Specific primers were designed with Primer3 [ 54] using cDNA sequences spotted on microarrays, and amplicons were controlled using Mfold [ 55].
The morphology of the 2D microarrays can be controlled by changing the solvent, reducer, and surfactant.
Among critical technical parameters that need to be controlled are microarray surface chemistry, probe sequence, probe deposition process, and hybridization conditions.
Therefore, a total number of 6 microarrays were developed (3 control pools, named C1, C2, C3, and 3 estradiol-treated pools named E1, E2 and E3).
Microarrays were scanned with Affymetrix scanner controlled by Affymetrix Microarray Suite software.
The 384 F. heteroclitus cDNA microarrays were printed using 55 control genes and 329 cDNAs which encode essential proteins for cellular metabolism (Table 1).
Using these benchmarks, we found the BayMiR scores consistently outperform both the sequence and expression scores and identify to what extent down-regulated genes on a global set of microarrays are under control of miRNAs.
Microarrays were scanned with an Affymetrix scanner controlled by the Affymetrix Microarray Suite software.
Analysis and quality control of 324 microarrays were performed using BeadArray R package v1.10.0.
Single dye hybridizations with L. infantum DNA microarrays were performed as a cross-hybridization control.
