RNA was extracted from Applied Biosystems Tempus Blood RNA Tubes using the Ambion MagMax-96 total RNA Isolation kits. Globin message reduction was conducted using Ambion GlobinClear Human 96 Kits.
Label
biotin
Label protocol
Biotinylated cRNA were prepared using Illumina Totalprep-96 Amplification Kits with 250ng input.
Hybridization protocol
Standard Illumina HT-12 V4 hybridization protocol.
Scan protocol
Standard Illumina iScan protocol.
Description
6116733072_G W44 Total RNA (globin reduced)
Data processing
We first applied a normal-exponential convolution model (Xie et al., Bioinformatics, 2009; Shi et al., Nucleic Acids Research, 2010) to correct for the background noise. An offset of 16 (the default value) was then added to the data (to improve precision and avoid a compression of the fold changes) before they were log2 transformed (to stabilize the variance). Finally, a quantile-quantile normalization was performed. The ComBat method (Johnson et al., Biostatistics, 2007) was used on those normalized data to correct for batch effects (namely a small hybridization chamber effect that was identified through Principal Variance Component Analysis - Li et al., chap. 12, Batch Effects and Noise in Microarray Experiments: Sources and Solutions, Wiley, 2009). At last, only probes which pval detection (provided by Genome Studio) was below 0.01 in at least one sample were kept for analysis.
