gender: male stimulus: baseline status: case age: 44 bmi: 19.88
Extracted molecule
total RNA
Extraction protocol
RNA was extracted from whole blood collected in PAXgene Blood RNA tubes using the PAXgene Blood RNA Kit (PreAnalytiX GmbH, Hombrechtikon, Switzerland).
Label
biotin
Label protocol
Sample labeling was performed using the Illumina TotalPrep RNA Amplification Kit (Ambion, TX, USA) according to the manufacturer's instructions.
Hybridization protocol
Biotin-labeled, amplified material was hybridized to Illumina Human-HT-12 v3 BeadChips, according to the manufacturer's instructions (Illumina, Inc., San Diego, CA, USA; 11322355 Rev. A, 11286331 Rev. A).
Scan protocol
Microarrays were scanned on the Illumina Bead Array Reader (Illumina, Inc., San Diego, CA) with default outlier detection according to the manufacturer's instructions and summarized raw probe intensities were exported using Illumina’s GenomeStudio v2011.1 Gene Expression module.
Description
Sample 33
Data processing
Microarray expression analysis was performed in R (http://www.r-project.org/). Summarized raw probe intensities (48,750 probes) were first filtered by an Illumina detection P value of 0.01 in at least 10% of the samples, leaving 14,168 expressed probes for further analysis. Second, each transcript was transformed and normalized through variance stabilization and normalization. Third, technical batches were adjusted using ComBat (http://jlab.byu.edu/ComBat/Abstract.html) with fixed effects of amplification round.
