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Analyzing CRISPR genome-editing experiments with CRISPResso

Nature Biotechnology volume 34, pages 695697 (2016) | Download Citation

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Acknowledgements

This work was supported by NHGRI Career Development Award K99HG008399 to L.P. M.C.C. is supported by F30DK103359-01A1. S.H.O. is supported by P01HL032262 and P30DK049216 (Center of Excellence in Molecular Hematology). D.E.B. is supported by NIDDK Career Development Award K08DK093705, Doris Duke Charitable Foundation, Charles H. Hood Foundation, Cooley's Anemia Foundation, American Society of Hematology and Burroughs Wellcome Fund. G.-C.Y. is supported by NIH R01HL119099 and R01HG005085.

Author information

Affiliations

  1. Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

    • Luca Pinello
    •  & Guo-Cheng Yuan
  2. Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, Massachusetts, USA.

    • Luca Pinello
    •  & Guo-Cheng Yuan
  3. Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA.

    • Matthew C Canver
    • , Stuart H Orkin
    •  & Daniel E Bauer
  4. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

    • Matthew C Canver
    • , Stuart H Orkin
    •  & Daniel E Bauer
  5. Department of Pediatrics, Harvard Medical School and Harvard Stem Cell Institute, Harvard University, Boston, Massachusetts, USA.

    • Matthew C Canver
    • , Stuart H Orkin
    •  & Daniel E Bauer
  6. Department of Microbiology, Immunology, and Molecular Genetics, Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los Angeles, Los Angeles, California, USA.

    • Megan D Hoban
    •  & Donald B Kohn
  7. Howard Hughes Medical Institute, Boston, Massachusetts, USA.

    • Stuart H Orkin

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Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Luca Pinello or Daniel E Bauer or Guo-Cheng Yuan.

Supplementary information

PDF files

  1. 1.

    Supplementary Figures and Texts

    Supplementary Figures 1–17, Supplementary Notes 1–8

Excel files

  1. 1.

    Supplementary Table 1

    SRR1046762 Report reads aligned to genome and amplicons

  2. 2.

    Supplementary Table 2

    SRR1046762 Report reads aligned to genome not matching amplicons

  3. 3.

    Supplementary Table 3

    SRR1046787 Report reads aligned to genome and amplicons

  4. 4.

    Supplementary Table 4

    SRR1046787 report reads aligned to genome not matching amplicons

  5. 5.

    Supplementary Table 5

    SRR1046762 Samples quantification summary

  6. 6.

    Supplementary Table 6

    SRR1046787 Samples quantification summary

  7. 7.

    Supplementary Table 7

    Comparison samples quantification summaries SRR1046762 VS SRR1046787

Zip files

  1. 1.

    Supplementary Data 1

    Report experiment 1

  2. 2.

    Supplementary Data 2

    Report experiment 2

  3. 3.

    Supplementary Data 3

    Report experiment 3

  4. 4.

    Supplementary Data 4

    Simulation Code Data Reports

  5. 5.

    Supplementary Data 5

    CRISPResso pooled on amplicons and genome SRR1046762

  6. 6.

    Supplementary Data 6

    CRISPRessoPooled on amplicons and genome SRR1046787

  7. 7.

    Supplementary Data 7

    CRISPRessoWGS

  8. 8.

    Supplementary Data 8

    CRISPRESSO Compare on VEGFA Site 1

  9. 9.

    Supplementary Data 9

    CRISPResso pooled WGS compare on SRR1046762 vs SRR104 6787

  10. 10.

    Supplementary Data 10

    CRISPResso source code

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DOI

https://doi.org/10.1038/nbt.3583

Editor's note: This article has been peer reviewed.

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