CRISPRz: a database of zebrafish validated sgRNAs

Varshney, Gaurav K.; Zhang, Suiyuan; Adomako-Ankomah, Ashrifia; Fohtung, Jacob; Schaffer, Katherine; Maskeri, Anoo; Slevin, Claire C; Wolfsberg, Tyra G.; Ledin, Johan; Burgess, Shawn M.

doi:10.1093/nar/gkv998

Cited by 43 publications

(33 citation statements)

References 30 publications

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“…Recent developments in high-throughput, multiplex mutagenesis using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and associated systems (Cas9) allow such experiments to be performed using in vivo model systems. 56 …”

Section: Discussionmentioning

confidence: 99%

Genome-wide analysis identifies 12 loci influencing human reproductive behavior

Barban¹,

Jansen²,

Vlaming³

et al. 2016

Nat Genet

315

265

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The genetic architecture of human reproductive behavior – age at first birth (AFB) and number of children ever born (NEB) – has a strong relationship with fitness, human development, infertility and risk of neuropsychiatric disorders. However, very few genetic loci have been identified and the underlying mechanisms of AFB and NEB are poorly understood. We report the largest genome-wide association study to date of both sexes including 251,151 individuals for AFB and 343,072 for NEB. We identified 12 independent loci that are significantly associated with AFB and/or NEB in a SNP-based genome-wide association study, and four additional loci in a gene-based effort. These loci harbor genes that are likely to play a role – either directly or by affecting non-local gene expression – in human reproduction and infertility, thereby increasing our understanding of these complex traits.

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Section: Discussionmentioning

confidence: 99%

Genome-wide analysis identifies 12 loci influencing human reproductive behavior

Barban¹,

Jansen²,

Vlaming³

et al. 2016

Nat Genet

315

265

View full text Add to dashboard Cite

show abstract

“…We generated a genetically defined zebrafish strain to simplify target site selection 19 , a rapid assay (CRISPR-STAT) for determining the somatic activity of sgRNA 20 , and a public database to curate published sgRNA targets and activities 21 in the belief that the transfer of sgRNA information is faster and cheaper than transferring actual mutant zebrafish. We used our high-throughput mutagenesis pipeline to generate the largest published germline transmission dataset in zebrafish 17 .…”

Section: Development Of the Protocolmentioning

confidence: 99%

A high-throughput functional genomics workflow based on CRISPR/Cas9-mediated targeted mutagenesis in zebrafish

et al. 2016

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Zebrafish is a popular model organism for studying development and disease and genetically modified zebrafish provide an essential tool for functional genomic studies. Numerous publications have demonstrated the efficacy of gene targeting in zebrafish using CRISPR/Cas9, and have included descriptions of a variety of tools and methods for guide RNA synthesis and mutant identification. However, most published techniques are not readily scalable to increase throughput. We recently described a CRISPR/Cas9-based high-throughput mutagenesis and phenotyping pipeline in zebrafish. Here, we present a complete workflow for this pipeline, including: target selection; cloning-free single-guide RNA (sgRNA) synthesis; microinjection; validation of the target-specific activity of the sgRNAs; founder screening to identify germline transmitting mutations by fluorescent PCR; determination of the exact lesion by Sanger or next- generation sequencing (including software for analysis); and genotyping in the F1 or subsequent generations. Using these methods, sgRNA's can be evaluated in 3 days, zebrafish transmitting germline mutations can be identified within 3 months and stable lines can be established within 6 months. Realistically, two researchers can target tens to hundreds of genes per year using this protocol.

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“…Several resources have been established to address this need. These include CRISPRz (12), a database of sgRNAs validated in zebrafish, WGE (13), a data resource that contains information about sgRNAs that can be used to target genes of interest and CrisprGE (14), a platform that provides knowledge about sequence mutations caused by sgRNAs previously used in various experimental settings. Nevertheless, a database that allows to compare screening results, such as perturbation phenotypes or sgRNA efficiency, of many different experiments on a genome-wide scale has so far not been available.…”

Section: Introductionmentioning

confidence: 99%

GenomeCRISPR - a database for high-throughput CRISPR/Cas9 screens

et al. 2016

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Over the past years, CRISPR/Cas9 mediated genome editing has developed into a powerful tool for modifying genomes in various organisms. In high-throughput screens, CRISPR/Cas9 mediated gene perturbations can be used for the systematic functional analysis of whole genomes. Discoveries from such screens provide a wealth of knowledge about gene to phenotype relationships in various biological model systems. However, a database resource to query results efficiently has been lacking. To this end, we developed GenomeCRISPR (http://genomecrispr.org), a database for genome-scale CRISPR/Cas9 screens. Currently, GenomeCRISPR contains data on more than 550 000 single guide RNAs (sgRNA) derived from 84 different experiments performed in 48 different human cell lines, comprising all screens in human cells using CRISPR/Cas published to date. GenomeCRISPR provides data mining options and tools, such as gene or genomic region search. Phenotypic and genome track views allow users to investigate and compare the results of different screens, or the impact of different sgRNAs on the gene of interest. An Application Programming Interface (API) allows for automated data access and batch download. As more screening data will become available, we also aim at extending the database to include functional genomic data from other organisms and enable cross-species comparisons.

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CRISPRz: a database of zebrafish validated sgRNAs

Cited by 43 publications

References 30 publications

Genome-wide analysis identifies 12 loci influencing human reproductive behavior

Genome-wide analysis identifies 12 loci influencing human reproductive behavior

A high-throughput functional genomics workflow based on CRISPR/Cas9-mediated targeted mutagenesis in zebrafish

GenomeCRISPR - a database for high-throughput CRISPR/Cas9 screens

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