normalization data transformation protocol
.CEL files were background adjusted, quantile normalized and summarized at the transcript level using only core probesets that mapped to RefSeq transcripts, by apt (Affymetrix Power Tool version 1.12.0) software that used the RMA algorithm. probe group file: HuEx-1_0-st-v2.r2.pgf meta-probeset file: HuEx-1_0-st-v2.na29.hg18.probeset.csv ID_REF = VALUE = Gene-level RMA value of core probesets representing RefSeq transcripts
array scanning protocol
Arrays were scanned using the Affymetrix GCS 3000 7G and Gene-Chip Operating Software v.1.3.0 to produce .CEL intensity files.
Samples were hybridized using Affymetrix hybridization kit materials per manufacturers recommendation. Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 (fluidics protocol FS450_0001).
Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)
nucleic acid extraction protocol
CLL samples were positively enriched by magnetic cell sorting using CD19 microbeads and MACS columns (Miltenyi Biotec Ltd, Surrey, UK). Total RNA was isolated using Trizol (Invitrogen) and RNeasy kit (QIAGEN).
Pretreatment specimens from relapsed chronic lymphocytic leukemia patients