FASTQ files of sequencing reads were retrieved from the sequencing machine and the sequences were then filtered and aligned to the genome and relative gene expression scores calculated
MCF-7 cells grown in 0.1% hypoxic conditions, after 72hrs the cells were sorted according to whether they expressed CA9 (CA9 +) or not (CA9-).
MCF7 cells were maintained in DMEM supplemented with 10% (v/v) FBS, penicillin (100 U/ml), streptomycin (100mg/ml) (Life Technologies). Incubation conditions were 37 C , 5% CO2
Total RNA extraction at 72 hrs
Data was background corrected and normalised using vsn package from Bioconductor
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
Standard Illumina scanning protocol
Standard Illumina hybridization protocol