Highly scalable generation of DNA methylation profiles in single cells (original) (raw)

Accession codes

Primary accessions

BioProject

Gene Expression Omnibus

References

  1. Varley, K.E. et al. Genome Res. 23, 555–567 (2013).
    Article CAS PubMed PubMed Central Google Scholar
  2. Lister, R. et al. Nature 462, 315–322 (2009).
    Article CAS PubMed PubMed Central Google Scholar
  3. Smallwood, S.A. et al. Nat. Methods 11, 817–820 (2014).
    Article CAS PubMed PubMed Central Google Scholar
  4. Farlik, M. et al. Cell Rep. 10, 1386–1397 (2015).
    Article CAS PubMed PubMed Central Google Scholar
  5. Farlik, M. et al. Cell Stem Cell 19, 808–822 (2016).
    Article CAS PubMed PubMed Central Google Scholar
  6. Angermueller, C. et al. Nat. Methods 13, 229–232 (2016).
    Article CAS PubMed PubMed Central Google Scholar
  7. Clark, S.J. et al. Nat. Protoc. 12, 534–547 (2017).
    Article CAS PubMed Google Scholar
  8. Luo, C. et al. Science 357, 600–604 (2017).
    Article CAS PubMed PubMed Central Google Scholar
  9. Amini, S. et al. Nat. Genet. 46, 1343–1349 (2014).
    Article CAS PubMed PubMed Central Google Scholar
  10. Adey, A. et al. Genome Res. 24, 2041–2049 (2014).
    Article CAS PubMed PubMed Central Google Scholar
  11. Vitak, S.A. et al. Nat. Methods 14, 302–308 (2017).
    Article CAS PubMed PubMed Central Google Scholar
  12. Cao, J. et al. Science 357, 661–667 (2017).
    Article CAS PubMed PubMed Central Google Scholar
  13. Cusanovich, D.A. et al. Science 348, 910–914 (2015).
    Article CAS PubMed PubMed Central Google Scholar
  14. Adey, A. et al. Genome Biol. 11, R119 (2010).
    Article CAS PubMed PubMed Central Google Scholar
  15. Karimzadeh, M. et al. bioRxiv (2017).
  16. Zerbino, D.R., Wilder, S.P., Johnson, N., Juettemann, T. & Flicek, P.R. Genome Biol. 16, 56 (2015).
    Article PubMed PubMed Central Google Scholar
  17. Roadmap Epigenomics Consortium. Nature 518, 317–330 (2015).
  18. The ENCODE Project Consortium. Nature 489, 57–74 (2012).
  19. Lister, R. et al. Science 341, 1237905 (2013).
    Article PubMed PubMed Central Google Scholar
  20. Guo, J.U. et al. Nat. Neurosci. 17, 215–222 (2014).
    Article CAS PubMed Google Scholar
  21. Adey, A. & Shendure, J. Genome Res. 22, 1139–1143 (2012).
    Article CAS PubMed PubMed Central Google Scholar
  22. Krueger, F. & Andrews, S.R. Bioinformatics 27, 1571–1572 (2011).
    Article CAS PubMed PubMed Central Google Scholar
  23. Lee, D. & Seung, S. Nature 401, 778 (1999).
    Article Google Scholar
  24. Ester, M. et al. Proc. 2nd Int. Conf. Knowl. Discov. Data Min. 226–231 (AAAI,1996).
  25. Heinz, S. et al. Mol. Cell 38, 576–589 (2010).
    Article CAS PubMed PubMed Central Google Scholar

Download references

Acknowledgements

We would like to thank B. DeRosa for culturing the primary fibroblast cell line for this project (Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, Oregon, USA). We would like to thank other members of the Adey laboratory for helpful suggestions and dialog pertaining to this work, particularly S. Vitak. We also thank G. Mandel for providing the mice used in this study and for helpful discussion and comments on the manuscript (Vollum Institute, Oregon Health & Science University, Portland, Oregon, USA). J.R.S. is supported by the Rett Syndrome Research Trust. A.C.A. is supported by an R35 from NIGMS (1R35GM124704-01), and the Knight Cardiovascular Institute. B.J.O. is supported a fellowship from the Sloan Foundation.

Author information

Authors and Affiliations

  1. Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, Oregon, USA
    Ryan M Mulqueen, Kristof A Torkenczy, Andrew J Fields, Brian J O'Roak & Andrew C Adey
  2. Illumina, Inc., San Diego, California, USA
    Dmitry Pokholok, Steven J Norberg & Frank J Steemers
  3. Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, Oregon, USA
    Duanchen Sun & Zheng Xia
  4. Computational Biology Program, Oregon Health & Science University, Portland, Oregon, USA
    Duanchen Sun & Zheng Xia
  5. Vollum Institute, Oregon Health & Science University, Portland, Oregon, USA
    John R Sinnamon
  6. Department of Genome Sciences, University of Washington, Seattle, Washington, USA
    Jay Shendure & Cole Trapnell
  7. Howard Hughes Medical Institute, Seattle, Washington, USA
    Jay Shendure
  8. Knight Cardiovascular Institute, Portland, Oregon, USA
    Andrew C Adey

Authors

  1. Ryan M Mulqueen
  2. Dmitry Pokholok
  3. Steven J Norberg
  4. Kristof A Torkenczy
  5. Andrew J Fields
  6. Duanchen Sun
  7. John R Sinnamon
  8. Jay Shendure
  9. Cole Trapnell
  10. Brian J O'Roak
  11. Zheng Xia
  12. Frank J Steemers
  13. Andrew C Adey

Contributions

A.C.A. and R.M.M. conceived the sci-MET assay. R.M.M. carried out all sci-MET preparations with contributions from A.J.F. A.C.A., R.M.M., F.J.S., D.P., and S.N. designed the sci-MET adaptors and primers and reduced the assay to practice. R.M.M., F.J.S., D.P., and S.N. carried out all sequencing. R.M.M. led the data analysis. D.S. and Z.X. performed the NMF-tSNE analysis. K.A.T. provided additional analyses. J.R.S. performed mouse cortex dissection. F.J.S., J.S., C.T., and B.J.O. contributed to analysis design and edited the manuscript. A.C.A. supervised all aspects of the study. All authors approved the manuscript.

Corresponding author

Correspondence toAndrew C Adey.

Ethics declarations

Competing interests

D.P., S.N., and F.J.S. are all employees of Illumina Inc. F.J.S., D.P., S.N., A.C.A., R.M.M., and J.S. all have one or more patents pertaining to one or more aspects of the technologies described here.

Supplementary information

Rights and permissions

About this article

Cite this article

Mulqueen, R., Pokholok, D., Norberg, S. et al. Highly scalable generation of DNA methylation profiles in single cells.Nat Biotechnol 36, 428–431 (2018). https://doi.org/10.1038/nbt.4112

Download citation