title: Concordance among digital gene expression, microarrays, and qPCR when measuring differential expression of microRNAs.
abstract: Profiling microRNA (miRNA) expression is of widespread interest given the critical role of miRNAs in many cellular functions. Profiling can be achieved via hybridization-based (microarrays), sequencing-based, or amplification-based (quantitative reverse transcription-PCR, qPCR) technologies. Among these, microarrays face the significant challenge of accurately distinguishing between mature and immature miRNA forms, and different vendors have developed different methods to meet this challenge. Here we measure differential miRNA expression using the Affymetrix, Agilent, and Illumina microarray platforms, as well as qPCR (Applied Biosystems) and ultra high-throughput sequencing (Illumina). We show that the differential expression measurements are more divergent when the three types of microarrays are compared than when the Agilent microarray, qPCR, and sequencing technology measurements are compared, which exhibit a good overall concordance.
authors.affiliation: Genomic Technologies Facility, Center for Integrative Genomics, University of Lausanne, Genopode Building, Lausanne, Switzerland. sylvain.pradervand@unil.ch
authors.forename: Sylvain
authors.initials: S
authors.lastname: Pradervand
authors.forename: Johann
authors.initials: J
authors.lastname: Weber
authors.forename: Frédéric
authors.initials: F
authors.lastname: Lemoine
authors.forename: Floriane
authors.initials: F
authors.lastname: Consales
authors.forename: Alexandra
authors.initials: A
authors.lastname: Paillusson
authors.forename: Mélanie
authors.initials: M
authors.lastname: Dupasquier
authors.forename: Jérôme
authors.initials: J
authors.lastname: Thomas
authors.forename: Hannes
authors.initials: H
authors.lastname: Richter
authors.forename: Henrik
authors.initials: H
authors.lastname: Kaessmann
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Beaudoing
authors.forename: Otto
authors.initials: O
authors.lastname: Hagenbüchle
authors.forename: Keith
authors.initials: K
authors.lastname: Harshman
mesh_terms: D001921:Brain / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D035683:MicroRNAs / Q000096:biosynthesis* / Q000235:genetics / Q000378:metabolism; D009206:Myocardium / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods*; D012044:Regression Analysis; D017423:Sequence Analysis, RNA / Q000379:methods
chemical_list: D035683:MicroRNAs