Sc-Seq of polyploid hepatocytes reveal increasing CNV with the basal ploidy state

Single-cell whole genome sequencing of wt and caspase-2 deficient murine hepatocytes before and after regeneration reveals increasing levels of copy number variation with basal ploidy.
Polyploid hepatocytes from wt and caspase-2 deficient mice were analyzed using single-cell whole genome sequencing. We addressed the question whether caspase-2, the polyploid state or the liver regeneration process impact on the degree of aneuploidy in the liver. We sequenced the ploidy states of 4c, 8c and 16c nuclei isolated form livers of these mice before and 7 days after 2/3 partial hepatectomy (PH). The data was analyzed using the R package AneuFinder (developer version 1.10.1) to call copy number variations (Bakker et al., 2016, van den Bos et al., 2019). The following settings for AneuFinder were used: Fixed ground ploidy for the respective ploidy state of the sample, variable bins (average size of 2Mb), 500kb step size, significance level < 0.05 and R = 20. Breakpoints located within 5 Mb from each other across libraries were grouped and centered using custom made R functions. We introduced an additional data curation step based on total read cound and spikiness of the data. The following cut offs were used: total read count >250kb, spikiness >= 0.11. The data deposited here includes all single profile plots of the sequenced and analyzed nuclei before and after curation based on spikiness and read count.

对野生型和caspase-2缺陷型小鼠肝细胞的单细胞全基因组测序，在再生前后的分析揭示了随着基本倍性的增加，拷贝数变异水平逐渐上升。通过单细胞全基因组测序对野生型和caspase-2缺陷型小鼠的多倍体肝细胞进行了分析。本研究旨在探讨caspase-2、多倍体状态或肝脏再生过程是否会影响肝脏的非整倍程度。对来自这些小鼠肝脏在2/3部分肝切除术（PH）前及术后7天的4c、8c和16c核进行了测序。数据采用R包AneuFinder（开发者版本1.10.1）进行分析，以调用拷贝数变异（Bakker等，2016；van den Bos等，2019）。AneuFinder使用的设置包括：针对样本各自倍性状态的固定基本倍性、可变大小为2Mb的区间、500kb的步长、显著性水平<0.05和R=20。通过自定义R函数将位于各文库中彼此相隔5Mb以内的断裂点进行分组和居中。我们引入了一个基于总读数和数据的尖峰度的额外数据整理步骤。使用的阈值如下：总读数>250kb，尖峰度>=0.11。此处存档的数据包括在基于尖峰度和读数计数整理后，测序和分析的核在整理前后的所有单细胞谱图。