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Related Concept Videos

Genetic Screens02:46

Genetic Screens

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Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...
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Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish
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CRISPRz: a database of zebrafish validated sgRNAs.

Gaurav K Varshney1, Suiyuan Zhang2, Wuhong Pei1

  • 1Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.

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CRISPRz is a new database that collects validated CRISPR/Cas9 target sequences for zebrafish genome editing. This resource helps researchers quickly find highly efficient target sites, accelerating genetic studies in zebrafish.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Zebrafish Research

Background:

  • CRISPR/Cas9 is an efficient genome editing tool increasingly used in zebrafish.
  • The effectiveness of CRISPR/Cas9 relies on specific guide RNA (sgRNA) sequences, which vary widely in activity.
  • Predictive models for sgRNA activity are imperfect, highlighting the need for validated target data.

Purpose of the Study:

  • To develop CRISPRz, a centralized database of experimentally validated CRISPR/Cas9 target sequences for zebrafish.
  • To provide researchers with a resource to identify zebrafish CRISPR target sites with high mutagenic efficiency.

Main Methods:

  • Collected validated CRISPR target sequences from published literature and an in-house large-scale mutagenesis project.
  • Compiled data into a searchable database, CRISPRz.
  • Enabled searching using various identifiers including ZFIN IDs, accession numbers, UniGene IDs, and gene symbols (zebrafish, human, mouse).

Main Results:

  • CRISPRz provides a curated collection of validated CRISPR/Cas9 target sequences for zebrafish.
  • The database includes information on the relative mutagenic activity of these validated target sites.
  • CRISPRz facilitates the selection of high-activity target sequences for efficient zebrafish genome editing.

Conclusions:

  • CRISPRz serves as a valuable resource for zebrafish researchers by consolidating validated CRISPR/Cas9 target sequences.
  • The database aids in the selection of efficient target sites, streamlining genome editing experiments.
  • CRISPRz supports the rapid and reproducible generation of zebrafish mutants for genetic research worldwide.