title: Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing.
abstract: We developed a targeted RNA sequencing method that couples microfluidics-based multiplex PCR and deep sequencing (mmPCR-seq) to uniformly and simultaneously amplify up to 960 loci in 48 samples independently of their gene expression levels and to accurately and cost-effectively measure allelic ratios even for low-quantity or low-quality RNA samples. We applied mmPCR-seq to RNA editing and allele-specific expression studies. mmPCR-seq complements RNA-seq for studying allelic variations in the transcriptome.
authors.affiliation: Department of Genetics, Stanford University, Stanford, California, USA.
authors.forename: Rui
authors.initials: R
authors.lastname: Zhang
authors.affiliation: Department of Pathology, Stanford University, Stanford, California, USA.
authors.forename: Xin
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Genetics, Stanford University, Stanford, California, USA.
authors.forename: Gokul
authors.initials: G
authors.lastname: Ramaswami
authors.affiliation: Department of Pathology, Stanford University, Stanford, California, USA.
authors.forename: Kevin S
authors.initials: KS
authors.lastname: Smith
authors.affiliation: McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada.
authors.forename: Gustavo
authors.initials: G
authors.lastname: Turecki
authors.affiliation: 1] Department of Genetics, Stanford University, Stanford, California, USA. [2] Department of Pathology, Stanford University, Stanford, California, USA.
authors.forename: Stephen B
authors.initials: SB
authors.lastname: Montgomery
authors.affiliation: Department of Genetics, Stanford University, Stanford, California, USA.
authors.forename: Jin Billy
authors.identifier: 0000000307131399
authors.initials: JB
authors.lastname: Li
mesh_terms: D000483:Alleles; D001921:Brain / Q000378:metabolism / Q000473:pathology; D058893:DNA Barcoding, Taxonomic; D018076:DNA, Complementary / Q000378:metabolism; D020869:Gene Expression Profiling; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D060885:Multiplex Polymerase Chain Reaction / Q000379:methods*; D012313:RNA / Q000032:analysis*; D017393:RNA Editing; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000191:economics / Q000379:methods; D017423:Sequence Analysis, RNA / Q000191:economics / Q000379:methods*; D059467:Transcriptome
chemical_list: D018076:DNA, Complementary; D012313:RNA