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Modeling allele-specific gene expression by single-cell RNA sequencing

By Yuchao Jiang, Nancy R Zhang, Mingyao Li

Posted 17 Feb 2017
bioRxiv DOI: 10.1101/109629 (published DOI: 10.1186/s13059-017-1200-8)

Allele-specific expression is traditionally studied by bulk RNA sequencing, which measures average expression across cells. Single-cell RNA sequencing (scRNA-seq) allows the comparison of expression distribution between the two alleles of a diploid organism and thus the characterization of allele-specific bursting. We propose SCALE to analyze genome-wide allele-specific bursting, with adjustment of technical variability. SCALE detects genes exhibiting allelic differences in bursting parameters, and genes whose alleles burst non-independently. We apply SCALE to mouse blastocyst and human fibroblast cells and find that, globally, cis control in gene expression overwhelmingly manifests as differences in burst frequency.

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