run_metadata: 9953
This data as json
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| 9953 | ERR5961096 | ERX5601617 | ERS6490236 | ERP123184 | PRJEB39643 | CRISPR tools for zebrafish | ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095 | Other | Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on and off target gene editing we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish we generated an RNA seq dataset of various control larvae at 5 dpf From this while we found no evidence of spontaneous somatic mutations of injected larvae we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments. | ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25 | RNA seq data of 5dpf larvae uninjected controls from the an additional batch. | Uninjected5 | SAMEA8805902 | UNIVERSITY OF CALIFORNIA - DAVIS | ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805902|INSDC center alias:UNIVERSITY OF CALIFORNIA DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Uninjected5|common name:zebrafish|sample name:Uninjected5 | Illumina HiSeq 4000 paired end sequencing | ena EXPERIMENT UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 11 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina HiSeq 4000 | ERP123184 | Illumina HiSeq 4000 paired end sequencing | ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26 | WT5_R1_001.fastq.gz WT5_R2_001.fastq.gz | fastq fastq | 9088444200.0 | 30294814.0 | ena RUN UNIVERSITY OF CALIFORNIA DAVIS 25 05 2021 08:56:51:032 11 | 0:150 1:150 | A:2404715160;C:2098546919;G:2330441921;T:2254532578;N:207622 | 150 | 150 | 2404715160 | 2098546919 | 2330441921 | 2254532578 | 207622 | ERX5601617 | ERS6490236 | ERA4417635 | UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive | UNIVERSITY OF CALIFORNIA - DAVIS | 2 | 0.95076 | 0.93857 | 0.06296 | 0.06222 | 0.68485 | 0.70047 | 0.47429 | 0.48524 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2020-10-31 | Larval | Larval | Undetermined | Undetermined |