Concordance among digital gene expression, microarrays, and qPCR when measuring differential expression of microRNAs.
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.
Pradervand
Sylvain
S
Genomic Technologies Facility, Center for Integrative Genomics, University of Lausanne, Genopode Building, Lausanne, Switzerland. sylvain.pradervand@unil.ch
Weber
Johann
J
Lemoine
Frédéric
F
Consales
Floriane
F
Paillusson
Alexandra
A
Dupasquier
Mélanie
M
Thomas
Jérôme
J
Richter
Hannes
H
Kaessmann
Henrik
H
Beaudoing
Emmanuel
E
Hagenbüchle
Otto
O
Harshman
Keith
K
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
D035683:MicroRNAs