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Raw Sanger sequences of the tyr fragment from crispant and control zebrafish embryos

Citation

Lauri, Antonella (2022), Raw Sanger sequences of the tyr fragment from crispant and control zebrafish embryos, Dryad, Dataset, https://doi.org/10.5061/dryad.qv9s4mwjc

Abstract

Thanks to the amenability to genetic modifications, the minimal or non-invasive phenotyping possibilities in early embryos and larvae and the presence of a high percentage of genes orthologous to humans, zebrafish is a successful alternative vertebrate to validate new disease genes and variants and to study mechanisms underlying human diseases. We developed an optimized method allowing early and gentle genotype detection to reduce further possible suffering associated with the generation of genetically modified zebrafish and valid to strategize the employment of “surplus” animals (e.g., those needed solely for line generation or without the desired genotype). The method is based on minimally-invasive tissue (fin) scratching (FS) to obtain genomic DNA material and perform genotyping in early zebrafish embryos. We showcase the method's usefulness for various genotyping needs, including screening both F0 and stable CRISPR/Cas9 lines and obtaining genomic material compatible with Sanger sequencing. Here we provide the raw sequences obtained from FS-derived genomic DNA of single mutant F0 embryos carrying mutations in the tyr gene generated with Base editor (BE) CRISPR/Cas9 technology. We compared the sequencing outcome of FS- vs whole embryos (WE)-based genomic DNA preparation (the WE sequencing results are also provided here). Sequences show the successful C>T (G>A) conversion generating crispant tyr mutants that FS-derived genomic DNA can capture. The resulting dataset demonstrates the compatibility of the method developed with sequencing-based genotyping of early crispant embryos.   

Methods

The data were obtained by Sanger sequencing using a 3500 Genetic Analyzer (Applied Biosystems). Data provided are not processed.

Usage Notes

To view the files common sequences analysis software are sufficient (Ape, Snapgene and Finch).

Funding

Fondazione Umberto Veronesi, Award: individual research fellowship

H2020 Marie Skłodowska-Curie Actions, Award: 844636

Agence Nationale de la Recherche, Award: IHU FOReSIGHT ANR-18-IAHU-0001

Fondation pour la Recherche Médicale, Award: ECO20170637481

Ligue Nationale Contre le Cancer, Award: fellowship

Ministero della Salute, Award: Ricerca 5x1000

Ministero della Salute, Award: CCR-2017-23669081

Ministero della Salute, Award: RCR-2020-23670068_001

Ministero della Salute, Award: RCR-2021-23671215

Ministero della Salute, Award: GR-2019-12368907