Higher numbers of microarray probes showing DE were observed in contrast between males of the two strains (n = 410) than in the corresponding female contrast (n = 270).
Generic primers to the ORF2 region of LINE- 1 and primers designed to detect the copies of LINE-1 that correspond to the upregulated microarray probes, all show a modest but statistically significant ∼1.6 2-fold (P < 0.05) upregulation in Tex19.1 −/− placentas by qRT-PCR (Fig. 6C).
Because of microarray technique or other unknown factors, some probes show higher expression level at 3h than at 0h.
More recently, tiling oligonucleotide microarrays with 42 million probes, showed that an average of 1,098 CNVs comprising 0.78% of the human genome were validated between two individuals [ 49].
Microarray experiments were performed on three independently prepared samples and probes showing at least a 3-fold change (p<0.05) in signal intensity were selected.
Probes showing the best combination of thermodynamic criteria and strain coverage were selected for microarray manufacturing (Fig. 1f).
Probes showing significant differential gene expression were identified using the Linear Models in Microarrays (LIMMA) library [ 93] of the Bioconductor software package [ 94].
A substantial fraction (31%) of the 55 gene probes showing inconsistent patterns were scored as differentially expressed in only one of the nodule samples examined by 16KPlus microarrays.
More than 38% of the microarray probes were found to show statistically significant differences in expression levels between the three cell states (FDR < 0.05).
The locations of real-time PCR probes and primers and of microarray probe sets are shown for the examples of IGF1 and EDNRA in Figure 3.
