ArticleGenome research2015
High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 306 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
306 citing papers in PubMed, 1 synthesis or guideline pooled it, 557 citations in OpenAlex.
- Transitioning from wet lab to artificial intelligence: a systematic review of AI predictors in CRISPR.Journal of translational medicine · 2025Pooled it
- Trial
- Catfish Transgenesis and Gene Editing: Overview, Recent Advances, and Future Perspectives.Biology · 2026Review
- Optimised genome editing for precise DNA insertion and substitution using prime editors in zebrafish.eLife · 2026Article
- Bi-allelic ATG12 variants impair autophagy and cause a neurodevelopmental disorder.American journal of human genetics · 2026Article
- Universal conditional knockout approach to multiple species, from fish to human induced pluripotent stem cells.Nucleic acids research · 2026Article
- Article
- Review
- Advancing knock-in approaches for robust genome editing in zebrafish.Biology open · 2026Article
- High-efficiency TadA cytosine base editors for precise modelling of human disease variants.Nature biomedical engineering · 2026Article
- Mass Spectrometry Proteomics: A Key to Faster Drug Discovery.Journal of medicinal chemistry · 2026Review
- Developmental regulation of intestinalbioRxiv : the preprint server for biology · 2025Article
- Advancing Knock-In Approaches for Robust Genome Editing in Zebrafish.bioRxiv : the preprint server for biology · 2025Article
- Zebrafish: A Versatile and Powerful Model for Biomedical Research.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- A cardiovascular, craniofacial, and neurodevelopmental disorder caused by loss-of-function variants in the eIF3 complex component genes EIF3A and EIF3B.American journal of human genetics · 2025Article
- CRISPR-GATE: a one-stop repository and guide to computational resources for genome editing experimentation.Briefings in bioinformatics · 2025Review
- Taperin bundles F-actin at stereocilia pivot points enabling optimal lifelong mechanosensitivity.The Journal of cell biology · 2025Article
- Creb3l3 deficiency promotes intestinal lipid accumulation and alters ApoB-containing lipoprotein kinetics.Journal of lipid research · 2025Article
- Zebrafishology, study design guidelines for rigorous and reproducible data using zebrafish.Communications biology · 2025Review
- A Rapid F0 CRISPR Screen in Zebrafish to Identify Regulator Genes of Neuronal Development in the Enteric Nervous System.Neurogastroenterology and motility · 2025Article
246 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
17 authors at 3 institutions in 2 countries.
Funding
Abstract
The use of CRISPR/Cas9 as a genome-editing tool in various model organisms has radically changed targeted mutagenesis. Here, we present a high-throughput targeted mutagenesis pipeline using CRISPR/Cas9 technology in zebrafish that will make possible both saturation mutagenesis of the genome and large-scale phenotyping efforts. We describe a cloning-free single-guide RNA (sgRNA) synthesis, coupled with streamlined mutant identification methods utilizing fluorescent PCR and multiplexed, high-throughput sequencing. We report germline transmission data from 162 loci targeting 83 genes in the zebrafish genome, in which we obtained a 99% success rate for generating mutations and an average germline transmission rate of 28%. We verified 678 unique alleles from 58 genes by high-throughput sequencing. We demonstrate that our method can be used for efficient multiplexed gene targeting. We also demonstrate that phenotyping can be done in the F1 generation by inbreeding two injected founder fish, significantly reducing animal husbandry and time. This study compares germline transmission data from CRISPR/Cas9 with those of TALENs and ZFNs and shows that efficiency of CRISPR/Cas9 is sixfold more efficient than other techniques. We show that the majority of published "rules" for efficient sgRNA design do not effectively predict germline transmission rates in zebrafish, with the exception of a GG or GA dinucleotide genomic match at the 5' end of the sgRNA. Finally, we show that predicted off-target mutagenesis is of low concern for in vivo genetic studies.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.