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

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.

本数据集包含本课题组在题为《用于植物应用的基因组编辑定量方法综合基准测试》的研究中产生的原始靶向扩增子测序读段（reads）。本研究中，我们通过遗传构建体瞬时转化本氏烟草（*Nicotiana benthamiana*）叶片，以表达SpCas9以及靶向内源基因的向导RNA（gRNA）。本研究共设计20条不同的gRNA并分别进行表达，同时采用8种方法对基因组编辑结果进行定量分析。基于下一代测序（Next Generation Sequencing, NGS）的靶向扩增子测序（AmpSeq）被用作基准参照方法，测序数据通过Illumina MiSeq平台的150 bp双端测序策略生成。在大多数样本中，我们将携带不同扩增子序列的两份样本混合后共同测序；测序得到的原始数据会直接与不同的扩增子序列进行比对，并通过设置序列同源性阈值的方式完成样本解多路复用。在本次提交的数据集中，所有包含混合样本的文件均进行了复制，并通过对应的gRNA与样本ID完成标注。