PT  - JOURNAL ARTICLE
AU  - Yuchao Jiang
AU  - Nancy R Zhang
AU  - Mingyao Li
TI  - Modeling allele-specific gene expression by single-cell RNA sequencing
AID  - 10.1101/109629
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 109629
4099  - http://biorxiv.org/content/early/2017/02/17/109629.short
4100  - http://biorxiv.org/content/early/2017/02/17/109629.full
AB  - 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.scRNA-seqsingle-cell RNA sequencingASEallele-specific expressionSNPsingle-nucleotide polymorphismRNA-seqRNA sequencingMEmonoallelic expressionRMErandom monoallelic expressionFISHfluorescence in situ hybridizationEMexpectation-maximizationFDRfalse discovery rateRPKMreads per kilo base per million readsPCAprincipal component analysisQCquality controlQTLquantitative trait loci