Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1272011 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We report transcriptome wide edits comparison between split-engineered base editors and intact base editors. Our results show that, split-engineered base editors show backgound levels of unique C>U edits when compared to intact base editors.
2021-10-18 | GSE181109 | GEO
Project description:We developed CROss-seq, a versatile, efficient and cost-effective method for genome-wide off-target profiling in multiple genome editing systems. Purpose: CRISPR-mediated genome editors have been widely deployed in basic research and therapeutic applications, yet the targeting specificity of these editors is still the major concern. Method to examine the genome-wide off-target effects of these editors remains lagging behind. Methods: in vivo CROss-seq, the transfected cells are labeled with N3-kethoxal for 45 minutes; in vitro CROss-seq, the genomic DNA are incubated with N3-kethoxal for 2 hours. The treated gDNA are processed with biotin click reaction, fragmentation, adapter ligation, and pull-down steps. The purified libraries were sequenced on Illumina HiSeq X Ten platform to generate paired-end reads. Results: Through CROss-seq we successfully both in vivo and in vitro to evaluate the off-target effects of CRISPR-Cas9 nuclease, base editors and prime editor. The in vivo assay was more specific while in vitro assay was more sensitive, highlighting the necessity of coupling in vivo and in vitro assays to achieve a comprehensive and precise assessment of the off-target effects. CROss-seq also revealed chromatin accessibility plays an important role in the off-target activity of the CRISPR-based editing. In addition, we identified limited genome-wide off-target sites of BE and PE in vivo, indicating that both editors were highly specific to target site.
2023-05-12 | GSE182568 | GEO
Project description:Genome-wide specificity of prime editors in plants
| PRJNA636219 | ENA
Project description:The continued development of novel genome editors calls for a universal method to analyze their off-target effects. Here we describe a versatile method, called Tracking-seq, for in situ identification of off-target effects that is broadly applicable to common genome-editing tools, including Cas9, base editors and prime editors. Through tracking replication protein A (RPA)-bound single-stranded DNA followed by strand-specific library construction, Tracking-seq requires a low cell input and is suitable for in vitro, ex vivo and in vivo genome editing, providing a sensitive and practical genome-wide approach for off-target detection in various scenarios. We show, using the same guide RNA, that Tracking-seq detects heterogeneity in off-target effects between different editor modalities and between different cell types, underscoring the necessity of direct measurement in the original system.
2024-05-31 | GSE236360 | GEO