RNAseq and microarray samples showed an overall high correlation between identical time-points (Additional file 6D).
UT501 tissue microarrays showed strong MST1 staining exclusively in normal endometrium, and EMC1021 tissue microarrays samples showed slightly weaker staining, but in the same high number of cells.
All genes were detected by rt-PCR in each sample, whereas by microarray the samples showed a continuum of detection frequency.
A hierarchical clustering of the microarray data identified two clusters of samples, shown in Figure 1 and in dendrogram form in Figure 2, a PC group and a healthy control group.
PPIA, a standard endogenous control from Applied Biosystems was chosen for the normalization of all target genes as it was consistently expressed in microarray samples, and showed no correlation with age or with the template.
To assess the extent to which observations from microarray analysis correlate with those from mass spectrometry, we isolated total RNA from the same eight samples shown in Figure 1 and analyzed them using spotted DNA microarrays described previously [19].
Microarray analysis on 178 samples showed a significant upregulation of the DHHC9 transcript in individual colorectal tumour samples, when compared to normal mucosa.
Overall, the miRNA microarray profiles generated for FFPE and FF samples showed high correlations across all 847 human miRNAs (R = 0.94, p < 0.0001, data not shown).
Microarray profiling of 101 RNA samples showed an average 65-fold range in ESR1 transcript levels across the entire collection of ER-positive breast cancers, with the older cohort showing significantly higher ESR1 levels as compared with the younger cohort, consistent with earlier biomarker studies [ 13].
Analysis of the microarray data of the MIND samples showed canonical Wnt signaling to be among the significantly upregulated pathways in our dataset (Fig 1c- d, Additional file 4) and BCL9 was significantly upregulated during the transition from DCIS to IDC (q value <5%%) (Fig. 1c- d and Additional file 3).
