Microarray experiments were performed at the Research Technologies Branch, Rocky Mountain Laboratories (NIAID, NIH). The miRNeasy Mini kit (Qiagen) was used to extract total RNA via the QIAcube robot (Qiagen). To prepare target, 50 ng of each RNA sample was used as template for the Ovation V2 RNA Amplification System (Nugen, Cat#3100) to make amplified cDNA, which was purified using QIAquick 96-well (Qiagen) protocol. The cDNA (3.75 μg) was fragmented and labeled using the Encore Biotin Labeling Kit (Nugen, Cat# 4200), hybridized onto the Rhesus Macaque GeneChip (Affymetrix, P/N 90065), washed, and scanned according to manufacturer’s instructions. Microarray data were normalized using Affymetrix Expression Console Software and gene expression analyzed using Affymetrix Transcriptome Analysis Console (Santa Clara, CA). Differentially expressed transcripts identified by ANOVA were arithmetically averaged and compared ratiometrically to average expression in control tissue for visualization using Spotfire Analyst (TIBCO; Palo Alto, CA) and fold changes (FC) ≤−2 and ≥2.0, false discovery rate (FDR) < 0.05 were used as cut-offs to define the significantly DEGs for subsequent functional genomic analyses. The NHP gene expression data have been deposited in NCBI's Gene Expression Omnibus (Edgar et al., 2002) and are accessible through GEO Series accession number GSE122798 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE122798).

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