We present GuideScan software for the design of CRISPR guide RNA libraries that can be used to edit coding and noncoding genomic regions. GuideScan produces high-density sets of guide RNAs (gRNAs) for single- and paired-gRNA genome-wide screens. We also show that the trie data structure of GuideScan enables the design of gRNAs that are more specific than those designed by existing tools.
At a glance
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- Supplementary Figure 1: Output of GuideScan and competitor tools. (602 KB)
(a) Genome-wide density of guides in GuideScan’s murine Cas9 database (blue), compared to the UCSC genome track from mit.edu (red). (b) Dot plot showing specificity scores and number of perfect off-target sites for promiscuous guides designed by the mit.edu gRNA web design tool. Data points are color-coded based on the specificity scores of the corresponding gRNAs following the guidelines of mit.edu web portal (red = low specificity, score 1-19; yellow = medium specificity, score 20-49; green = high specificity, score 50-100).
- Supplementary Figure 2: Uncropped gel images. (232 KB)
(a) Uncropped gel of T7 cleavage assay shown in Figure 2d. First lane shows the separations of the 1kb+ (Invitrogen) molecular size ladder. The size of selected bands of the ladder is shown on the left. Numbers above gel refer to gel lanes on which T7 assays were run. Red and Blue bars below gel highlight assays unrelated to this work (red; lanes 1—4), and those shown in Fig. 2 (blue; lanes 5—10); (b) Uncropped gel of PCR shown on Figure 2f; (c) Uncropped gel of PCRs shown in Fig. 2e. Bars below gels in panels b—c highlight the chromosomal region amplified.
- Supplementary Text and Figures (689 KB)
Supplementary Figures 1,2 and Supplementary Note 1
- Supplementary Table 1 (67 KB)
Off-target reporting by competitor tools for a subset of promiscuous gRNAs.
- Supplementary Table 2 (80 KB)
Number of gRNAs with off-targets with 0 or 1 mismatches.
- Supplementary Table 3 (51 KB)
Genomic Coordinates used for tool comparison experiment.
- Supplementary Code (27,970 KB)