Epigenome analysis of alcohol consumption in lymphocyte cell (LC) samples
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE57853 | GEO | 2014/09/24
SECONDARY ACCESSION(S): PRJNA248237
REPOSITORIES: GEO
Similar Datasets
Project description:Genome-wide DNA methylation profiling of individuals consuming alcohol and controls in LC samples. Individuals consuming alcohol were profiled at time of intake (T1) into treatment facility and four weeks into treatment (T2). Controls were profiled once. The Illumina Infinium 450k Human DNA Methylation BeadChip v1.0 was used to obtain DNA methylation profiles across 485,577 CpGs in LC samples. Samples included 33 case subjects at T1, 26 case subjects at T2 and 33 controls. Bisulfite-converted DNA from 92 samples were hybridized to the Illumina Infinium 450k Human Methylation BeadChip v1.0.
2014-09-24 | E-GEOD-57853 | biostudies-arrayexpress
Project description:To investigate maternal whole blood gene expression profiles associated with spontaneous preterm birth (SPTB, <37 weeks) in asymptomatic pregnant women. The â??All Our Babiesâ?? (AOB) community based cohort in Calgary recruited pregnant women between May 2008 and December 2010. Maternal blood at 17-23 (time point 1, T1) and 27-33 weeks of gestation (T2) were collected. Fifty-one SPTBs were matched to 114 term delivery controls. Microarray was performed on 326 samples from 165 women. Univariate analyses determined significant clinical factors and differential gene expression associated with SPTB. Thirteen genes were validated using qRT-PCR. Three multivariate models were constructed to identify gene expressions associated with SPTB at T1 (Model A) and T2 (Model B), and temporal gene expressions (T2-T1) associated with SPTB at T2 (Model C).
2016-06-01 | E-GEOD-59491 | biostudies-arrayexpress
Project description:Decompression sickness (DCS) is a potentially fatal condition usually observed after scuba diving. It involves bubble formation in blood and tissues from dissolved inert gas (usually nitrogen or helium), secondary to decreases in ambient pressure (decompression).To the best of our knowledge, no study has evaluated a DCS-induced transcriptomic signature in humans. In this study, we aim to explore the evolution of leukocyte gene expression in human subjects with DCS compared to closely matched divers after uneventful diving using a hypothesis-free RNA sequencing approach .Recruitment of DCS cases (n = 7) and controls (n = 6) was carried out using specific criteria. For both DCS cases and controls, whole blood was sampled at two time points, T1 - within 8 hours of surfacing from diving and T2 - at 40-44 hours after surfacing. Prior to sampling at T2, subjects were fasted for 10 hours. Specific exclusion criteria included a) age < 18 years b) self-reported consumption of alcohol and/or strenuous physical activity before T2 c) symptoms suggestive of delayed DCS presentation in controls at T2 d) acute life-threatening clinical complications or death within 72 hours of surfacing. All cases received emergency HBO as per United States Navy Treatment Table Six between T1 and T2.For RNA isolation, 2.5mL of whole blood was collected in a PAXgene® Blood RNA Tube (PreAnalytiX, Qiagen/BD) from DCS cases and controls at both T1 and T2. The quality of RNA was evaluated by RNA Integrity Number (RIN) determination using the RNA6000 Nano protocol on an Agilent 2100 Bioanalyzer system (Agilent, USA). The RIN values for samples undergoing transcriptome analysis ranged from 7.8 to 9.3. Depletion of alpha and beta globin mRNA was carried out using the GLOBINclear™ kit (ThermoFisher Scientific). To minimize batch effects, all samples were processed simultaneously by the same investigator. RNA samples were submitted for library generation and sequencing by the Beijing Genomics Institute (BGI-Shenzhen). Briefly, poly(A) mRNA was enriched using poly(T) oligo-attached magnetic beads, followed by fragmentation. First strand cDNA synthesis was carried out using random hexamer N6 primers and reverse transcriptase. Following adaptor ligation to cDNA fragments, PCR amplification and purification, single stranded DNA circles were generated in a final library. DNA nanoballs (DNBs) were subsequently generated by rolling circle replication, which underwent paired end sequencing (100bp) on the BGI DNBseq platform.
2021-05-23 | E-MTAB-10388 | biostudies-arrayexpress
Project description:Objective: to focus on the molecular mechanisms involved in the dystrophic process that leads to selective wasting of single muscles or muscle groups in Facioscapulohumeral muscular dystrophy (FSHD). By muscle MRI we observed that T2-short tau inversion recovery (T2-STIR) sequences identify two different patterns in which each muscle can be found before the irreversible dystrophic alteration, marked as T1-weighted sequence hyperintensity. We studied these conditions in order to obtain further information on the disease pathogenesis. Design: histopathology, gene expression profiling and real time PCR were performed on muscle biopsies. Subjects: muscles (n=8) with different MRI pattern (T1-weighted normal/T2-STIR normal and T1-weighted normal/T2-STIR hyperintense) from FSHD patients. Data were also compared with inflammatory myopathies (n=7), dysferlinopathies (n=4) and normal controls (n=7). Results: myopathic and inflammatory changes characterize T2-STIR hyperintense FSHD muscles, at variance with T2-STIR normal muscles. These two states can be easily distinguished from each other by their transcriptional profile. Comparison of T2-STIR hyperintense FSHD muscles with muscles of inflammatory myopathies shows peculiar changes, although many alterations are shared among these conditions. Conclusions: at the single muscle level, different stages of the disease correspond to the two MRI patterns. T2-STIR hyperintense FSHD muscles are more similar to inflammatory myopathies than to T2-STIR normal FSHD muscles or other muscular dystrophies, and share with them upregulation of genes involved in innate and adaptive immunity. Our data suggest that selective inflammation, together with perturbation in biological processes such as neoangiogenesis, lipid metabolism and adipokine production, may play a role in FSHD progression.
2012-09-14 | GSE26852 | GEO
Project description:A bovine oligo microarray platform (GPL7053) was used to evidence differences in gene expression profiles from eight (8) lymphocytes samples from prednisolone-treated cows and seven (7) from control animals at two sampling times (T1 and T2). T-test found 539 up-regulated and 368 down-regulated transcripts at T1 sampling time (31 days treatment) and 768 up-regulated and 648 down-regulated transcripts at T2 sampling time (6 days after drug withdrawal) in the prednisolone-treated animal group respect to the controls.
2016-12-22 | GSE50757 | GEO
Project description:Gene expression was profiled in peripheral blood samples collected over three time points from patients during acute anaphylaxis and from healthy controls. Patients presented to the Emergency Department (ED) at Royal Perth Hospital with acute, moderately severe anaphylaxis. Samples were collected at ED arrival (T0), 1 hour later (T1), and 3 hours post arrival (T2). The study design consisted of 12 subjects, 3 time points, and 2 clinical states (acute anaphylaxis, healthy controls).
2014-07-02 | E-GEOD-47655 | biostudies-arrayexpress
Project description:DNA of 124 normal mucosa biopsies from cecum (proximal) and sigmoid (distal) colon obtained at baseline (t1) and after 10years (t2) from 31 screening females was subjected to measure DNA methylation profiles by Illumina Infinium EPIC Human Methylation BeadChip across approximately 850,000 CpGs.
2020-11-09 | GSE142257 | GEO
Project description:Objective: to focus on the molecular mechanisms involved in the dystrophic process that leads to selective wasting of single muscles or muscle groups in Facioscapulohumeral muscular dystrophy (FSHD). By muscle MRI we observed that T2-short tau inversion recovery (T2-STIR) sequences identify two different patterns in which each muscle can be found before the irreversible dystrophic alteration, marked as T1-weighted sequence hyperintensity. We studied these conditions in order to obtain further information on the disease pathogenesis. Design: histopathology, gene expression profiling and real time PCR were performed on muscle biopsies. Subjects: muscles (n=8) with different MRI pattern (T1-weighted normal/T2-STIR normal and T1-weighted normal/T2-STIR hyperintense) from FSHD patients. Data were also compared with inflammatory myopathies (n=7), dysferlinopathies (n=4) and normal controls (n=7). Results: myopathic and inflammatory changes characterize T2-STIR hyperintense FSHD muscles, at variance with T2-STIR normal muscles. These two states can be easily distinguished from each other by their transcriptional profile. Comparison of T2-STIR hyperintense FSHD muscles with muscles of inflammatory myopathies shows peculiar changes, although many alterations are shared among these conditions. Conclusions: at the single muscle level, different stages of the disease correspond to the two MRI patterns. T2-STIR hyperintense FSHD muscles are more similar to inflammatory myopathies than to T2-STIR normal FSHD muscles or other muscular dystrophies, and share with them upregulation of genes involved in innate and adaptive immunity. Our data suggest that selective inflammation, together with perturbation in biological processes such as neoangiogenesis, lipid metabolism and adipokine production, may play a role in FSHD progression. 26 samples of human muscle muscle tissue were analysed using the Illumina beadchip technology.
2012-09-14 | E-GEOD-26852 | biostudies-arrayexpress
Project description:Human brain tumor cystic fluids collected from 3 different subjects:
P1_SM --> Secretory meningioma
P2_CS --> Cystic schwannoma
P3_CG --> Cystic high-grade glioma
Samples were collected at different times (t0, t1 and t2 (only for SM))
Rep1 and rep2 indicate technical replicates.
All P1 samples were analyzed by LTQ ORBITRAP XL.
All P2 and P3 samples were analyzed by LTQ.
2023-04-17 | MSV000091725 | MassIVE
Project description:The feasibility of longitudinal metastatic biopsies for gene expression profiling in breast cancer is unexplored. Dynamic changes in gene expression can potentially predict efficacy of targeted cancer drugs. Patients enrolled in a phase III trial of metastatic breast cancer with sunitinib combined with docetaxel (SU+DOC) versus docetaxel alone (DOC) were offered to participate in a translational substudy comprising longitudinal fine needle aspiration biopsies (FNAB) and positron emission imaging before (T1) and two weeks after start of treatment (T2). Aspirated tumor material was used for microarray analysis, and treatment-induced changes (T2 versus T1) in gene expression and standardized uptake values were investigated. Twenty-one patients were included in the docetaxel ± sunitinib trial at Karolinska and 18 of them agreed to participate in the substudy. Of the 18 women enrolled, 8 were randomly assigned to SU+DOC and 10 to DOC. Metastatic FNAB were carried out in 17 of the 18 patients at both time points with no complications reported. Representative tumor material, sufficient for RNA extraction was obtained in 15 patients at T1 and 14 patients at T2. Matched samples both at T1 and T2 were obtained for 14 subjects, 7 in each arm. The main objective was to determine whether gene expression profiling is feasible using sequential, intra-patient FNAB. Secondary objectives were to identify potential biomarkers of early response by gene expression and/or functional imaging and to explore drug action in vivo by changes in gene expression.
2015-04-14 | GSE54323 | GEO