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Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA

Nature Methods volume 7, pages 4749 (2010) | Download Citation

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Abstract

Chromatin structure and transcription factor localization can be assayed genome-wide by sequencing genomic DNA fractionated by protein occupancy or other properties, but current technologies involve multiple steps that introduce bias and inefficiency. Here we apply a single-molecule approach to directly sequence chromatin immunoprecipitated DNA with minimal sample manipulation. This method is compatible with just 50 pg of DNA and should thus facilitate charting chromatin maps from limited cell populations.

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Change history

  • 12 April 2010

    In the version of this supplementary file originally posted online, Figure 1 was truncated. The error has been corrected in this file as of 12 April 2010.

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Acknowledgements

We thank J. Robinson and members of the IGV platform for their help with data presentation. A.G. is supported by an EMBO long-term postdoctoral fellowship. M.K. is supported by a Croucher Foundation fellowship. A.R. is an investigator of the Merkin Foundation for Stem Cell Research at the Broad Institute. This research was supported by funds from the Burroughs Wellcome Fund (to B.E.B. and A.R.), Howard Hughes Medical Institute (to B.E.B. and A.R.), Partnership for Cures Culpeper Scholarship (to B.E.B.) and the US National Human Genome Research Institute.

Author information

Author notes

    • Alon Goren
    • , Fatih Ozsolak
    •  & Noam Shoresh

    These authors contributed equally to this work.

Affiliations

  1. Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

    • Alon Goren
    • , Noam Shoresh
    • , Manching Ku
    • , Mazhar Adli
    • , Melissa Gymrek
    • , Or Zuk
    • , Aviv Regev
    •  & Bradley E Bernstein
  2. Howard Hughes Medical Institute, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.

    • Alon Goren
    • , Manching Ku
    • , Mazhar Adli
    • , Melissa Gymrek
    • , Aviv Regev
    •  & Bradley E Bernstein
  3. Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.

    • Alon Goren
    • , Manching Ku
    • , Mazhar Adli
    • , Melissa Gymrek
    •  & Bradley E Bernstein
  4. Center for Systems Biology and Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts, USA.

    • Alon Goren
    • , Manching Ku
    • , Mazhar Adli
    • , Melissa Gymrek
    •  & Bradley E Bernstein
  5. Helicos BioSciences Corporation, Cambridge, Massachusetts, USA.

    • Fatih Ozsolak
    • , Chris Hart
    •  & Patrice M Milos
  6. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

    • Aviv Regev

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Contributions

A.G., N.S. and B.E.B. processed and analyzed the data, wrote the paper and made the figures; F.O., C.H. and P.M.M. developed the method for sequencing ChIP-DNA and performed the sequencing; M.K. performed the chromatin experiments; M.A., M.G., O.Z. and A.R. helped with data analysis.

Competing interests

F.O., C.H. and P.M.M. are employees of Helicos BioSciences Corporation.

Corresponding author

Correspondence to Bradley E Bernstein.

Supplementary information

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  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–13 and Supplementary Tables 1–4

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DOI

https://doi.org/10.1038/nmeth.1404

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