Dong Meichen, Jiang Yuchao
Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA.
Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA.
Methods Mol Biol. 2019;1935:155-174. doi: 10.1007/978-1-4939-9057-3_11.
Allele-specific expression is traditionally studied by bulk RNA sequencing, which measures average gene expression across cells. Single-cell RNA sequencing (scRNA-seq) allows the comparison of expression distribution between the two alleles of a diploid organism, and characterization of allele-specific bursting. Here we describe SCALE, a bioinformatic and statistical framework for allele-specific gene expression analysis by scRNA-seq. SCALE estimates genome-wide bursting kinetics at the allelic level while accounting for technical bias and other complicating factors such as cell size. SCALE detects genes with significantly different bursting kinetics between the two alleles, as well as genes where the two alleles exhibit non-independent bursting processes. Here, we illustrate SCALE on a mouse blastocyst single-cell dataset with step-by-step demonstration from the upstream bioinformatic processing to the downstream biological interpretation of SCALE's output.
传统上,等位基因特异性表达是通过批量RNA测序来研究的,该方法测量细胞间的平均基因表达。单细胞RNA测序(scRNA-seq)能够比较二倍体生物两个等位基因之间的表达分布,并对等位基因特异性爆发进行表征。在此,我们描述了SCALE,这是一个用于通过scRNA-seq进行等位基因特异性基因表达分析的生物信息学和统计框架。SCALE在考虑技术偏差和其他复杂因素(如细胞大小)的同时,估计全基因组等位基因水平的爆发动力学。SCALE可检测两个等位基因之间爆发动力学显著不同的基因,以及两个等位基因表现出非独立爆发过程的基因。在这里,我们通过从上游生物信息学处理到SCALE输出的下游生物学解释的逐步演示,在小鼠囊胚单细胞数据集上展示了SCALE。