gender: male sample type: cell line disease state: cancer cell line: PC3 cell line
Growth protocol
HepG2, SKHep1 and MCF-7 cells were maintained in MEM medium (Gibco, Invitrogen, Life Technologies). MCF7 cells were cultured with 0.01 mg/ml of insulin (Invitrogen, Carlsbad, California). MDA-MB-231 cells were cultured in Dulbecco’s modified Eagle’s medium (Invitrogen). PC3 and LNCaP were cultured in RPMI1640 media (Gibco, Invitrogen, Life Technologies). All media were supplemented with 2 mmol/L glutamine (Sigma-Aldrich), 10% FBS (Gibco), 1 U/mL penicillin and 1 mg/mL streptomycin (Gibco).
Extracted molecule
genomic DNA
Extraction protocol
Cell were resuspended first in cell lysis buffer lysate and incubated with RNAase A (50 U/mg; 30 min; Roche) followed by incubation with proteinase K (20 μl; 20 mg/ml; Roche, Basel, Switzerland) at 55 C for 12 h. Samples were treated and phenol-chloroform (1:1). To precipitate DNA, ethanol [95% (vol/vol)] was added. The pellet was washed and redissolved in buffer DNAse free double distillued water.
Label
Cy5 and Cy3
Label protocol
Standard Illumina Protocol (Cy5 and Cy3)
Hybridization protocol
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol
Scan protocol
Standard Illumina procedures using Illumina iScan scanner
Description
replicate 3
Data processing
Genome Studio (Illumina; version 2011.1, Methylation module (Version 1.9.0)
A common promoter hypomethylation signature in invasive breast, liver and prostate cancer cell lines reveals novel targets involved in cancer invasiveness (methylation)
A common promoter hypomethylation signature in invasive breast, liver and prostate cancer cell lines reveals novel targets involved in cancer invasiveness