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1,375 genes represented by both microarray platforms and spanning a wide dynamic range in gene expression levels, were selected for TaqMan® Gene Expression Assay based real-time PCR validation.
It is important to note that not all genes were measurable with all three technologies, therefore our analyses focused on the subset of genes that were represented on both microarray platforms and contained a Dpn II site detectable by MPSS (16,269 genes).
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Rankprod analysis identified 8 miRNAs that were found to be concordantly up-regulated in both microarray platforms (Agilent, Exiqon) and by small RNA-seq sequencing (Illumina).
To compare the microRNA profile between two different microarray platforms, we used all overlapped microRNAs available in both microarray platforms.
In total 8,125 orthologous genes were represented on both microarray platforms (Additional file 5).
In these graphs all 10,763 uniquely represented genes, common between both microarray platforms, are illustrated.
The probe annotations for all microarray platforms and qRT-PCR were provided by the manufacturer.
The approach also allows the analysis of different microarray experiments, microarray platforms, and cancer types simultaneously.
In general, microarray platforms and associated technologies and tools have improved greatly over the past decade.
An increasing number of studies have profiled tumor specimens using distinct microarray platforms and analysis techniques.
Microarray platforms, and more recently RNAseq, have made studying the early embryo transcriptome almost routine.
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