Project description:Deep sequencing of mRNA from two macaques, crab-eating macaque and Indian rhesus macaque Analysis of ploy(A)+ RNA of different specimens:brain,ileum,kidney,liver,testes and white adipose for crab-eating macaque while brain,heart,,kidney,liver,quadriceps and testes for Indian rhesus macaque
Project description:In this study three Indian rhesus macaques were infected with Simian Immunodeficiency Virus (SIVmac251). This generates a chronic infection mirroring AIDS in the animals. Prior to infection (day 0) and at two different time-points post-infection (day 21 and day 90), intestinal resection biopsies were performed. The intestinal tissue was then separated into different sub-sections including lamina-propria lymphocytes (LPL), intra-epithelial lymphocytes (IEL), stroma or matrix and epithelium. In this study we report the genome-wide transcriptional response at the two different time-points, specific to LPL, relative to pre-infection samples. For this purpose we have used the Affymetrix Rhesus Macaque GeneChip. 3 Rhesus Macaques prior to infection and 21 and 90 days of infection
Project description:Sixteen individual rhesus macaque genomes were compared to a reference macaque genome (R354) on custom-designed sure-print 1M oligonucleotide microarray Agilent (Agilent Technologies) aCGH slide per manufacturer’s recommendations. a custom designed Agilent array-based comparative genomic hybridization (aCGH) platform, which comprises 950,843 unique 60-mer oligonucleotide probes specific to the rhesus macaque reference genome (rheMac2), to compare the genomic DNAs of 17 unrelated rhesus macaques of Indian origin to the genome of an unrelated sample from the same species.
Project description:This SuperSeries is composed of the following subset Series: GSE33090: Dramatic effects of social behavior on gene regulation in rhesus macaques [Individual_expression] GSE34127: Dramatic effects of social behavior on gene regulation in rhesus macaques [Cell type_expression] GSE34128: Dramatic effects of social behavior on gene regulation in rhesus macaques [Bisulfite_seq] Refer to individual Series
Project description:Impact of CD8 depletion on peripheral CD4+ T cells transcriptome during ART-treated SIV infection of rhesus macaques. Analysis of CD8+ T cells, CD4+ T cells, and NK cell transcriptomes following administration of HIV/SIV latency reversing agent IL-15 superagonist N-803 in ART-suppressed SIV infected rhesus macaques. Methods: RNA-Seq of sorted CD4+ T cells from SIV-infected, ART-suppressed rhesus macaques before intervention with the anti-CD8a depleting antibody MT807R1 and then again on day 3, week 2, and week 4 following the start of intervention. Some animals also had an intervention that includes four weekly administrations of the IL-15 superagonist complex N-803 initiated at the time of CD8 depletion. Methods: RNA-Seq of sorted CD4+ T cells, CD8+ T cells, and NK cells from SIV-infected, ART-suppressed rhesus macaques before intervention with four weekly administrations of the IL-15 superagonist complex N-803, then again on day 3, week 2, and week 4 following the start of intervention. Methods: RNA from sorted cells was collected and extracted and DNA was digested. Libraries were prepared and normalized, pooled, and clustered on a flow cells for sequencing. RNAseq data were aligned to the MacaM v7.8 assembly of the Indian rhesus macaque genome. To identify pathways differentially modulated, Gene Set Enrichment Analysis (GSEA)34 was performed on the ranked transcript lists using 1000 phenotype permutations and random seeding. Gene sets used included the MSigDB H (hallmark) gene sets