NGS data from: Detection of unintended on-target effects in CRISPR genome editing by DNA donors carrying diagnostic mutations

We developed a method to detect copy number variation and loss of heterozygosity in genome-edited cell lines by only sequencing the edited site. We introduced different substitutions on both chromosomes of diploid H9 human embryonic stem cells using CRISPR/Cas9 and a mixture of homology-directed repair donor DNAs carrying different substitutions. Here, we deposit the associated sequencing data (BAM-files) generated by extracting genomic DNA from genome-edited H9 cells, PCR amplifying the region of interest and sequencing on a MiSeq platform. We sequenced the edited site of cell bulks to investigate the editing efficiencies of individual donors from the donor mixtures. For proof of concept, we isolated over 850 cellular clones from the edited cell bulks and sequenced the edited site and heterozygous positions flanking the edited site to determine the number of alleles at the edited site and detect copy-neutral loss of heterozygosity. Additionally, we sequenced the DNA donors to assess, t..., ,

本研究开发了一种仅通过测序编辑位点，即可检测基因组编辑细胞系中拷贝数变异（copy number variation, CNV）与杂合性缺失（loss of heterozygosity, LOH）的方法。本研究利用CRISPR/Cas9系统与携带不同碱基替换的同源定向修复（homology-directed repair, HDR）供体DNA混合物，对二倍体H9人胚胎干细胞的两条染色体分别引入了不同的碱基替换。本研究在此上传相关测序数据（BAM文件）：该数据通过提取基因组编辑后的H9细胞的基因组DNA，对目标区域进行PCR扩增，并在MiSeq测序平台上完成测序获得。我们对批量编辑细胞的编辑位点进行测序，以探究供体混合体系中各单一供体的编辑效率。为验证方法可行性，我们从批量编辑的细胞中分离得到850余株细胞克隆，并对编辑位点及其侧翼的杂合位点进行测序，以确定编辑位点的等位基因数量，同时检测拷贝中性杂合性缺失（copy-neutral loss of heterozygosity, CN-LOH）。此外，我们还对供体DNA进行了测序，以开展相关评估，原文后续内容未完整提供。