Transcriptome profiling in five vitally important tissues of Cynomolgus monkeys using customized NimbleGen microarrays

Cynomolgus monkeys are well-established translational models for biomedical research and drug testing. To evaluate organ transcriptomes and gene expression variability in Cynomolgus monkeys, we used Customized NimbleGen Microarrays (Design ID: 120419_Cynomolgus_v5_TH_exp_HX12) for genome-wide gene expression profiling on 5 different tissues (heart, kidney, liver, lung, spleen) from 21 Cynomolgus monkeys. Cynomolgus monkey samples were derived from breeding centers located in the Philippines (3 females and 3 males), in Vietnam (2 females and 2 males), in China for animals from Mainland Southeast Asia (3 females), or in Mauritius (4 females and 4 males). Furthermore, genome-wide copy number variation was analyzed in tissue samples from the same animals using a custom NimbleGen 4.2 million probes comparative genomic hybridization (CGH) array to associate CNV genotypes with expression changes of proximal genes. A NimbleGen customized 12x135K Gene Expression Array [Design ID: 120419_Cynomolgus_v5_TH_exp_HX12] study using total RNA recovered from tissues of drug-naive Cynomolgus monkeys. Each microarray measures the expression level of 22,731 probe sets covering 18,943 genes with six 60-mer probes (PM) per probe set. The number of replicates is 1 - i.e., only one set of probes on the array. The design includes 3420 RANDOM_MK1 control probes for the estimation of the signal threshold and 1536 ERCC probes for ERCC RNA Spike-In Control Mixes. The gene expression results analyzed in this study are further described in Gschwind A.R. et al. (2016) Diversity and regulatory impact of copy number variation in the primate Macaca fascicularis, under submission.