ArticleNature protocols2018
Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments.
Article in Nature protocols, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
What it found
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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.
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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.
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Who cites it
53 citing papers in PubMed.
- Patient-Derived Organoid-Based CRISPR Screens in Cancer Research: Applications, Advances, and Challenges.Cancer medicine · 2026Review
- Targeted single-cell RNA and perturbation sequencing with TAP-seq.Nature protocols · 2026Review
- Metabolic Engineering ofJournal of fungi (Basel, Switzerland) · 2026Article
- Scaffolding-dependent CASP1 constrains excessive cell-intrinsic inflammatory signaling in leukemia.Cell chemical biology · 2026Article
- Dissecting Epigenetic Drug Response Mechanisms Using CRISPR Knockout Screens.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Functional Genomics: Principles and Methods.Advances in experimental medicine and biology · 2026Review
- High-throughput chemical genomic screening: a step-by-step workflow from plate to phenotype.mSystems · 2025Article
- TERT promoter methylation predicts overall survival, immune cell infiltration and response to immunotherapy in clear cell renal cell carcinoma.Clinical epigenetics · 2025Article
- Article
- PtWAVE: a high-sensitive deconvolution software of sequencing trace for the detection of large indels in genome editing.BMC bioinformatics · 2025Article
- Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancers.Nature communications · 2025Article
- CRISPR-Cas and CRISPR-based screening system for precise gene editing and targeted cancer therapy.Journal of translational medicine · 2024Review
- Aggresome formation promotes ASK1/JNK signaling activation and stemness maintenance in ovarian cancer.Nature communications · 2024Article
- Next-generation forward genetic screens: uniting high-throughput perturbations with single-cell analysis.Trends in genetics : TIG · 2024Review
- Stem cell-like reprogramming is required for leukemia-initiating activity in B-ALL.The Journal of experimental medicine · 2024Article
- CRISPR/Cas9-gene editing approaches in plant breeding.GM crops & food · 2023Review
- CRISPR/SaCas9-based gene editing rescues photoreceptor degeneration throughout a rhodopsin-associated autosomal dominant retinitis pigmentosa mouse model.Experimental biology and medicine (Maywood, N.J.) · 2023Article
- Genome-scale CRISPRi screening: A powerful tool in engineering microbiology.Engineering microbiology · 2023Review
- A Digital PCR Method Based on Highly Specific Taq for Detecting Gene Editing and Mutations.International journal of molecular sciences · 2023Article
- Repurposing CRISPR/Cas to Discover SARS-CoV-2 Detecting and Neutralizing Aptamers.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats) genome-editing experiments offer enormous potential for the evaluation of genomic loci using arrayed single guide RNAs (sgRNAs) or pooled sgRNA libraries. Numerous computational tools are available to help design sgRNAs with optimal on-target efficiency and minimal off-target potential. In addition, computational tools have been developed to analyze deep-sequencing data resulting from genome-editing experiments. However, these tools are typically developed in isolation and oftentimes are not readily translatable into laboratory-based experiments. Here, we present a protocol that describes in detail both the computational and benchtop implementation of an arrayed and/or pooled CRISPR genome-editing experiment. This protocol provides instructions for sgRNA design with CRISPOR (computational tool for the design, evaluation, and cloning of sgRNA sequences), experimental implementation, and analysis of the resulting high-throughput sequencing data with CRISPResso (computational tool for analysis of genome-editing outcomes from deep-sequencing data). This protocol allows for design and execution of arrayed and pooled CRISPR experiments in 4-5 weeks by non-experts, as well as computational data analysis that can be performed in 1-2 d by both computational and noncomputational biologists alike using web-based and/or command-line versions.
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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.