8 protocols
AccessionType
bioassay_data_transformation
ID_REF =
VALUE = log2 RMA
feature_extraction
The data was normalized using the Robust Multichip Average (RMA). RMA consists of three steps: a background adjustment, quantile normalization and summarization (Irizarry, R.A., et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 2003. 4(2): p. 249-64.). The quality of the arrays data was assessed through affyQCReport (Parman, C., C. Halling, and R. Gentleman, affyQCReport: QC Report Generation for affyBatch objects. R package version 1.32.0.). The microarray data was then analyzed using the S-score algorithm, which is a comparative method for gene expression data analysis that uses probe level data. The microarray data was then analyzed using the S-score algorithm, which is a comparative method for gene expression data analysis that uses probe level data to calculate p-value of differential expression for each gene (Kennedy, R.E., K.J. Archer, and M.F. Miles, Empirical validation of the S-Score algorithm in the analysis of gene expression data. BMC Bioinformatics, 2006. 7: p. 154.). Differential gene expression was defined as genes with a p-value (generated by Sscore, described in data processing section above) less than 0.05 and a 2-fold or greater difference in normalized fluorescence intensity between the 143B (numerator) and HOS (denominator), and LM7 (numerator) and SaOS-2 (denominator) cells.
labeling
The purified RNA were labelled by the Genechip 3” IVT express kit (Affymetrix, Santa Clara, CA) following the manufacturer’s protocol.
hybridization
The labelled RNA was hybridized with the Human U133 plus 2 array using the GeneChip hybridization, wash and stain kit (Affymetrix).
image_aquisition
The hybridization signals were obtained from the GeneChip 7G Scanner (Affymetrix).
nucleic_acid_extraction
The TRIzol reagent (Invitrogen, San Diego, CA) was used to extract RNA from the cell lines, and the RNA was further purified by the RNeasy kit (QIAGEN, Valencia, CA).
specified_biomaterial_action
None
grow
The cell lines were maintained in GIBCO Minimum Essential Media supplemented with 10% fetal bovine serum at 37oC in 5% CO2, and they were tested to be mycoplasma-free.