The CodeLink Expression Assay Reagent Kit (GE Healthcare, Piscataway, NJ) is used. It is called the 'CodeLink' method in the paper. Approximately 1 µg of total RNA was processed to produce biotinylated cRNA targets. UTP-biotin was used for labeling and the in vitro transcription reaction lasts for 14 hours.
Hybridization protocol
standard Affymetrix procedures
Scan protocol
standard Affymetrix procedures
Description
Stratagene’s Universal Human Reference RNA is composed of total RNA from 10 human cell lines. The reference RNA is designed to be used as a reference for microarray gene-profiling experiments. Since RNA species differ in abundance between cell lines, an ideal reference sample should represent these different RNAs. Equal quantities of DNase-treated total RNA from each cell line were pooled to make the Universal Human Reference RNA. The ten cell lines are cell lines of the adenocarcinoma of the mammary gland, melanoma, liver hepatoblastoma, liposarcoma, adenocarcinoma of the cervix, histocytic lymphoma (macrophage, histocyte), embryonal carcinoma of the testis, lymphoblastic leukemia (T lymphoblast), glioblastoma of brain, and plasmacytoma (myeloma; B lymphocyte).
Data processing
Affymetrix Microarray Suite version 5.0 for detection calls and detection p-value; dChip v1.3 algorithm is used to calculate the signal intensity values with the invariant set normalization and the PM-only model.
