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General Information
Name
DRSC_sgRNA_designs
Species
D. melanogaster
Result type
FlyBase ID
FBlc0003481
Project
Data Provider
Title
A set of predicted sgRNAs designed to be suitable for genome engineering using CRISPR/Cas9.
Status
Current
Accessions
    Biosample Source
    Overview
    Strain
    Stage
    Sex
    Tissue isolated
    Other tissues studied
    Cell component
    Cell line
    Key genes
    Methods
    Sample preparation
    Data Analyzed
    Assay
    Assay methods
    Key genes
    Protocol
    Mode of Assay
    Raw Data Analyzed (0)
    Assay / Reagent collection
    Type
    Title
    Processed Data Analyzed (0)
    Result
    Type
    Title
    Analysis
    Methods
    Reference Genome
    Reference Annotation
    Dmel R6.24
    Data analysis
    All 23-mers having a 3-prime proto-spacer adjacent motif (PAM) sequence (NGG) and a 15 base sequence unique to the genome (including the PAM) were identified in the D. melanogaster Release6 genome assembly (forward and reverse strands); these constituted all possible 23-mer designs that could possibly be suitable as sgRNA. These designs were further assessed for predicted efficiency and off-target effects. Because base pair mismatches can be tolerated outside the seed region, predicted sgRNAs were evaluated for potential off-target sites allowing for 3, 4 or 5 mismatches, corresponding to low, medium and high stringencies, respectively.
    The "efficiency" scores range from 1.47-12.32 (higher is better, > 5 recommended, see FBrf0229582 for details).
    The "seed" score measures the number of bases in the 15 bases next to the PAM that are unique in the genome; these scores range from 12 to 15.
    The "frameshift" score represents the percent of frameshift changes predicted by micro-homology around the target site; these scores range from 0-100 (higher is better, >50 recommended, see PMID:24972169 for details).
    The "machine learning" score was developed by training and testing against a fly cell-based screen dataset (scores not yet validated in cells or in vivo); scores range from 0-1 (higher is better, see FBrf0239612 for details).
    The "OT" (off-target) score represents a weighted sum of the number of off-target sites at various mismatch stringencies (low_stringency_mismatches + 0.1*med_stringency_mismatches + 0.01*high_stringency_mismatches); scores range from 0-5441.73 (lower is better, less than 1 recommended).
    These designs were assessed for overlapping genomic variants in lines commonly used for CRISPR work (S2R+, TRiP Cas9 lines); these variants could prevent sgRNA targeting.
    Comments
    First data version provided (2018-09-24) has been deprecated.
    This data update incorporates newer FlyBase gene model anntotations, information on genomic variants overlapping sgRNA designs, and a new machine learning prediction score.
    At FlyBase, these sgRNA designs are viewable in JBrowse, sorted into five different JBrowse tracks based on their specificity (predicted off-target matches): 1. no off-target sites (high stringency), 2. no off-target sites (medium stringency), 3. no off-target sites (low stringency), 4. 1-3 off-target sites (low stringency), 5. more than 3 off-target sites and/or at least 1 off-target site in a CDS (low stringency).
    For additional information on overlappng genomic variants and off-target sites, use the sgRNA design's sequence to search the DRSC CRISPR tool (http://www.flyrnai.org/crispr/).
    Associated Data
    Size
    10613118 predicted sgRNAs
    Additional Information
    Synonyms and Secondary IDs (3)
    Reported As
    Symbol Synonym
    DRSC_sgRNA_designs
    Name Synonyms
    A set of predicted sgRNAs designed to be suitable for genome engineering using CRISPR/Cas9.
    Secondary FlyBase IDs
      References (3)