CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters
Description
CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters
Collected and generated data for the paper
## Data Tables
Off-target score data for the ROC analysis using Haeussler dataset [2].
Data from the table below is used to generate the Figure-2, Table-1 and Supplementary Figure-1 in the corresponding paper [1]. Don't forget to cite the corresponding studies as well if you use this table.
- Haeussler_mm6_scores.csv.gz: This table includes the off-targeting scores of 1167036 off-target sequences, computed with CRISPRoff[1], CCTop[3], CFD[4], Cropit[5], Elevation (Elevation-score)[6], MIT[2,7] and VfoldCAS[8] methods. Off-target data has been taken from the Haeussler dataset [2].
Analysis with CIRCLE-seq dataset [9]
Data in all the three tables below has been generated to analyze the CIRCLE-seq dataset [9]. This data is further used to generate the Figure-3, Figure-4, and Supplementary Figure-4 in the corresponding paper. Don't forget to cite the corresponding studies as well if you use these tables.
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CIRCLEseq_known_off_scores.csv.gz: This table is used when generating the Figure-3 in the paper. It includes the 7 different off-targeting scores of CIRCLE-seq reported off-target sequences and the read counts from CIRCLE-seq experiments.
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CIRCLEseq_mm6_off_scores.csv.gz: This table is used when generating the Figure-4 in the paper. It includes the 7 different off-targeting scores of RIsearch2(v2.1)[10] based off-target predictions for CIRCLE-seq gRNAs.
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CIRCLEseq_specificities.csv.gz: This table is used when generating the Supplementary Figure-4 in the supplementary document of the paper. It includes the specificty scores of CIRCLE-seq gRNAs, computed with CRISPRspec[1], MIT[2,7], MIT*[1,2,7] and Elevation (Elevation-aggregate)[6] methods.
Analysis with SITE-seq dataset [11]
Data in all the three tables below has been generated to analyze the SITE-seq dataset [11]. This data is further used to generate the Figure-5, Supplementary Figure-2 and Supplementary Figure-3 in the corresponding paper. Don't forget to cite the corresponding studies as well if you use these tables.
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SITEseq_known_off_scores.csv.gz: This table is used when generating the Supplementary Figure-2 in the supplementary document of the paper. It includes the 7 different off-targeting scores of SITE-seq reported off-target sequences and the read counts from SITE-seq experiments.
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SITEseq_mm6_off_scores.csv.gz: This table is used when generating the Supplementary Figure-3 in the supplementary document of the paper. It includes the 7 different off-targeting scores of RIsearch2(v2.1) based off-target predictions for SITE-seq gRNAs.
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SITEseq_specificities.csv.gz: This table is used when generating the Figure-5 in the paper. It includes the 4 different specificty scores of SITE-seq gRNAs.
Specificity-Efficiency Analysis
This data is used to generate the Figure-6 and Supplementary Figure-5 in the corresponding paper. Don't forget to cite the corresponding studies as well if you use these tables.
- Doench_Wang_specificity_grps.csv.gz: This table includes the specificity group of 3802 gRNA/on-target sequences, computed with CRISPRspec and MIT methods. gRNA sequence and modulation frequency data have been taken from the Haeussler dataset [2].
## Citation
If you find this data useful for your research, please cite the following works where appropriate:
- [Our citation comes here]
- Haeussler, M., Schonig, K., Eckert, H., Eschstruth, A., Mianne, J., Renaud, J.B., Schneider-Maunoury, S., Shkumatava, A., Teboul, L., Kent, J., Joly, J.S., Concordet, J.P.: Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol. 17(1), 148 (2016). PMID 27380939
- Stemmer, M., Thumberger, T., Del Sol Keyer, M., Wittbrodt, J., Mateo, J.L.: CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool. PLoS ONE 10(4), 0124633 (2015). PMID 25909470
- Doench, J.G., Fusi, N., Sullender, M., Hegde, M., Vaimberg, E.W., Donovan, K.F., Smith, I., Tothova, Z., Wilen, C., Orchard, R., Virgin, H.W., Listgarten, J., Root, D.E.: Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat. Biotechnol. 34(2), 184–191 (2016). PMID 26780180
- Singh, R., Kuscu, C., Quinlan, A., Qi, Y., Adli, M.: Cas9-chromatin binding information enables more accurate CRISPR off-target prediction. Nucleic Acids Res. 43(18), 118 (2015). PMID 26032770
- Listgarten, J., Weinstein, M., Kleinstiver, B.P., Sousa, A.A., Joung, J.K., Crawford, J., Gao, K., Hoang, L., Elibol, M., Doench, J.G., Fusi, N.: Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs. Nature Biomedical Engineering 2, 38–47 (2018). PMID 29998038
- Hsu, P.D., Scott, D.A., Weinstein, J.A., Ran, F.A., Konermann, S., Agarwala, V., Li, Y., Fine, E.J., Wu, X., Shalem, O., Cradick, T.J., Marraffini, L.A., Bao, G., Zhang, F.: DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol. 31(9), 827–832 (2013). PMID 23873081
- Xu, X., Duan, D., Chen, S.J.: CRISPR-Cas9 cleavage efficiency correlates strongly with target-sgRNA folding stability: from physical mechanism to off-target assessment. Sci Rep 7(1), 143 (2017). PMID 28273945
- Tsai, S.Q., Nguyen, N.T., Malagon-Lopez, J., Topkar, V.V., Aryee, M.J., Joung, J.K.: CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets. Nat. Methods 14(6), 607–614 (2017). PMID 28459458
- Alkan, F., Wenzel, A., Palasca, O., Kerpedjiev, P., Rudebeck, A.F., Stadler, P.F., Hofacker, I.L., Gorodkin, J.: RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets. Nucleic Acids Res. (2017). PMID 28108657
- Cameron, P., Fuller, C.K., Donohoue, P.D., Jones, B.N., Thompson, M.S., Carter, M.M., Gradia, S., Vidal, B., Garner, E., Slorach, E.M., Lau, E., Banh, L.M., Lied, A.M., Edwards, L.S., Settle, A.H., Capurso, D., Llaca, V., Deschamps, S., Cigan, M., Young, J.K., May, A.P.: Mapping the genomic landscape of CRISPR-Cas9 cleavage. Nat. Methods 14(6), 600–606 (2017). PMID 28459459
## Contact
ferro@rth.dk gorodkin@rth.dk
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