Project description:Callset of filtered SNP and indel genotypes of 163 vervet monkeys (genus Chlorocebus) from several African and Caribbean countries as described in Svardal et al. Nature Genetics 2017. Sample information can be found in Data S1 of the publication above. There is one VCF file per chromosome. Genotypes are not imputed and unphased. There is missing data. Note that there also is a imputed and phased dataset of biallelic SNPs available as a separate submission which might be more useful for many applications. Fixed differences between vervet and macaque have been added to the VCFs (mainly the sites with AC=0 and AF=0.000) so that variant effects are also annotated for divergent sites between vervet and macaque. Where available, the macaque state is given by the INFO tag 'AA'. Variant effects have been annotated. Please refer to the methods section of the article cited above for a full description of the data. <hannes.svardal@gmail.com>
Project description:This report is based on an ongoing study to examine gene expression differences in monkey lateral geniculate nucleus (LGN). For this study, samples from an Old World species, vervet monkey (Cercopithecus aethiops), were cross-hybridized to the Rhesus Macaque Genome Array (Affymetrix). Microarray analysis was performed using laser capture microdissected populations of individual neuronal cell bodies isolated from the LGN compared to heterogeneous samples from whole lamina. We show here that cross-species hybridization of microdissected brain tissue samples from vervet monkeys to the Rhesus array produced reliable and biologically relevant data sets. We present the first list of genes enriched in the large neuronal cell bodies of the LGN. We found that these cell bodies are concentrated with genes involved in metabolic processes and protein synthesis, whereas signaling molecules including chemokines and integrins were expressed at higher levels within heterogeneous samples. Our data set provides support for a contribution of Wnt signaling in adult monkey LGN. Keywords: gene expression profile
2007-11-12 | GSE8859 | GEO
Project description:16S rRNA sequencing in vervet monkeys
Project description:Mechanisms by which non-coding genetic variation influences gene expression remain only partially understood but are considered to be major determinants of phenotypic diversity and disease risk. To investigate these mechanisms with respect to signal-dependent gene expression, we evaluated effects of > 50 million SNPs and InDels provided by five inbred strains of mice on the responses of macrophages to the anti-inflammatory cytokine IL-4. Remarkably, of the > 600 genes observed to be induced >2-fold across the five strains after 24 hours of IL-4 treatment, only 26 genes reached this threshold in all strains and more than half of the induced genes were observed in only a single strain. By examining the effects of SNPs and InDels on transcription factor binding and enhancer activity under basal and IL-4 treatment conditions, we identified dominant collaborative roles of the signal-dependent transcription factors (SDTFs) STAT6, PPARg and EGR2 in driving late enhancer activation that were dependent on general macrophage lineage determining factors (LDTFs). As expected, SNPs and InDels that affected the relative affinities of SDTFs primarily influenced the ability of enhancers with similar basal activities to respond to IL-4. In contrast, SNPs and InDels that altered the relative binding affinities of macrophage LDTFs had divergent effects on basal and activated enhancer activity. Variants resulting in strong reductions in LDTF binding affinity were associated with low basal enhancer activity and failure to recruit SDTFs, whereas variants that increased LDTF binding affinities were associated with constitutively high levels of enhancer activity and a blunted response to SDTF recruitment. Together, these studies reveal mechanisms by which noncoding genetic variation influences absolute levels of enhancer activity and their dynamic responses to IL-4, thereby contributing to strain-specific patterns of gene expression and phenotypic diversity.
Project description:To identify genes involved in responses to psychosocial stressor, we analysed RNAseq transcriptomic profiles in whole blood of 15 juvenile male vervet monkeys from the Caribbean island of St. Kitts at three experimental time points: day 0 (baseline), day 3 and day 5 of exposure to the stressor.
Project description:High-throughput profiling of gene expression in the livers of vervet monkeys fed a high fructose diet or chow diet. Analysis of differentially expressed genes revealed sirtuin signaling and a network of genes regulated by the peroxisome proliferator activated receptor alpha were significantly altered in response to the high fructose diet.
Project description:Characterization of transcriptomic variation is emerging as a critical tool for understanding how quantitative trait loci (QTL) contribute to complex phenotypes. Human transcriptomic studies are limited by factors such as the feasibility of invasive tissue collection or variable environmental exposures that can be readily overcome in non-human primate (NHP) models. We characterized transcriptomic variation across multiple tissues and developmental stages and between individuals in 59 vervet monkeys from the Vervet Research Colony extended pedigree. We conducted RNA sequencing across early (7, 90 days, and one year) and later (1.25, 1.5, 1.75, 2, 2.5, 3, and 4+ years old) developmental time points in 6 individuals at each stage in five tissue types: two brain tissues from hippocampus and caudate, two endocrine tissues (pituitary and adrenal) and two peripheral tissues serving as a source of biomarkers (blood and fibroblasts)
Project description:High-throughput profiling of miRNA expression in the livers of vervet monkeys fed a high fructose or chow diet. Analysis of differentially expressed miRNAs revealed miR-148a-3p, miR-181a-5p, miR-342-5p and miR-574-5p may have regulatory roles in coordinating changes in hepatic gene expression in response to a high fructose diet.
Project description:Objective: The dietary xanthophylls, lutein and zeaxanthin, accumulate in primate brain and may be beneficial for cognition. Brain xanthophyll content varies greatly among individuals and genetic factors are likely to be significant contributors. Subspecies of rhesus macaques originating from different geographic locations differ genetically, but the effect of origin on gene expression and carotenoid status has not been determined. The study objective was to determine whether xanthophyll status and expression of carotenoid-related genes, as well as genes with known variants between subspecies, differ between the brains of adult rhesus monkeys of Indian and Chinese origin. Methods: Next generation RNA sequencing was used to determine differentially expressed carotenoid-related genes and genes with known variants among rhesus monkey subspecies in the prefrontal cortex, cerebellum, and striatum of Indian-origin monkeys (n=3) versus Chinese-origin monkeys (n=3). Serum and brain xanthophylls were determined using HPLC. FastQC was performed on raw sequenced reads to determine the quality of each read. Reads were mapped to the Rhesus Macaque reference genome and differences in gene expression (FPKM) were determined using TopHat and Cuffdiff, respectively. Findings from RNAseq were validated using RT-PCR. Results: Indian-origin monkeys had higher xanthophyll levels in brain tissue compared to Chinese-origin monkeys despite consuming similar amounts of dietary carotenoids. In a region-specific manner, 4 genes related to carotenoid and fatty acid metabolism (BCO2, RPE65, ELOVL4, FADS2) and 4 genes involved in the immune response (CD4, CD74, CXCL12 LTBR) were differentially expressed between Indian- and Chinese-origin monkeys. Expression of all four genes involved in carotenoid and fatty acid metabolism were correlated with brain xanthophyll concentration in a region-specific manner. Conclusions: These results indicate that origin is related to differences in both gene expression and xanthophyll content in the brain. Findings from this study may have important implications regarding genetic diversity, lutein status, and cognition in primates.
