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. 2021 Aug 20;22:236. doi: 10.1186/s13059-021-02462-4

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© The Author(s) 2021

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 6 — Analysis of large deletions in iPSC single-cell clones. a Raw deletion indexes of iPSC single-cell clones. Clone #31 highlighted in red indicated the only one clone with significant deletion mutation on one allele among 52 gene-edited iPSC single-cell clones. See details of all the clones in Additional file 1: Fig. S10. b Heterozygous genotype of the two SNPs identified on the BCL11A alleles. c No loss of heterozygosity in all the iPSC single-cell clones by SNP analysis. A total of 52 edited single-cell clones were analyzed by PCR and nanopore sequencing. d Assessment of mega-deletions in edited iPSC single-cell clones by qPCR analysis. We conducted qPCR to assess copies of gDNA at 40, 80, and 160 kb away from the target site BCL11A-1. AAVS1, located on another chromosome, served as a control. The data from WT cells were used to normalize the copy numbers of edited cells. We aggregated all the data points surrounding the BCL11A-1 editing site of each clone to increase statistical power. The data in c and d were statistically analyzed by a two-way ANOVA test. “ns” means no significance (P > 0.05).