Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing (original) (raw)

This is a preview of subscription content, access via your institution

References

  1. Johnson, J.M. et al. Science 302, 2141–2144 (2003).
    Article CAS Google Scholar
  2. Zahler, A.M. WormBook 2005, 1–13 (2005).
    Google Scholar
  3. Schuster, S.C. Nat. Methods 5, 16–18 (2008).
    Article CAS Google Scholar
  4. Margulies, M. et al. Nature 437, 376–380 (2005).
    Article CAS Google Scholar
  5. Shendure, J. et al. Science 309, 1728–1732 (2005).
    Article CAS Google Scholar
  6. Moore, M.J. et al. BMC Plant Biol. 6, 17 (2006).
    Article Google Scholar
  7. Oh, J.D. et al. Proc. Natl. Acad. Sci. USA 103, 9999–10004 (2006).
    Article CAS Google Scholar
  8. Torres, T.T., Metta, M., Ottenwalder, B. & Schlotterer, C. Genome Res. 18, 172–177 (2008).
    Article CAS Google Scholar
  9. Porreca, G.J. et al. Nat. Methods 4, 931–936 (2007).
    Article CAS Google Scholar
  10. Emrich, S.J., Barbazuk, W.B., Li, L. & Schnable, P.S. Genome Res. 17, 69–73 (2007).
    Article CAS Google Scholar
  11. Wicker, T. et al. BMC Genomics 7, 275 (2006).
    Article Google Scholar
  12. Walhout, A.J. et al. Methods Enzymol. 328, 575–592 (2000).
    Article CAS Google Scholar
  13. The MGC Project Team. Genome Res. 14, 2121–2127 (2004).
  14. Rual, J.F. et al. Genome Res. 14, 2128–2135 (2004).
    Article CAS Google Scholar
  15. Lamesch, P. et al. Genomics 89, 307–315 (2007).
    Article CAS Google Scholar
  16. Hamosh, A., Scott, A.F., Amberger, J.S., Bocchini, C.A. & McKusick, V.A. Nucleic Acids Res. 33, D514–D517 (2005).
    Article CAS Google Scholar
  17. Clamp, M. et al. Proc. Natl. Acad. Sci. USA 104, 19428–19433 (2007).
    Article CAS Google Scholar
  18. Yamasaki, C. et al. Nucleic Acids Res. 36, D793–D799 (2008).
    Article CAS Google Scholar

Download references

Acknowledgements

This work was funded in part by a grant from the Ellison Foundation (awarded to M.V.) and in part by the Dana Farber Cancer Institute Strategic Initiative in support of Center for Cancer Systems Biology. F.P.R. acknowledges support from US National Institutes of Health grants NS054052, HG003224, HL081341. W.T. was supported in part by National Institutes of Health grant DK070078. We thank the West Quad Computing Group at Harvard Medical School as well as Research Computing at Massachusetts General Hospital for assistance with computational resources. We thank G. Temple for helpful comments on the manuscript.

Author information

Author notes

  1. Kourosh Salehi-Ashtiani, Xinping Yang, Adnan Derti, Weidong Tian and Tong Hao: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Cancer Biology, Center for Cancer Systems Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, 02115, Massachusetts, USA.
    Kourosh Salehi-Ashtiani, Xinping Yang, Adnan Derti, Weidong Tian, Tong Hao, Chenwei Lin, Ryan R Murray, David Szeto, Michael E Cusick, David E Hill, Frederick P Roth & Marc Vidal
  2. Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, 02115, Massachusetts, USA
    Kourosh Salehi-Ashtiani, Xinping Yang, Tong Hao, Chenwei Lin, Ryan R Murray, David Szeto, Michael E Cusick, David E Hill & Marc Vidal
  3. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, 02115,, Massachusetts, USA
    Adnan Derti, Weidong Tian & Frederick P Roth
  4. Agencourt Bioscience Corporation, 500 Cummings Center, Beverly, 01915, Massachusetts, USA
    Kathryn Makowski, Lei Shen, Nadeem Tusneem & Douglas R Smith

Authors

  1. Kourosh Salehi-Ashtiani
    You can also search for this author inPubMed Google Scholar
  2. Xinping Yang
    You can also search for this author inPubMed Google Scholar
  3. Adnan Derti
    You can also search for this author inPubMed Google Scholar
  4. Weidong Tian
    You can also search for this author inPubMed Google Scholar
  5. Tong Hao
    You can also search for this author inPubMed Google Scholar
  6. Chenwei Lin
    You can also search for this author inPubMed Google Scholar
  7. Kathryn Makowski
    You can also search for this author inPubMed Google Scholar
  8. Lei Shen
    You can also search for this author inPubMed Google Scholar
  9. Ryan R Murray
    You can also search for this author inPubMed Google Scholar
  10. David Szeto
    You can also search for this author inPubMed Google Scholar
  11. Nadeem Tusneem
    You can also search for this author inPubMed Google Scholar
  12. Douglas R Smith
    You can also search for this author inPubMed Google Scholar
  13. Michael E Cusick
    You can also search for this author inPubMed Google Scholar
  14. David E Hill
    You can also search for this author inPubMed Google Scholar
  15. Frederick P Roth
    You can also search for this author inPubMed Google Scholar
  16. Marc Vidal
    You can also search for this author inPubMed Google Scholar

Corresponding authors

Correspondence toKourosh Salehi-Ashtiani, Frederick P Roth or Marc Vidal.

Ethics declarations

Competing interests

K.M., L.S., N.T. and D.R.S. are employed by Agencourt Corp.

Supplementary information

Rights and permissions

About this article

Cite this article

Salehi-Ashtiani, K., Yang, X., Derti, A. et al. Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing.Nat Methods 5, 597–600 (2008). https://doi.org/10.1038/nmeth.1224

Download citation