Total RNA extracted with Qiagen's Rneasy Plus Mini kit per manufacturer's instructions. cDNA synthesis carried out as previously described (Figueroa et al. PLoS One, 2008)
Label
Cy5
Label protocol
Random priming with 7-mers pre-labeled with either Cy3 or Cy5 according to manufacturer's instructions using the NimbleGen Dual-Color DNA Labeling Kit (cat # 05223547001)
Hybridization protocol
See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details
Scan protocol
Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.
Description
Sample name: 17640
Data processing
RMA normalization using the RMA algorithm found in the oligo package (version 1.8.3)(Carvalho et al.) in BioConductor
