Cells were cultured in RPMI-1640 Medium with GlutaMAX (Gibco, Invitrogen), supplemented with 10% (v/v) Fetal calf serum, and 1% (v/v) penicillin and streptomycin at 37oC in 5% CO2
Extracted molecule
total RNA
Extraction protocol
TRIzol reagent (Invitrogen, Carlsbad, NM, USA), cleaned on RNeasy columns (Qiagen) according to the manufacturers' instructions
Label
biotin
Label protocol
200ng of total RNA were amplified and labeled using the Message Amp II-biotin Enhanced reagents (Ambion; catalog #AM1791)
Hybridization protocol
Affymetrix HG-U133 Plus 2.0 arrays were hybridized with 11 microgramme of labeled, amplified cRNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol EukGeWS2v5_450)
Scan protocol
Scanning was done on an Affymetrix GeneChip Scanner 7G
Description
Comparison of the transcriptomes of cell lines from control and t(11;22)(q23;q11) individuals.
Data processing
Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).
