HCT116 cells were grown in vehicle (DMSO), IC50, IC90 or the 3xIC90 dose of R547 for 0,1, 2, 4, 6, and 24 hours
Growth protocol
Cell lines were maintained in the recommended medium and supplemented with 10% heat-inactivated fetal bovine serum (Life Technologies, Gaithersburg, MD) and 2 mmol/L L-glutamine (Life Technologies)
Extracted molecule
total RNA
Extraction protocol
Total RNA was extracted from cells using the Qiagen RNeasy Mini Kit
Label
biotin
Label protocol
RNA was converted into cDNA and cRNA according to the manufacturer’s recommendation and using manufacturer’s kits (Affymetrix, Santa Clara, CA). 15 ug of total RNA was converted to cDNA with the One-cycle cDNA Synthesis Kit with the addition of reagents from the Poly-A RNA Control Kit. cRNA was produced with the IVT Labeling Kit
Hybridization protocol
Hybridization Mix contained, in addition to cRNA, reagents from the Hybridization Control Kit and Control Oligo B2. Staining and washing steps were performed as suggested by the manufacturer (Affymetrix, Santa Clara, CA).
Scan protocol
Each hybridized Affymetrix GeneChip array was scanned with a GeneChip Scanner 3000 7G (Agilent/Affymetrix).
Description
n/a
Data processing
Affymetrix gene expression microarray data was first background corrected and normalized via the RMA procedure followed by QQ normalization (R/Bioconductor)
