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Pettitt SJ, Krastev DB, Pemberton HN, et al. Genome-wide barcoded transposon screen for cancer drug sensitivity in haploid mouse embryonic stem cells. Sci Data. 2017;4:170020doi: 10.1038/sdata.2017.20.
Pettitt, S. J., Krastev, D. B., Pemberton, H. N., Fontebasso, Y., Frankum, J., Rehman, F. L., Brough, R., Song, F., Bajrami, I., Rafiq, R., Wallberg, F., Kozarewa, I., Fenwick, K., Armisen-Garrido, J., Swain, A., Gulati, A., Campbell, J., Ashworth, A., & Lord, C. J. (2017). Genome-wide barcoded transposon screen for cancer drug sensitivity in haploid mouse embryonic stem cells. Scientific data, 4170020. https://doi.org/10.1038/sdata.2017.20
Pettitt, Stephen J, et al. "Genome-wide barcoded transposon screen for cancer drug sensitivity in haploid mouse embryonic stem cells." Scientific data vol. 4 (2017): 170020. doi: https://doi.org/10.1038/sdata.2017.20
Pettitt SJ, Krastev DB, Pemberton HN, Fontebasso Y, Frankum J, Rehman FL, Brough R, Song F, Bajrami I, Rafiq R, Wallberg F, Kozarewa I, Fenwick K, Armisen-Garrido J, Swain A, Gulati A, Campbell J, Ashworth A, Lord CJ. Genome-wide barcoded transposon screen for cancer drug sensitivity in haploid mouse embryonic stem cells. Sci Data. 2017 Mar 01;4:170020. doi: 10.1038/sdata.2017.20. PMID: 28248920; PMCID: PMC5332012.
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Sci Data. 2017 Mar 01;4:170020. doi: 10.1038/sdata.2017.20.

Genome-wide barcoded transposon screen for cancer drug sensitivity in haploid mouse embryonic stem cells.

Scientific data

Stephen J Pettitt, Dragomir B Krastev, Helen N Pemberton, Yari Fontebasso, Jessica Frankum, Farah L Rehman, Rachel Brough, Feifei Song, Ilirjana Bajrami, Rumana Rafiq, Fredrik Wallberg, Iwanka Kozarewa, Kerry Fenwick, Javier Armisen-Garrido, Amanda Swain, Aditi Gulati, James Campbell, Alan Ashworth, Christopher J Lord

Affiliations

  1. The CRUK Gene Function Laboratory, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK.
  2. Breast Cancer Now Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK.
  3. Tumour Profiling Unit, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK.

PMID: 28248920 PMCID: PMC5332012 DOI: 10.1038/sdata.2017.20

Abstract

We describe a screen for cellular response to drugs that makes use of haploid embryonic stem cells. We generated ten libraries of mutants with piggyBac gene trap transposon integrations, totalling approximately 100,000 mutant clones. Random barcode sequences were inserted into the transposon vector to allow the number of cells bearing each insertion to be measured by amplifying and sequencing the barcodes. These barcodes were associated with their integration sites by inverse PCR. We exposed these libraries to commonly used cancer drugs and profiled changes in barcode abundance by Ion Torrent sequencing in order to identify mutations that conferred sensitivity. Drugs tested included conventional chemotherapeutics as well as targeted inhibitors of topoisomerases, poly(ADP-ribose) polymerase (PARP), Hsp90 and WEE1.

References

  1. Nature. 2011 Sep 07;479(7371):131-4 - PubMed
  2. Science. 2015 Nov 27;350(6264):1092-6 - PubMed
  3. Cell Stem Cell. 2014 Mar 6;14(3):385-93 - PubMed
  4. Cancer Res. 2014 Jan 1;74(1):287-97 - PubMed
  5. Sci Data. 2017 Mar 01;4:170020 - PubMed
  6. Science. 2009 Nov 27;326(5957):1231-5 - PubMed
  7. Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1531-6 - PubMed
  8. J Exp Med. 2011 Dec 19;208(13):2675-89 - PubMed
  9. Bioinformatics. 2009 Jul 15;25(14):1754-60 - PubMed
  10. Cell Stem Cell. 2010 May 7;6(5):468-78 - PubMed
  11. PLoS One. 2013 Apr 25;8(4):e61520 - PubMed
  12. Genome Res. 2009 Apr;19(4):667-73 - PubMed
  13. Clin Cancer Res. 2013 Sep 15;19(18):5003-15 - PubMed
  14. Nature. 2011 Aug 24;477(7364):340-3 - PubMed
  15. Science. 2014 Jan 3;343(6166):84-87 - PubMed
  16. Genome Biol. 2011 Oct 21;12(10):R104 - PubMed
  17. Development. 2012 Sep;139(18):3301-5 - PubMed
  18. Nat Methods. 2008 Dec;5(12):1005-10 - PubMed
  19. Nat Biotechnol. 2014 Mar;32(3):267-73 - PubMed
  20. Methods Enzymol. 2010;477:217-42 - PubMed
  21. Nature. 2005 Apr 14;434(7035):917-21 - PubMed
  22. Nat Methods. 2009 Jul;6(7):493-5 - PubMed
  23. Cell. 2013 Aug 15;154(4):914-27 - PubMed
  24. Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):11756-65 - PubMed
  25. Cell Stem Cell. 2011 Dec 2;9(6):563-74 - PubMed
  26. Bioinformatics. 2010 Jan 1;26(1):139-40 - PubMed
  27. EMBO J. 2001 Sep 3;20(17):4704-16 - PubMed

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