gRNA Designer for Zebrafish

In this websever, we scanned all potential CRISPR/Cas9 targets on zebrafish genome exons (Refseq annotation, with NGG as PAM sequence) and evaluated each targets from the following four aspects:

1. Chromatin Accessibility status labeled by "OC" or "CC"

2. Sequence feature evaluation calculated by SSC

3. Potential off-target site evaluated by sequence similarity with other site of genome

Once an user submitting a query via a gene name (both Refseq ID and official gene symbol are supported), the matching records on NL/OC region and with few potential off-target site will be given high priority to return to users. If no preferential targets returned, all matching result will be returned.

Briefly, the three aspects of evaluation standard were identified as follow:

1. Chromatin Accessibility Status Identification
  • The ATAC-seq reads of 256-cell and dome stages were aligned to the zebrafish genome built using zv9/danRer7 using bowtie2 (v 2.2.3). We removed the reads that were mapped to the scaffold chromosome and the reads with MAPQ lower than 30. The remaining reads were used to call peaks using the MACS2 (v (callpeak function with parameter -q 0.01 –SPMR. We combined the peaks called from the two stages. Each peak summit was extended 1000 bp upstream and 1000 bp downstream, and the merged regions were identified as open chromatin (OC) regions. The remaining regions on the genome were regarded as close chromatin regions (CC) regions.
  • We regard gRNAs targeting on OC region as potential high efficiency gRNAs.
  • 2. Sequence Feature Score Calculation
  • For sequence feature evaluation, we used the source code of Sequence Scan for CRISPR (SSC source code) which includes two core command Fasta2Spacer and SSC. Firstly, we used bedtools getfasta function to generate 40bp sequence for each target. Secondly, Fasta2Spacer command was used to scan each fasta record to get target site. Then SSC scores for each targets were calculated by SSC command.
  • We regard gRNAs with higher SSC score as potential high efficiency gRNAs.
  • 3. Potential Off-target Sites Counting
  • For each potential target, we evaluated the possibility of off-target binding by calculating 0-2 mismatched sites on the zebrafish genome. We used bowtie version 1.0.1 to output all 0-2 mismatched sites on the genome with -v 2 -a parameters, and then a custom Python code was used to calculate the mismatched site number for each target. We regard targets with more similar site on genome as high-possibility-off-target sites.
  • The result format 'x:y:z' represents for each gRNA targets, there are x other sites in zebrafish genome which are 0-mismatch similar with target site, y sites for 1-mismach and z sites for 2-mismatch. Generally, CRISPR/Cas9 potential off-target sites tend to locate at similar-sequence sites on genome. Therefore, we recommand users to design gRNA on the targets with less similar sequence site.
  • Reference:

    Chen Y, Zeng S, Hu R, et al. Using local chromatin structure to improve CRISPR/Cas9 efficiency in zebrafish.[J]. Plos One, 2017, 12(8):e0182528.


    You can submit a gene name (both Refseq ID and official gene symbol are supported) and exon number (also chromatin accessibility status, optional) to get potential Cas9 cleavage target sites with following information:

    1. Genomic location

    2. Chromatin Accessibility status

    3. Sequence feature evaluation

    4. Potential off-target site evaluation

    Gene name query

    Your gene:

    Exon number:

    Chromatin accessibility status: