Ht 12 beadchips

Within pharmacokinetics of the Qishe pill, standardized workflows for the omics characterization of biosamples will be developed. Currently, genomic variants will be analyzed for 144 subjects with the aid of the Human- CoreExome + v1.1-Psych Array. For a subset of 144 subjects, whole blood expression data will be generated using Illumina’s HT-12 bead chips. The findings will be complemented with proteomic and metabolomic data using established workflows. Cytochrome P450 genes, such as CYP1A1, CYP1A2, CYP2D6, CYP2C9, CYP2C19, CYP2E1, CYP3A4 and CYP3A5, among other, will be the targets.
Metabolomics provide comprehensive snapshots of the metabolome of body fluids such as plasma or urine. High-throughput metabolomic analyses mainly based on 1H nuclear magnetic resonance (NMR) spectroscopy, a nondestructive analysis with minimal preparation requirements, will be performed. NMR spectroscopy provides robust and reproducible measurements. Mass spectrometry (MS) with high analytical sensitivity will be used for additional detailed studies.
Integrated analyses of these data for associations with clinical and subclinical phenotypes will be performed using the bioinformatics groups of the TCM constitutional type classification.

Full details of mRNA expression measurement and analysis are provided in Koussounadis et al32 (link). Briefly, total mRNA was prepared from 10-50 mg of frozen tissue, and divided into two aliquots for two technical replicates per sample. Total RNA (0.5 mg) was amplified and biotinylated, diluted to 150 ng/ml, and hybridized to Illumina HT-12 BeadChips (Illumina, San Diego, CA, USA). This platform had been previously validated via PCR in a breast cancer xenograft study34 (link). Expression values were processed with Bioconductor’s lumi package35 (link). mRNA expression was measured in 3-4 biological replicates per time point per condition (except one which had 2 replicates; Supplementary Table 1); controls were only measured on days 0, 1, 7, and 14. Agreement among biological replicates was good as measured by Pearson correlation coefficients (mean 95% confidence interval r = 0.987 – 0.990; Supplementary Table 1).