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Analyzing CRISPR genome-editing experiments with CRISPResso

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Figure 1: Quantification and visualization of NHEJ and HDR mutagenesis profiles.

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Gene Expression Omnibus

References

  1. 1

    Cong, L. et al. Science 339, 819–823 (2013).

    CAS  Article  Google Scholar 

  2. 2

    Mali, P. et al. Science 339, 823–826 (2013).

    CAS  Article  Google Scholar 

  3. 3

    Ran, F.A. et al. Nat. Protoc. 8, 2281–2308 (2013).

    CAS  Article  Google Scholar 

  4. 4

    Sander, J.D. & Joung, J.K. Nat. Biotechnol. 32, 347–355 (2014).

    CAS  Article  Google Scholar 

  5. 5

    Canver, M.C. et al. J. Biol. Chem. 289, 21312–21324 (2014).

    Article  Google Scholar 

  6. 6

    Ran, F.A. et al. Cell 154, 1380–1389 (2013).

    CAS  Article  Google Scholar 

  7. 7

    Güell, M., Yang, L. & Church, G.M. Bioinformatics 30, 2968–2970 (2014).

    Article  Google Scholar 

  8. 8

    Hsu, P.D. et al. Nat. Biotechnol. 31, 827–832 (2013).

    CAS  Article  Google Scholar 

  9. 9

    Fu, Y. et al. Nat. Biotechnol. 31, 822–826 (2013).

    CAS  Article  Google Scholar 

Download references

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.

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

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The authors declare no competing financial interests.

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

Supplementary information

Supplementary Figures and Texts

Supplementary Figures 1–17, Supplementary Notes 1–8 (PDF 28900 kb)

Supplementary Table 1

SRR1046762 Report reads aligned to genome and amplicons (XLSX 13 kb)

Supplementary Table 2

SRR1046762 Report reads aligned to genome not matching amplicons (XLSX 922 kb)

Supplementary Table 3

SRR1046787 Report reads aligned to genome and amplicons (XLSX 12 kb)

Supplementary Table 4

SRR1046787 report reads aligned to genome not matching amplicons (XLSX 1835 kb)

Supplementary Table 5

SRR1046762 Samples quantification summary (XLSX 10 kb)

Supplementary Table 6

SRR1046787 Samples quantification summary (XLSX 10 kb)

Supplementary Table 7

Comparison samples quantification summaries SRR1046762 VS SRR1046787 (XLSX 11 kb)

Supplementary Data 1

Report experiment 1 (ZIP 1198 kb)

Supplementary Data 2

Report experiment 2 (ZIP 180 kb)

Supplementary Data 3

Report experiment 3 (ZIP 1571 kb)

Supplementary Data 4

Simulation Code Data Reports (ZIP 36513 kb)

Supplementary Data 5

CRISPResso pooled on amplicons and genome SRR1046762 (ZIP 1892 kb)

Supplementary Data 6

CRISPRessoPooled on amplicons and genome SRR1046787 (ZIP 2386 kb)

Supplementary Data 7

CRISPRessoWGS (ZIP 344 kb)

Supplementary Data 8

CRISPRESSO Compare on VEGFA Site 1 (ZIP 247 kb)

Supplementary Data 9

CRISPResso pooled WGS compare on SRR1046762 vs SRR104 6787 (ZIP 393 kb)

Supplementary Data 10

CRISPResso source code (ZIP 675 kb)

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Pinello, L., Canver, M., Hoban, M. et al. Analyzing CRISPR genome-editing experiments with CRISPResso. Nat Biotechnol 34, 695–697 (2016). https://doi.org/10.1038/nbt.3583

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