ArticleNucleic acids research2022
CRISPRroots: on- and off-target assessment of RNA-seq data in CRISPR-Cas9 edited cells.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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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.
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Who cites it
17 citing papers in PubMed.
- CRISPR/Cas9 Mediated Genome Editing for Enhancing Abiotic Stress Tolerance in Rice: An Omics Guided Perspective.Molecular biotechnology · 2026Review
- From Bench to Bedside: Ethical and Clinical Best Practices for Genome Editing Applications.International journal of molecular sciences · 2026Review
- Review
- Off-target effects in CRISPR-Cas genome editing for human therapeutics: Progress and challenges.Molecular therapy. Nucleic acids · 2025Review
- CRISPR-GATE: a one-stop repository and guide to computational resources for genome editing experimentation.Briefings in bioinformatics · 2025Review
- Enhancing human NK cell antitumor function by knocking out SMAD4 to counteract TGFβ and activin A suppression.Nature immunology · 2025Article
- Accelerating crop improvement via integration of transcriptome-based network biology and genome editing.Planta · 2025Review
- The Evolution of Nucleic Acid-Based Diagnosis Methods from the (pre-)CRISPR to CRISPR era and the Associated Machine/Deep Learning Approaches in Relevant RNA Design.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Combining Off-flow, a Nextflow-coded program, and whole genome sequencing reveals unintended genetic variation in CRISPR/Cas-edited iPSCs.Computational and structural biotechnology journal · 2024Article
- Generating universal anti-CD19 CAR T cells with a defined memory phenotype by CRISPR/Cas9 editing and safety evaluation of the transcriptome.Frontiers in immunology · 2024Article
- Progress and harmonization of gene editing to treat human diseases: Proceeding of COST Action CA21113 GenE-HumDi.Molecular therapy. Nucleic acids · 2023Review
- Review of CRISPR/Cas Systems on Detection of Nucleotide Sequences.Foods (Basel, Switzerland) · 2023Review
- Review
- Golgi fragmentation - One of the earliest organelle phenotypes in Alzheimer's disease neurons.Frontiers in neuroscience · 2023Article
- DANGER analysis: risk-averse on/off-target assessment for CRISPR editing without a reference genome.Bioinformatics advances · 2023Article
- CRISPRon/off: CRISPR/Cas9 on- and off-target gRNA design.Bioinformatics (Oxford, England) · 2022Article
- Advances in CRISPR/Cas9.BioMed research international · 2022Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The CRISPR-Cas9 genome editing tool is used to study genomic variants and gene knockouts, and can be combined with transcriptomic analyses to measure the effects of such alterations on gene expression. But how can one be sure that differential gene expression is due to a successful intended edit and not to an off-target event, without performing an often resource-demanding genome-wide sequencing of the edited cell or strain? To address this question we developed CRISPRroots: CRISPR-Cas9-mediated edits with accompanying RNA-seq data assessed for on-target and off-target sites. Our method combines Cas9 and guide RNA binding properties, gene expression changes, and sequence variants between edited and non-edited cells to discover potential off-targets. Applied on seven public datasets, CRISPRroots identified critical off-target candidates that were overlooked in all of the corresponding previous studies. CRISPRroots is available via https://rth.dk/resources/crispr.
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What Socratic 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 Socratic graph.