Publications

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

Jiang, Y., Zhang, N.R., Li, M.

Allele-specific expression is traditionally studied by bulk RNA sequencing, which measures average expression across cells. Single-cell RNA sequencing allows the comparison of expression distribution between the two alleles of a diploid organism and the characterization of allele-specific bursting. Here, 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 cis control in gene expression overwhelmingly manifests as differences in burst frequency.

Citation

Jiang, Y., Zhang, N.R., Li, M. "SCALE: modeling allele-specific gene expression by single-cell RNA sequencing" Genome Biology (2017): 74