title: Concordance between RNA-sequencing data and DNA microarray data in transcriptome analysis of proliferative and quiescent fibroblasts.
abstract: DNA microarrays and RNA sequencing (RNA-seq) are major technologies for performing high-throughput analysis of transcript abundance. Recently, concerns have been raised regarding the concordance of data derived from the two techniques. Using cDNA libraries derived from normal human foreskin fibroblasts, we measured changes in transcript abundance as cells transitioned from proliferative growth to quiescence using both DNA microarrays and RNA-seq. The internal reproducibility of the RNA-seq data was greater than that of the microarray data. Correlations between the RNA-seq data and the individual microarrays were low, but correlations between the RNA-seq values and the geometric mean of the microarray values were moderate. The two technologies had good agreement when considering probes with the largest (both positive and negative) fold change (FC) values. An independent technique, quantitative reverse-transcription PCR (qRT-PCR), was used to measure the FC of 76 genes between proliferative and quiescent samples, and a higher correlation was observed between the qRT-PCR data and the RNA-seq data than between the qRT-PCR data and the microarray data.
authors.affiliation: Department of Computer Science , University of Saskatchewan , Saskatoon Canada S7N 5C9.
authors.forename: Brett
authors.initials: B
authors.lastname: Trost
authors.affiliation: Department of Life Sciences , Brunel University , Uxbridge UB8 3PH, UK ; Nuclear Dynamics Programme , Babraham Institute , Cambridge CB22 3AT, UK.
authors.forename: Catherine A
authors.initials: CA
authors.lastname: Moir
authors.affiliation: Department of Food and Bioproduct Sciences , University of Saskatchewan , Saskatoon Canada S7N 5A8.
authors.forename: Zoe E
authors.initials: ZE
authors.lastname: Gillespie
authors.affiliation: Department of Computer Science , University of Saskatchewan , Saskatoon Canada S7N 5C9.
authors.forename: Anthony
authors.initials: A
authors.lastname: Kusalik
authors.affiliation: Department of Cell and Systems Biology , University of Toronto , Toronto, Canada M5S 3G5 ; Centre for the Analysis of Genome Evolution and Function , University of Toronto , Toronto Canada M5S 3G5.
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Mitchell
authors.affiliation: Department of Life Sciences , Brunel University , Uxbridge UB8 3PH, UK ; Department of Food and Bioproduct Sciences , University of Saskatchewan , Saskatoon Canada S7N 5A8.
authors.forename: Christopher H
authors.initials: CH
authors.lastname: Eskiw
keywords: RNA-seq; fibroblasts; gene expression; microarrays; transcriptome analysis