6 protocols
AccessionNameType
P-MTAB-26584
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).
P-MTAB-26585
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)
P-MTAB-26589
grow
Melanoma cell lines are grown in DMEM 10%FBS supplemented
(Parameters: time unit = seconds, temperature unit = C)
P-MTAB-26587
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)
P-MTAB-26586
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)
P-MTAB-26588
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)