Transcriptome Analysis of Whole Blood

We made use of pre-processed gene expression data extracted from WPB samples of individuals as provided by the LIFE database. Participant's recruitment, blood collection, storage and mRNA preparation, microarray measurements, and primary data pre-processing was realized by different groups of the LIFE center (Loeffler et al., 2015 (link)). WPB was collected in tempus blood RNA tubes (ThermoFisher, Waltham, MA, USA) and stored at −80°C until further processing. RNA was isolated and then hybridized to Illumina HT-12 v4 Expression BeadChips (Illumina, San Diego, CA, USA) and measured on an Illumina HiScan device. Raw probe level data were extracted using Illumina GenomeStudio and then further pre-processing including batch correction, outlier and missing value removal, log-transformation, quantile normalization, and centralization of the expression value of each gene using an in-house pipeline as described in detail in Supplementary Methods (Supplementary File 1) was undertaken. The final transcriptome data consists of more than 48,000 probe IDs including the expression values of 19,049 genes for each of the individuals.