42490c86-cdd1-4cd2-8cea-ee99adce56f8 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001011118 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Using the Infinium HM450 platform, we have performed a longitudinal study of DNA methylation at birth and age 18 months in DNA from buccal swabs from 10 monozygotic (MZ) and 5 dizygotic (DZ) twin pairs from the Peri/postnatal Epigenetic Twins Study (PETS) cohort.
2013-03-06 | GSE42700 | GEO
Project description:The purpose of the current study was to use an epigenome-wide association approach (EWAS) to identify a potential DNA methylation alterations associated with obesity using twins discordant on obesity status. Buccal cells (from a cheek swab) were used as a purified marker cell for the epigenetic analysis. Analysis of differential DNA methylation regions (DMRs) was used to identify epigenetic associations with metabolic and dietary measures in obesity parameters discordant twins. An edgeR analysis provided a DMR signature with p<1e-04, but a false discovery rate analysis demonstrated a lack of significance due to low sample size and known multivariant origins of obesity.
2023-02-18 | GSE218363 | GEO
Project description:This study mapped the genome wide DNA methylation changes in whole blood and buccal swab samples of 2 year old male rhesus monkeys subjected to parental deprivation in their first months of life (surrogate peer-reared condition). Equal numbers of control mother-reared (MR) and surrogate peer-reared (SPR) male monkeys whole blood (5 vs 5) and buccal swab samples (3 vs 3) were analyzed by methylated DNA immunoprecipitation (MeDIP) coupled with promoter tiling arrays.
2016-07-06 | E-GEOD-84020 | biostudies-arrayexpress
Project description:Male infertility has been a primary cause of global infertility, affecting 8-12% of couples worldwide. Previous studies have shown that semen quality decreases with advanced aging with an increased presence of inflammatory cells. In this study, we examined the DNA methylation of seminal fluid to understand how the methylome changes with age and infertility. We also compare the age associated changes in semen to those observed in buccal swabs in order to characterize differences in epigenetic aging across diverse tissues. We found that infertility associated changes in the DNA methylation of semen are driven by changes in cell composition, while those associated with aging are linked to inflammatory genes. Many age associated sites are demethylated with advanced aging and are associated with the activation of inflammatory pathways. By contrast, we do not observe age associated changes in inflammatory genes in buccal swab methylomes, which instead are characterized by changes to bivalent promoters. Our study suggests that DNA methylation could serve as a biomarker for male infertility assessment in addition to the standard semen analysis.
2023-12-22 | GSE250598 | GEO
Project description:This study mapped the genome wide DNA methylation changes in whole blood and buccal swab samples of 2 year old male rhesus monkeys subjected to parental deprivation in their first months of life (surrogate peer-reared condition).
2016-07-06 | GSE84020 | GEO
Project description:Small molecules extracted from mouse mesenteric lymph nodes.
| MSV000080181 | GNPS
Project description:To elucidate key pathways in the host transcriptome of patients infected with SARS-CoV-2, we used RNA sequencing (RNA Seq) to analyze nasopharyngeal (NP) swab and whole blood (WB) samples from 333 COVID-19 patients and controls, including patients with other viral and bacterial infections. Analyses of differentially expressed genes (DEGs) and pathways was performed relative to other infections (e.g. influenza, other seasonal coronaviruses, bacterial sepsis) in both NP swabs and WB. Comparative COVID-19 host responses between NP swabs and WB were examined. Both hospitalized patients and outpatients exhibited upregulation of interferon-associated pathways, although heightened and more robust inflammatory and immune responses were observed in hospitalized patients with more clinically severe disease. A two-layer machine learning-based classifier, run on an independent test set of NP swab samples, was able to discriminate between COVID-19 and non-COVID-19 infectious or non-infectious acute respiratory illness using complete (>1,000 genes), medium (<100) and small (<20) gene biomarker panels with 85.1%-86.5% accuracy, respectively. These findings demonstrate that SARS-CoV-2 infection has a distinct biosignature that differs between NP swabs and WB and can be leveraged for differential diagnosis of COVID-19 disease.
2020-12-15 | GSE163151 | GEO
Project description:Using the Infinium HM450 platform, we have performed a longitudinal study of DNA methylation at birth and age 18 months in DNA from buccal swabs from 10 monozygotic (MZ) and 5 dizygotic (DZ) twin pairs from the Peri/postnatal Epigenetic Twins Study (PETS) cohort. Beta methylation measurements from bisulphite-converted DNA and raw intensity values from 53 samples. Samples were collected at birth ('_B') or 18 months ('_18m'). Data were preprocessed using the Minfi package in R by the 'illumina' method and normalized to control probes. Subset quantile normalization was performed on type 1 and type 2 probes. Probes failing P detection cutoff of <0.01 were removed. Probes on the X and Y chromosomes have been removed from the processed data. Outlier samples were removed. Between-array quantile normalization was performed to arrive at the final data set of 330168 probes and 53 samples.
2013-03-06 | E-GEOD-42700 | biostudies-arrayexpress
Project description:Epigenetic misregulation is consistent with the various non-Mendelian features of Alzheimer's disease (AD) and may even play an etiological role in the disease. We performed DNA modification profiling of post-mortem brain samples from twins who differed for age of AD onset and buccal samples from twins who were discordant for AD at the time of sample collection. We performed DNA methylome analysis on frontal cortex, cerebellum, or buccal tissues from monozygotic twins and dizygotic twins discordant for Alzheimerâs disease (AD) or disease age of onset. DNA samples were enriched for unmodified fraction of the genome using DNA-modification sensitive restriction enzyme digestion followed by adaptor-mediated PCR. The enriched fractions were labelled with a fluorescent dye (Cy3) and hybridized onto the array with a common reference pool (Cy5).
2016-04-04 | E-GEOD-61242 | biostudies-arrayexpress
Project description:Lymph nodes from canine patients with head and neck caner were sequenced to determine differences in gene expression after irradiation.
2022-11-02 | GSE217028 | GEO