Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA172385 | ENA |
REPOSITORIES: ENA
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Project description:The objective of this study was analysis of the whole saliva transcriptome to search for biomarkers of psychosocial stressor exposure and substance use in young adults drawn from a population-based longitudinal cohort, the Oregon Youth Substance Use Project. We conducted genome-wide gene expression analysis on whole saliva RNA from 48 individuals stratified by psychosocial stressor exposure using an Affymetrix Gene ST 1.0 array. We applied Weighted Gene Co-expression Network Analysis (WCGNA) to characterize the high-level structure in the data and to relate expression patterns among samples to participant clinical characteristics. This approach finds clusters of correlated genes (modules) which can reflect clinical, histological, or intracellular organization and function. Using WCGNA, we constructed a gene expression network from saliva genome-wide gene expression data, which we found to be similar to a network we constructed from publicly available cell-free saliva genome-wide gene expression data. Functional characterization of the WGCNA modules suggested that the samples varied in composition between an expression profile similar to circulating antigen presenting cell types and a glycoprotein-containing expression profile. We identified a significant relation between one module of whole saliva genome-wide gene expression and smoking behavior, and one with psychosocial stressor exposure. The smoking-related module was related to mitochondrial gene expression, and ever-smokers were found to have reduced overall mitochondrial gene expression. To determine whether reduced expression could be explained by reduction in mitochondrial DNA, we measured mtDNA copy number variation within genomic DNA from 400 OYSUP participants. Surprisingly, we found that more frequent smoking is associated with increased mtDNA copy number. The network structure of whole saliva and its association with clinically assessed exposures and behaviors are reported here for the first time.
2014-09-04 | GSE40013 | GEO
Project description:Differences in the transcriptional profile of the menigococcal strains MC58 and α710 were compared upon growth in PPM+ and on exposure to human saliva, whole blood and cerebrospinal fluid
2016-12-31 | GSE38051 | GEO
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.
2019-12-12 | GSE120900 | GEO
Project description:This study investigated the impact of psychosocial stress experienced during adolescence on the development of the brain dopaminergic system. The experiment was designed to evaluate the transcriptomic changes in the ventral tegmental area of mouse brain after one week of repeated exposure to a threatening mouse during preadolescence (P14-P21).
2022-03-31 | GSE199136 | GEO
Project description:High resolution microRNA signatures in human whole saliva
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Project description:Time series analysis of healthy individuals response to a psychosocial stress test (Trier Social Stress Test (TSST))
2012-06-01 | E-MTAB-1039 | biostudies-arrayexpress
Project description:Illumina Infinium EPIC HumanMethylation BeadChip data from saliva DNA samples from a healthy elderly cohort with individuals in the age range 70-95 in Southwest Sweden. The cohort was stratified into study groups based on participants´answers to a questionnaire of different lifestyle factors including vitamin supplementations, smoking and drinking habits, physical activity (per year), sun exposure and eating habits. Vitamin D intake was evaluated from the vitamin D supplementation (alone or in a multivitamin complex), dietary vitamin D intake (fish and seafood frequency) and vitamin D synthesis in the skin (sunlight exposure and use of sunscreen). Differential methylation analysis was performed for all the study groups and the combination of different factors with vitamin D supplementation. Gender, age, smoking and alcohol (SD and frequency) were used as covariates in the analyses. Only the study groups referred to the conclusions of the study are shown.
2022-07-23 | E-MTAB-11445 | biostudies-arrayexpress
Project description:The goal of this study was to compare transcriptional profiles of the amygdala from control and (PS) prenatally stressed male and female offspring to elucidate sex-specific molecular mechanisms underlying behavioral and neuroendocrine abnormalities observed after in-utero psychosocial stress exposure. Amygdalar mRNA profiles of 28 day old control and PS male and female mice were generated by preparing sequencing libraries using the NEBNext Ultr II Directional RNA Library Prep Kit for Illumina. After indexing, enrichment through 8 cycles of PCR, and passing initial quality control metrics, individually indexed and compatible libraries were proportionally pooled and sequenced using Nextseq 550 sequencer. The sequencing setting of single read 1 × 85 bp to generate ∼50 M reads per sample was used. Differentially expressed genes (DEGs) were analyzed using RUVseq and EdgeR. Results were validated via qPCR We find psychosocial PS results in the emergence of anxiety-like behaviors, an altered behavioral coping strategy to stress, and anhedonia in male and female offspring. Neuroendocrine abnormalities, evidenced by acute stress-induced HPA axis hyperactivity, are only observed in PS female offspring. Our RNA-seq analysis reveals these phenotypic changes in PS offspring to be associated with sex-specific disturbances in genes associated with synaptic transmission, including genes associated with glutamatergic and GABAergic signaling in PS males, and upregulation of DBH, known to regulate NE synthesis, in PS females. Our study represents one of the first detailed analysis of amygdalar transcriptomes generated by RNA-seq comparing control vs prenatally stressed offspring, identifying sex-specific changes in response to in-utero psychosocial stress exposure.
2022-02-08 | GSE189330 | GEO
Project description:Recent studies have reported both mRNA and microRNA (miRNA) in saliva, but little information has been documented on the quality and yield of RNA collected. Therefore, the aim of the present study was to develop an improved RNA isolation method from saliva and to identify major miRNA species in human whole saliva.
2014-04-12 | GSE28659 | GEO