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SCALE: modeling allele specific gene expression by single cell RNA sequencing

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Figure

Fig. 1 Allele-specific transcriptional bursting and gene categorization by single-cell ASE.genes switch between the a Transcription from DNA to RNA occurs in bursts, where “ON” and the “OFF” states
Fig. 2 Overview of analysis pipeline of SCALE. SCALE takes as inputallele-specific read counts at heterozygous loci and carries out threemajor steps: (i) gene classification using an empirical Bayes method,(ii) estimation of allele-specific transcriptional kinetics using aPoisson-Beta hierarchical model with adjustment of technicalvariability and cell size, (iii) testing of the two alleles of a gene todetermine if they have different bursting kinetics and/or non-independent firing using a hypothesis testing framework
Fig. 3 Allele-specific transcriptional kinetics of 7486 genes from 122 mouse blastocyst cells
Fig. 4 Examples of significant genes from hypothesis testing. a The two alleles of the gene have significantly different burst frequencies from thebootstrap-based testing
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