6 protocols
AccessionType
bioassay_data_transformation
Microarray results were analyzed by using the GeneSpring GX 11 software (Agilent Technologies). Data transformation was applied to set all the negative raw values at 1.0, followed by a Quantile normalization. A filter on low gene expression was used to keep only the probes expressed in at least one sample (flagged as Marginal or Present).
labeling
Labeled cRNA is synthesized from 500 ng of total RNA using the Low RNA Input Linear Amplification Kit (Agilent Technologies) in the presence of cyanine 3-CTP (Perkin-Elmer Life Sciences, Boston, MA).
(Parameters: Mass unit = Micro gram, Amplification = none)
grow
Melanoma cell lines are grown in DMEM 10%FBS supplemented
(Parameters: time unit = seconds, temperature unit = C)
image_acquisition
Images at 5 um resolution were generated by Agilent scanner and the Feature Extraction 10.5 software (Agilent Technologies) was used to obtain the microarray raw-data.
(Parameters: Scanning hardware = OTHER: Agilent Technologies, Scanning software = Scanning software)
hybridization
Hybridizations were performed at 65?C for 17 hours in a rotating oven.
(Parameters: Chamber type = OTHER: Agilent Techologies, Quantity of label target used = 500, Mass unit = Nano gram, Tiny time unit = seconds, Volume unit = Nano litre, temperature = 65)
nucleic_acid_extraction
Total RNA fraction is obtained from samples by using the Trizol standar protocol. RNA quality is assessed by the use of Agilent 2100 Bioanalyzer (Agilent Technologies)
(Parameters: Extracted product = total_RNA, Amplification = none)