Following manufacturer's instructions, 250 ng total RNA was used for cRNA in vitro transcritpion and labeling with the Illumina TotalPrep RNA Amplication Kit using biotinylated-UTP (Ambion, Austin, TX)
Hybridization protocol
Hybridization is carried out in Illumina Intellihyb chambers at 58 °C (Whole-Genome Gene Expression with IntelliHyb Seal System Manual, 2006, Illumina)
Scan protocol
Following hybridization, washing, and staining with streptavidin-Cy3, the chips were scanned using an Illumina BeadArray reader.
Description
NA
Data processing
Data analyses were performed with Illumina BeadStudio (v3.1.7) and Bioconductor packages (v2.3) in the R programming environment (v 2.7.1). The image data were analyzed using the BeadStudio, the output files of which were imported into the R using the lumi package (v1.8.3). Probe set signal intensities were averaged. Expression profiles were then log2 transformed and quantile normalized for downstream analyses.
The Illumina Human6 V2 Expression BeadChip platform runs each sample in duplicates, but BeadStudio has collapsed the duplicates prior to our normalization in R. Therefore, each sample is associated with two raw TXT files, one for each technical replicate on the chip.
Raw data files column header definitions are as follows: Code: Array address id (corresponds to the Array_Address_Id field of GPL6102; Illumina refers to it as ProbeID in the BeadStudio summary output as well as their array annotation file) Grn: Bead signal intensity GrnX: X-coordinate of the bead GrnY: Y-coordinate of the bead
