RT Journal Article
SR Electronic
T1 Modeling allele-specific gene expression by single-cell RNA sequencing
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 109629
DO 10.1101/109629
A1 Yuchao Jiang
A1 Nancy R Zhang
A1 Mingyao Li
YR 2017
UL http://biorxiv.org/content/early/2017/02/17/109629.abstract
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