Data

Raw AmpSeq reads for the quantification of CRISPR/SpCas9 genome edits in Nicotiana benthamiana plants

The University of Queensland
Miss Kimmy Zhang (Aggregated by)
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ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=info:doi10.48610/a32ca0d&rft.title=Raw AmpSeq reads for the quantification of CRISPR/SpCas9 genome edits in Nicotiana benthamiana plants&rft.identifier=10.48610/a32ca0d&rft.publisher=The University of Queensland&rft.description=This dataset consists of the raw targeted amplicon sequencing reads that was produced in our study titled Comprehensive benchmarking of genome editing quantification methods for plant applications. In the study, we transiently transformed Nicotiana benthamiana leaves with genetic constructs for the expression of SpCas9 and gRNAs targeting endogenous genes. 20 different gRNAs were individually expressed and genome edits were quantified using 8 methods. The NGS-based targeted AmpSeq was used as the benchmark. Illumina MiSeq pair end 150 bp sequencing was used to generate the data. In the majority of samples, two samples with different amplicon sequences were mixed and sequenced together. The output were directly mapped to the different amplicon sequences with a sequence homology threshold as a way of de-multiplexing. In the submitted dataset, files where two samples were multiplexed were duplicated and labelled with the corresponding gRNA and sample ID.&rft.creator=Miss Kimmy Zhang&rft.date=2025&rft_rights= https://guides.library.uq.edu.au/deposit-your-data/license-reuse-data-agreement&rft_subject=eng&rft_subject=CRISPR&rft_subject=Genome editing&rft_subject=Plants&rft_subject=GENETICS&rft_subject=BIOLOGICAL SCIENCES&rft_subject=AGRICULTURAL BIOTECHNOLOGY&rft_subject=TECHNOLOGY&rft.type=dataset&rft.language=English Access the data
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zheng.gong@uq.net.au

Full description

This dataset consists of the raw targeted amplicon sequencing reads that was produced in our study titled "Comprehensive benchmarking of genome editing quantification methods for plant applications". In the study, we transiently transformed Nicotiana benthamiana leaves with genetic constructs for the expression of SpCas9 and gRNAs targeting endogenous genes. 20 different gRNAs were individually expressed and genome edits were quantified using 8 methods. The NGS-based targeted AmpSeq was used as the benchmark. Illumina MiSeq pair end 150 bp sequencing was used to generate the data. In the majority of samples, two samples with different amplicon sequences were mixed and sequenced together. The output were directly mapped to the different amplicon sequences with a sequence homology threshold as a way of de-multiplexing. In the submitted dataset, files where two samples were multiplexed were duplicated and labelled with the corresponding gRNA and sample ID.

Issued: 31 03 2025

Data time period: 06 2023 to 30 06 2023

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Subjects
Agricultural Biotechnology | Biological Sciences | CRISPR | Genetics | Genome editing | Plants | Technology | eng |

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local : UQ:289097

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