Nimblegen one color dna labeling kit

Global gene expression analysis was done for MDA-MB-231 cells transfected with miR-944 precursor (50 nM) or scramble (30 nM) using the NimbleGen array (Roche). RNA samples were used to synthesize double-stranded labeled cDNA using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and NimbleGen One-Color DNA Labeling Kit. Samples were hybridized in NimbleGen array 12x135K (12 x 135,000 features). After hybridization and washing, the processed slides were scanned using a NimbleGen MS200 Microarray Scanner. Raw data were extracted as pair files by NimbleScan software (version 2.5), background was corrected and data were normalized. The probe level files and gene summary files were produced and imported into ANAIS software (Analysis of NimbleGen arrays Interface) for further analysis. The Student test with Varmixt package was used and raw P values were adjusted by the Benjamini and Yekutieli method to control the false discovery rate (FDR). Only genes with a Benjamini/Yekutieli value <0.05, and expression fold change >1.5 were considered as being differentially expressed.

Global gene expression analysis was done for MDA-MB-231 cells transfected with pre-miR-204 (30 nM) or scramble (30 nM) using the NimbleGen array (Roche). RNA samples were used to synthesize double-stranded labeled cDNA using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and NimbleGen One-Color DNA Labeling Kit. Samples were hybridized in NimbleGen array 12 × 135 K (12 × 135,000 features). After hybridization and washing, the processed slides were scanned using a NimbleGen MS200 Microarray Scanner. Raw data were extracted as pair files by NimbleScan software (version 2.5), background corrected and data were normalized. The probe level files and gene summary files were produced and imported into ANAIS software (Analysis of NimbleGen arrays Interface) for further analysis. DNA microarrays data for 10 selected genes was validated by RT-qPCR using specific oligonucleotides.