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Evaluating the impact of sleep on genome-wide methylation levels in college students

ABSTRACT: Approximately 4 μg of DNA was isolated from blood of each of 16 subjects using the Qiagen DNEasy Blood and Tissue Kit. Of the 16 samples, 8 were from group 1 (CESD-H/TST-H; 5 female, 3 male) and 8 were from group 2 (CESD-H/TST-L; 5 female, 3 male). All DNA samples were confirmed to be of high purity (A260/280: 1.7-2.0). Pooled samples were prepared for each group by combining approximately 75 ng of DNA from each of the eight subjects. These two samples were submitted to the Yale Genomics Core for epigenome-wide methylation profiling using the Illumina Infinium HumanMethylation450 BeadChip, which measures the level of methylation β (a value ranging from 0 to 1, where 0 represents a completely unmethylated site and 1 a completely methylated site) at each of the 485,577 CpG sites on the array. Illumina’s GenomeStudio software was used to calculate the degree of differential methylation by group for each CpG site on the array, and FDR-adjusted p-values (Q-values) were calculated for each site in order to adjust for multiple comparisons. CESD=depression score; TST=sleep score

ORGANISM(S): Homo sapiens

PROVIDER: GSE80559 | GEO | 2016/08/01

SECONDARY ACCESSION(S): PRJNA319268

REPOSITORIES: GEO

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Evaluating the impact of sleep on genome-wide methylation levels in college students

Project description:Approximately 4 Î¼g of DNA was isolated from blood of each of 16 subjects using the Qiagen DNEasy Blood and Tissue Kit. Of the 16 samples, 8 were from group 1 (CESD-H/TST-H; 5 female, 3 male) and 8 were from group 2 (CESD-H/TST-L; 5 female, 3 male). All DNA samples were confirmed to be of high purity (A260/280: 1.7-2.0). Pooled samples were prepared for each group by combining approximately 75 ng of DNA from each of the eight subjects. These two samples were submitted to the Yale Genomics Core for epigenome-wide methylation profiling using the Illumina Infinium HumanMethylation450 BeadChip, which measures the level of methylation Î² (a value ranging from 0 to 1, where 0 represents a completely unmethylated site and 1 a completely methylated site) at each of the 485,577 CpG sites on the array. Illuminaâs GenomeStudio software was used to calculate the degree of differential methylation by group for each CpG site on the array, and FDR-adjusted p-values (Q-values) were calculated for each site in order to adjust for multiple comparisons. CESD=depression score; TST=sleep score Blood-derived genomic DNA was isolated from 16 subjects; 8 each with high and low total sleep scores, respectively. DNA was pooled by group and genome-wide methylation profiling was performed.

2016-08-01 | E-GEOD-80559 | biostudies-arrayexpress

Whole genome gene expression profiles of normo- and dyslipidemic men after fish oil supplementation

Project description:Beneficial effects of long-chain omega-3 polyunsaturated fatty acids (n-3 FAs) are generally well-known from epidemiological studies, but the various mechanisms of action are not completely clarified. Regulation of gene expression is one known mechanism of action, but only very limited data of regulated pathways in humans after n-3 FA supplementation are available. Up to now, no studies compared gene expression changes after n-3 FA supplementation between normolipidemic and dyslipidemic subjects. Therefore, the aim of this study was to investigate the effects of n-3 FA administration on whole genome expression profiles in the blood of normo- and dyslipidemic subjects. We conducted an intervention study with normo- and dyslipidemic men aged between 29 and 51 years, which were subdivided into four groups with a balanced age distribution and randomized to either six fish oil capsules per day providing 1.5 g docosahexaenoic acid and 1.0 g eicosapentaenoic acid or corn oil capsules rich in linoleic acid per day for a period of 12 weeks. Venous blood samples were collected at baseline as well as after 4 hours, 1 week and 12 weeks of supplementation. For each investigation time point, the samples of each group were pooled together to minimize inter-individual variability. All subjects have successfully completed the study, but for the microarray experiments, nine subject samples were excluded. Therefore, the microarray experiments are based on the following group characteristics: normolipidemic fish oil group (FO-N): pool of nine RNAs from normolipidemic subjects supplemented with fish oil; normolipidemic corn oil group (CO-N): pool of six RNAs from normolipidemic subjects supplemented with corn oil; dyslipidemic corn oil group (CO-D): pool of eight RNAs from dyslipidemic subjects supplemented with corn oil; dyslipidemic fish oil group (FO-D): pool of nine RNAs from dyslipidemic subjects supplemented with fish oil.

2012-05-30 | GSE34898 | GEO

DNA methylation in the superior temporal gyrus of 44 subjects with schizophrenia and 44 non-psychiatric control subjects

Project description:DNA methylation (DNAm) signal from the planum temporale of superior temporal gyrus (STG) of forty-four subjects with schizophrenia (SZ) and forty-four non-psychiatric control (NPC) subjects was measured on the Illumina MethylationEPIC BeadChip Infinium (EPIC) array. Averaged, normalized beta-values at each site were correlated with dendritic spine density (DSD) previously measured per subject to identify site-specific DNAm-DSD correlations that met methylome-wide significance, or a suggestive-level of significance. We tested the hypothesis that DNAm correlates with DSD in human STG at several sites across the methylome and that this relationship is disrupted in SZ. DSD measures were available for 40 of the subjects with SZ and 40 of the NPC subjects. We found DNAm to correlate with DSD at more sites than expected by chance in NPC, but not SZ, subjects. In addition, we show that the slopes of the linear DNAm-DSD correlations differed between SZ and NPC subjects at more sites than expected by chance. Together, these data suggest that alterations in the intercation between DNAm and neurobiology in SZ may be a mechanism for SZ-related DSD reductions.

2020-06-30 | GSE144910 | GEO

Gene Expression Profiling of Scleroderma Skin

Project description:We have analyzed the genome-wide patterns of gene expression with DNA microarrays in skin biopsies from 34 subjects: 17 patients with SSc with diffuse scleroderma (dSSc), 7 patients with SSc with limited scleroderma (lSSc), 3 patients with morphea and 6 healthy controls. In total, 61 skin biopsies were analyzed. The addition of 14 technical replicates resulted in a total of 75 microarray hybridizations. The Intrinsic_scleroderma_genes.txt supplementary file lists the 995 genes with the most consistent expression between each forearm-back pair and technical replicates, but with the highest variance across all samples analyzed. An intrinsic gene identifier algorithm was used to select a set of intrinsic scleroderma genes. A total of 34 experimental groups were defined, each representing the 34 different subjects in our study. Replicate hybridizations for a given patient were assigned to the same experimental group. Each gene was analyzed and assigned a score that is inversely related to how intrinsic the gene's expression is across the samples analyzed. The analysis was repeated on randomized data in order to estimate a False Discovery Rate (FDR). An intrinsic score of 0.3 selected 995 genes with an FDR of 4% (39 ± 7 genes) while retaining reproducible clustering of technical replicates. Keywords: global gene expression profiling using Agilent Whole Human genome oligo arrays

2008-07-15 | GSE9285 | GEO

Comparative miRNA Expression Profiles in Individuals with Latent and Active Tuberculosis

Project description:To study the role of miRNAs in the transition from latent to active TB and to discover candidate biomarkers that may help predict TB progression, we have employed miRNA microarray expression profiling as a discovery platform to probe the transcriptome of peripheral blood mononuclear cells (PBMCs) with active TB, latent TB infection (LTBI), and healthy donors.Patients were recruited at the Shanghai Public Health Clinical Centre (Shanghai, China) from December, 2008 to May, 2009. The diagnosis of active TB was based on clinical presentation, chest radiography, and acid-fast stain of sputum smear.All the patients were HIV negative, as diagnosed by the Livzon Anti-HIV1/2 EIA Kit (Livzon Pharmaceutical Group Inc., Guangdong, China). Additional tests were also performed to detect hepatitis B virus (HBV) and hepatitis C virus (HCV) by using the Abbott AxSYM anti-HBsAg and HCV 3.0 antibody assay kit (Abbott Laboratories, Illinois) to exclude HBV- and HCV-positive patients (these 2 diseases are highly prevalent in China). Patients with a diabetes history were also excluded because diabetes could increase the risk of TB. Peripheral venous blood was drawn before treatment. Subjects with LTBI and healthy donors both without a history of clinical TB or other infectious diseases were recruited from the staff at the Shanghai Public Health Clinical Centre. TST and IGRA (T-SPOTM-BM-..TB, Oxford Immunuotec, Oxfordshire, U.K) results were used to distinguish the two groups. The LTBI group was TST-positive (TST>10 mm) and IGRA-positive while the healthy donors were TST-negative (TST<5 mm) and IGRA-negative. RNA of PBMC from 6 patients with active TB, 6 donors with Latent TB, and 3 healthy controls (total of 15 biologically independent samples) were used to perform Agilent Human miRNA (version 3) microarray , No replicates were included

2011-05-10 | E-GEOD-29190 | biostudies-arrayexpress

Comparative miRNA Expression Profiles in Individuals with Latent and Active Tuberculosis

Project description:To study the role of miRNAs in the transition from latent to active TB and to discover candidate biomarkers that may help predict TB progression, we have employed miRNA microarray expression profiling as a discovery platform to probe the transcriptome of peripheral blood mononuclear cells (PBMCs) with active TB, latent TB infection (LTBI), and healthy donors.Patients were recruited at the Shanghai Public Health Clinical Centre (Shanghai, China) from December, 2008 to May, 2009. The diagnosis of active TB was based on clinical presentation, chest radiography, and acid-fast stain of sputum smear.All the patients were HIV negative, as diagnosed by the Livzon Anti-HIV1/2 EIA Kit (Livzon Pharmaceutical Group Inc., Guangdong, China). Additional tests were also performed to detect hepatitis B virus (HBV) and hepatitis C virus (HCV) by using the Abbott AxSYM anti-HBsAg and HCV 3.0 antibody assay kit (Abbott Laboratories, Illinois) to exclude HBV- and HCV-positive patients (these 2 diseases are highly prevalent in China). Patients with a diabetes history were also excluded because diabetes could increase the risk of TB. Peripheral venous blood was drawn before treatment. Subjects with LTBI and healthy donors both without a history of clinical TB or other infectious diseases were recruited from the staff at the Shanghai Public Health Clinical Centre. TST and IGRA (T-SPOT®.TB, Oxford Immunuotec, Oxfordshire, U.K) results were used to distinguish the two groups. The LTBI group was TST-positive (TST>10 mm) and IGRA-positive while the healthy donors were TST-negative (TST<5 mm) and IGRA-negative.

2011-05-10 | GSE29190 | GEO

Whole blood DNA methylation samples from HIV positive men [2012 study]

Project description:Genome wide DNA methylation profiles of whole blood from HIV positive men. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Dataset included 24 subjects from the USA. This data set was used as validation set for studying the effect of HIV viral load on host DNA methylation levels. Bisulphite converted DNA from the 24 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. Subjects had different levels of HIV viral load. This dataset reports DNA methylation data set on 24 subjects that were generated in 2012 (while the other data set of 120 subjects reports DNA meth data generated in 2013). Details on what each sample characteristics and their values represent are provided in the 'characteristics_readme.txt' file.

2015-06-09 | E-GEOD-53841 | biostudies-arrayexpress

PGE2-induced OSM expression

Project description:The objective of the study was to compare the wound macs with corresponding macs derived from peripheral blood monocytes (MDMs). Wound site macrophage (wound macs were isolated from human subjects with chronic wounds. Matching blood monocyte derived macrophages (MDM) were obtained from same subjects. Transcriptome profiling (GeneChip, Affymetrix) was performed.The expression values of genes were normalized using global scaling approach. Blood monocyte derived macrophages or human wound macrophages were isolated and transcriptome analysis was performed using affymetrix gene chip analysis. Group -1 MDMs (n=3) Mac-1 Mac-2 Mac-3 Group -2 Wound macs (n=3) Wmac-1 Wmac-2 Wmac-3

2012-08-01 | E-GEOD-36995 | biostudies-arrayexpress

Ursolic acid regulates inflammatory cell infiltration to prevent ulcerative colitis

Project description:Total RNA was isolated from 3 colonic tissues of each treatment group using the Qiagen RNeasy kit following the manufacturers' protocol. RNA samples with good quality control (RIN values>8) were sequenced using Hiseq-2500 by Novogene. Ursolic acid (UA), Dextran sulfate sodium (DSS)."Con" group stands for normal group, "DSS" group stands for DSS induced group, "UA_DSS" group stands for UA Preventive DSS induced group, "DSS_UA" group stands for UA Treatment DSS induced group.

2020-05-16 | GSE150688 | GEO

RNA-seq analysis of HuH-7, NCI-H1299 and HEK-293T cells

Project description:The diversity and complexity of the cancer transcriptome hold the potential to yield tumor-specific transcripts (TSTs) in cancer. We report a novel LIN28B variant, LIN28B-TST, which is specifically expressed in hepatocellular carcinoma (HCC) and many other cancer types. LIN28B-TST initiates from a de novo alternative transcription initiation site. We found that LIN28B-TST was expressed in HuH-7 HCC cells and NCI-H1299 lung cancer cells, while wild-type LIN28B (LIN28B-WT) was expressed in HEK-293T human embryo kidney cells.

2018-01-24 | GSE109528 | GEO

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