Total RNA isolated using mirVana total RNA isolation kit and procedure.
Label
Cy3
Label protocol
microRNAs end labled with Cy3-ppCpp using the Agilent labeling kit as described in the manufacturer's protocol
Hybridization protocol
End-labeled samples hybridized and washed on arrays according to manufacturer's protocol.
Scan protocol
Scanned using Agilent G2505B array scanner according to manufacturer's protocol.
Description
Proliferating, cell line 3
Data processing
Probe intensities were filtered to eliminate any probes that, for any sample, had signals that were flagged as saturated or below background by Feature Extractor. Intensities of probes to identical microRNAs were averaged and then log2 transformed. The log2 transformed signals for each microRNA were then individually normalized and analyzed using multiple linear regression on the experimental design and surrogate variable analysis. Experimental design variables included in the regression were cell line identity, slide on which array was hybridized, cell proliferation state, serum concentration state, and mean sample intensity. Values represented in data matrix are the sum contributions of residual error, cell proliferation state, and serum concentration state, i.e. the biological variables of interest. log2 transformed sum changes normalized for cell line, overall signal intensity, date of hybridization, and date of sample collection
