MGH-U3 cells were transfected for 72h either with siRNA FGFR3 (Si1 FGFR3, Ambion, 144467), siRNA FGFR3 (Si2 FGFR3, Ambion, 144468),or a pool of siRNA FGFR3 (SiPool FGFR3, Dharmacon, L-0031333-00-0005) using LipofectaminRNAimax (Invitrogen) according to the manufacturer's instructions (reverse protocol)
Growth protocol
The bladder cancer cells, MGH-U3, have been culture in DMEM 10% fetal bobine serum
Extracted molecule
total RNA
Extraction protocol
mRNAs were extracted and purified using RNeasy Mini kits (Qiagen).
Label
biotin
Label protocol
100ng of total RNA were amplified to produced biotinylated complementary RNAs, as recommended by Affymetrix.
Hybridization protocol
Affymetrix microarrays were hybridized with 10µg of biotinylated cRNA according the supplier recommendations. Microarrays were washed and stained using FS450 fluidics upon a protocol provided by Affymetrix, corresponding to the GeneChip Human Exon 1.0 ST (Affymetrix) array
Scan protocol
Microarrays were scanned using a 7G, Affymetrix GCS3000 scanner, raw data were acquired with Affymetrix Genechip Command Console.
Description
MGH-U3 treated with Si1 FGFR3 ( Ambion, 144467)
Data processing
Signal reconstruction was performed with the RMA algorithm as implemented in Bioconductor affy package on R statistical software using the Dai custom CDF package: HuEx10stv2_Hs_ENTREZG Brainarray Custom CDF EntrezG version 12.1.0
