Labeled cRNAs were generated from 500 ng of total RNA for each of AG1 and AGL using Agilent’s Low RNA Input Linear Amplification Kit (P/N 5188-5339). The two-color protocol was modified such that 1.5 µg of labeled cRNA was hybridized per dye channel per microarray.
Channel 2
Source name
MAQC sample A, i.e., Stratagene Universal Human Reference RNA (UHRR, Catalog #740000)
Labeled cRNAs were generated from 500 ng of total RNA for each of AG1 and AGL using Agilent’s Low RNA Input Linear Amplification Kit (P/N 5188-5339). The two-color protocol was modified such that 1.5 µg of labeled cRNA was hybridized per dye channel per microarray.
Scan protocol
Microarrays were scanned using Agilent’s DNA Microarray Scanner BA (P/N G2565BA) and data extracted using Agilent's Feature Extraction software, version 8.5 (P/N G2567AA).
Description
AGL sample-pair convention: A (A/A, Cy3/Cy5), B (B/B, Cy3/Cy5), C (A/B, Cy3/Cy5), and D (B/A, Cy3/Cy5). Only MAQC samples A and B were used in AGL two-color experiments.
Data processing
Data were extracted using Agilent's Feature Extraction software, version 8 (P/N G2567AA), Cy3 corresponding to the gProcessedSignal column of FE file, Cy5 corresponding to the rProcessedSignal column of FE file.
Channel 1 median intensity (background subtracted) (Cy3)
CH2_Median
Channel 2 median intensity (background subtracted) (Cy5)
Flags
For AGL data points that did not have detectable signal in both dye channels and those that represent microarray controls were labeled as Absent, those representing either non-uniform or saturated features in either channel were labeled as Marginal, and all remaining data points were labeled as Present.
