The dynamics of genome-wide DNA methylation 40. Tang, F. et al. RNA-seq analysis to capture the transcriptome landscape of
reprogramming in mouse primordial germ cells. Mol. Cell 48, 849–862 (2012). a single cell. Nat. Protoc. 5, 516–535 (2010).
14. Xie, W. et al. Epigenomic analysis of multilineage differentiation of human 41. Tang, F. et al. mRNA-seq whole-transcriptome analysis of a single cell.
embryonic stem cells. Cell 153, 1134–1148 (2013). Nat. Methods 6, 377–382 (2009).
15. Reik, W. & Kelsey, G. Epigenetics: cellular memory erased in human 42. Yan, L. et al. Single-cell RNA-seq profiling of human preimplantation
embryos. Nature 511, 540–541 (2014). embryos and embryonic stem cells. Nat. Struct. Mol. Biol. 20, 1131–1139
16. Burgess, D.J. Stem cells: epigenome reprogramming—of mice and men. (2013).
Nat. Rev. Genet. 15, 571 (2014). 43. Evrony, G.D. et al. Single-neuron sequencing analysis of L1
17. Guo, H. et al. Single-cell methylome landscapes of mouse embryonic stem retrotransposition and somatic mutation in the human brain. Cell 151,
cells and early embryos analyzed using reduced representation bisulfite 483–496 (2012).
sequencing. Genome Res. 23, 2126–2135 (2013). 44. Frumkin, D. et al. Amplification of multiple genomic loci from single cells
18. Lister, R. et al. Human DNA methylomes at base resolution show isolated by laser micro-dissection of tissues. BMC Biotechnol. 8, 17
widespread epigenomic differences. Nature 462, 315–322 (2009). (2008).
19. Shirane, K. et al. Mouse oocyte methylomes at base resolution reveal 45. Ma, C. et al. A clinical microchip for evaluation of single immune cells
genome-wide accumulation of non-CpG methylation and role of DNA reveals high functional heterogeneity in phenotypically similar T cells.
methyltransferases. PLoS Genet. 9, e1003439 (2013). Nat. Med. 17, 738–743 (2011).
20. Molaro, A. et al. Sperm methylation profiles reveal features of epigenetic 46. Fan, H.C., Wang, J., Potanina, A. & Quake, S.R. Whole-genome molecular
inheritance and evolution in primates. Cell 146, 1029–1041 (2011). haplotyping of single cells. Nat. Biotechnol. 29, 51–57 (2011).













nature protocols \| VOL.10 NO.5 \| 2015 \| 659

468–481 (2011).

28. Smallwood, S.A. & Kelsey, G. Genome-wide analysis of DNA methylation in

Reprints and permissions information is available online at http://www.nature. low cell numbers by reduced representation bisulfite sequencing. Methods

com/reprints/index.html. Mol. Biol. 925, 187–197 (2012).

29. Smith, Z.D., Gu, H., Bock, C., Gnirke, A. & Meissner, A. High-throughput

1. Bird, A. DNA methylation patterns and epigenetic memory. Genes Dev. 16, bisulfite sequencing in mammalian genomes. Methods 48, 226–232

6–21 (2002). (2009).

2. Smith, Z.D. et al. A unique regulatory phase of DNA methylation in the 30. Gu, H. et al. Genome-scale DNA methylation mapping of clinical samples

early mammalian embryo. Nature 484, 339–344 (2012). at single-nucleotide resolution. Nat. Methods 7, 133–136 (2010).

3. Smallwood, S.A. et al. Dynamic CpG island methylation landscape in 31. Boyle, P. et al. Gel-free multiplexed reduced representation bisulfite

oocytes and preimplantation embryos. Nat. Genet. 43, 811–814 (2011). sequencing for large-scale DNA methylation profiling. Genome Biol. 13,

4. Gu, T.P. et al. The role of Tet3 DNA dioxygenase in epigenetic R92 (2012).

reprogramming by oocytes. Nature 477, 606–610 (2011). 32. Smallwood, S.A. et al. Single-cell genome-wide bisulfite sequencing for

5. Hackett, J.A. et al. Germline DNA demethylation dynamics and imprint assessing epigenetic heterogeneity. Nat. Methods 11, 817–820 (2014).

erasure through 5-hydroxymethylcytosine. Science 339, 448–452 (2013). 33. Miura, F., Enomoto, Y., Dairiki, R. & Ito, T. Amplification-free whole-

6. Iqbal, K., Jin, S.G., Pfeifer, G.P. & Szabo, P.E. Reprogramming of the genome bisulfite sequencing by post-bisulfite adaptor tagging.

paternal genome upon fertilization involves genome-wide oxidation of Nucleic Acids Res. 40, e136 (2012).

5-methylcytosine. Proc. Natl. Acad. Sci. USA 108, 3642–3647 (2011). 34. Guo, F. et al. Active and passive demethylation of male and female

7. Mayer, W., Niveleau, A., Walter, J., Fundele, R. & Haaf, T. Demethylation pronuclear DNA in the mammalian zygote. Cell Stem Cell 15, 447–458

of the zygotic paternal genome. Nature 403, 501–502 (2000). (2014).

8. Wossidlo, M. et al. 5-Hydroxymethylcytosine in the mammalian zygote is 35. Krueger, F. & Andrews, S.R. Bismark: a flexible aligner and methylation

linked with epigenetic reprogramming. Nat. Commun. 2, 241 (2011). caller for bisulfite-seq applications. Bioinformatics 27, 1571–1572

9. Okada, Y., Yamagata, K., Hong, K., Wakayama, T. & Zhang, Y. A role for (2011).

the elongator complex in zygotic paternal genome demethylation. Nature 36. Xi, Y. & Li, W. BSMAP: whole-genome bisulfite sequence mapping program.

463, 554–558 (2010). BMC Bioinformatics 10, 232 (2009).

10. Guo, H. et al. The DNA methylation landscape of human early embryos. 37. Chen, P.Y., Cokus, S.J. & Pellegrini, M. BS Seeker: precise mapping for

Nature 511, 606–610 (2014). bisulfite sequencing. BMC Bioinformatics 11, 203 (2010).

11. Smith, Z.D. et al. DNA methylation dynamics of the human 38. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-

preimplantation embryo. Nature 511, 611–615 (2014). efficient alignment of short DNA sequences to the human genome. Genome

12. Hackett, J.A. & Surani, M.A. DNA methylation dynamics during the Biol. 10, R25 (2009).

mammalian life cycle. Philos. Trans. R. Soc. Lond. B Biol. Sci. 368, 39. Li, H. et al. The Sequence Alignment/Map format and SAMtools.

20110328 (2013). Bioinformatics 25, 2078–2079 (2009).

13. Seisenberger, S. et al. The dynamics of genome-wide DNA methylation 40. Tang, F. et al. RNA-seq analysis to capture the transcriptome landscape of

reprogramming in mouse primordial germ cells. Mol. Cell 48, 849–862 (2012). a single cell. Nat. Protoc. 5, 516–535 (2010).

14. Xie, W. et al. Epigenomic analysis of multilineage differentiation of human 41. Tang, F. et al. mRNA-seq whole-transcriptome analysis of a single cell.

embryonic stem cells. Cell 153, 1134–1148 (2013). Nat. Methods 6, 377–382 (2009).

15. Reik, W. & Kelsey, G. Epigenetics: cellular memory erased in human 42. Yan, L. et al. Single-cell RNA-seq profiling of human preimplantation

embryos. Nature 511, 540–541 (2014). embryos and embryonic stem cells. Nat. Struct. Mol. Biol. 20, 1131–1139

16. Burgess, D.J. Stem cells: epigenome reprogramming—of mice and men. (2013).

Nat. Rev. Genet. 15, 571 (2014). 43. Evrony, G.D. et al. Single-neuron sequencing analysis of L1

17. Guo, H. et al. Single-cell methylome landscapes of mouse embryonic stem retrotransposition and somatic mutation in the human brain. Cell 151,

cells and early embryos analyzed using reduced representation bisulfite 483–496 (2012).

sequencing. Genome Res. 23, 2126–2135 (2013). 44. Frumkin, D. et al. Amplification of multiple genomic loci from single cells

18. Lister, R. et al. Human DNA methylomes at base resolution show isolated by laser micro-dissection of tissues. BMC Biotechnol. 8, 17

widespread epigenomic differences. Nature 462, 315–322 (2009). (2008).

19. Shirane, K. et al. Mouse oocyte methylomes at base resolution reveal 45. Ma, C. et al. A clinical microchip for evaluation of single immune cells

genome-wide accumulation of non-CpG methylation and role of DNA reveals high functional heterogeneity in phenotypically similar T cells.

methyltransferases. PLoS Genet. 9, e1003439 (2013). Nat. Med. 17, 738–743 (2011).

20. Molaro, A. et al. Sperm methylation profiles reveal features of epigenetic 46. Fan, H.C., Wang, J., Potanina, A. & Quake, S.R. Whole-genome molecular

inheritance and evolution in primates. Cell 146, 1029–1041 (2011). haplotyping of single cells. Nat. Biotechnol. 29, 51–57 (2011).

nature protocols | VOL.10 NO.5 | 2015 | 659