Transcriptome and open chromatin analysis of 5-month mouse liver and blood by the TaRGET II consortium
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE146508 | GEO | 2020/05/20
REPOSITORIES: GEO
Similar Datasets
Project description:The NIEHS data set (endpoint C) was provided by the National Institute of Environmental Health Sciences (NIEHS) of the National Institutes of Health (Research Triangle Park, NC, USA). The study objective was to use microarray gene expression data acquired from the liver of rats exposed to hepatotoxicants to build classifiers for prediction of liver necrosis. The gene expression compendium data set was collected from 418 rats exposed to one of eight compounds (1,2-dichlorobenzene, 1,4-dichlorobenzene, bromobenzene, monocrotaline, N-nitrosomorpholine, thioacetamide, galactosamine, and diquat dibromide). All eight compounds were studied using standardized procedures, i.e. a common array platform (Affymetrix Rat 230 2.0 microarray), experimental procedures and data retrieving and analysis processes. For each compound, four to six male, 12 week old F344 rats were exposed to a low dose, mid dose(s) and a high dose of the toxicant and sacrificed at 6, 24 and 48 hrs later. At necropsy, liver was harvested for RNA extraction, histopathology, and clinical chemistry assessments.
2010-09-25 | E-GEOD-24363 | biostudies-arrayexpress
Project description:The NIEHS data set (endpoint C) was provided by the National Institute of Environmental Health Sciences (NIEHS) of the National Institutes of Health (Research Triangle Park, NC, USA). The study objective was to use microarray gene expression data acquired from the liver of rats exposed to hepatotoxicants to build classifiers for prediction of liver necrosis. The gene expression compendium data set was collected from 418 rats exposed to one of eight compounds (1,2-dichlorobenzene, 1,4-dichlorobenzene, bromobenzene, monocrotaline, N-nitrosomorpholine, thioacetamide, galactosamine, and diquat dibromide). All eight compounds were studied using standardized procedures, i.e. a common array platform (Affymetrix Rat 230 2.0 microarray), experimental procedures and data retrieving and analysis processes.
2010-09-25 | GSE24363 | GEO
Project description:Paternal exposure to a range of environmental and lifestyle factors elicits distinct changes to the sperm sncRNA profile; modifications that have significant post-fertilization consequences. Despite this knowledge, there remains limited mechanistic understanding of how paternal exposures effect the sperm sncRNA landscape. Here, we report the acute sensitivity of the sperm sncRNA profile to the potent reproductive toxicant, acrylamide. Further, we traced the differential accumulation of acrylamide responsive sncRNAs to coincide with sperm transit of the proximal (caput) segment of the epididymis, wherein acrylamide exposure altered the expression of several transcription factors implicated in the expression of acrylamide-sensitive sncRNAs. We also identified extracellular vesicles secreted from the caput epithelium in relaying altered sncRNA profiles to maturing spermatozoa, the implications of which manifest in the form of dysregulated gene expression during early embryonic development. These data provide a causative mechanistic link to account for how environmental insults can alter the sperm epigenome and compromise the transcriptomic profile of early embryos
2021-10-07 | PXD022865 | Pride
Project description:AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana; The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate. Wild-type and ARR22 overexpressing seedlings were treated with t-zeatin for 3 hours; Experimenter name = Takatoshi Kiba , Takeshi Mizuno; Experimenter institute = AtGenExpress Experiment Overall Design: 12 samples were used in this experiment
2008-06-14 | E-GEOD-5698 | biostudies-arrayexpress
Project description:To determine toxicant specific effects of Ordnance Related Compound (ORC) exposure we performed microarray hybridizations with RNA isolated from Daphnia magna following different ORC exposures at the 1/10 LC50. The gene expression profiles revealed toxicant specific gene expression profiles allowed for the identification of specific biomarkers of exposure. Keywords: ecotoxicogenomic exposure study We exposed Daphnia magna the 1/10 LC50 of different Ordnance Related Compounds (Cu, Zn, Pb, WO4, RDX, TNT, 2-ADNT, 2-ADNT, TNB, DNB, 2,4-DNT, and 2,6-DNT) for 24 hours. For each exposure condition, we performed 3 exposures and 2 technical replicates (as dye swap) for each exposure (6 microarrays total, except TNT and Cu). All exposures were compared to a unexposed laboratory control (MHRW media).
2010-05-18 | E-GEOD-13169 | biostudies-arrayexpress
Project description:To determine toxicant specific effects of Ordnance Related Compound (ORC) exposure we performed microarray hybridizations with RNA isolated from Daphnia magna following different ORC exposures at the 1/10 LC50. The gene expression profiles revealed toxicant specific gene expression profiles allowed for the identification of specific biomarkers of exposure. Keywords: ecotoxicogenomic exposure study
2008-10-16 | GSE13169 | GEO
Project description:In this paper, a nonlinear mathematical model is proposed and analyzed to study the
effect of environmental toxicant on the immune response of the body. Criteria for local
stability, instability and global stability are obtained. It is shown that the immune
response of the body decreases as the concentration of environmental toxicant increases,
and certain criteria are obtained under which it settles down at its equilibrium level.
In the absence of toxicant, an oscillatory behavior of immune system and pathogenic
growth is observed. However, in the presence of toxicant, oscillatory behavior is not
observed. These studies show that the toxicant may have a grave effect on our body’s
defense mechanism.
Keywords: Pathogen; Immune Response; Toxicant; Stability.
2024-09-02 | BIOMD0000000905 | BioModels
Project description:In this paper, a nonlinear mathematical model is proposed and analyzed to study the
effect of environmental toxicant on the immune response of the body. Criteria for local
stability, instability and global stability are obtained. It is shown that the immune
response of the body decreases as the concentration of environmental toxicant increases,
and certain criteria are obtained under which it settles down at its equilibrium level.
In the absence of toxicant, an oscillatory behavior of immune system and pathogenic
growth is observed. However, in the presence of toxicant, oscillatory behavior is not
observed. These studies show that the toxicant may have a grave effect on our body’s
defense mechanism.
Keywords: Pathogen; Immune Response; Toxicant; Stability.
2024-09-02 | BIOMD0000000906 | BioModels
Project description:AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana (Hybridisations done at NASC). The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate. Series 1: Growth conditions: Sterilized seeds will be stratified at 4degreeC for 3 days, exposed to white light for 2 h to induce germination, and grown on MS agar plates (0.9 % agar) without sugar in total darkness for 4 days at 22degreeC. Seedlings will then be transferred to the light conditions described for each slide below for 1 h (to identify early induced genes) and 4 hrs (maximum expression of the first initial light response of most target genes), respectively. All light treatments will be done in parallel to minimize the number of dark controls. All samples will be done in triplicate and only with shoots. Experimenter name = Thomas Kretsch; Experimenter institute = AtGenExpress Experiment Overall Design: 48 samples were used in this experiment
2008-06-13 | E-GEOD-5617 | biostudies-arrayexpress
Project description:The developing epigenome changes rapidly, potentially making it more sensitive to toxicant exposures. DNA modifications, including methylation and hydroxymethylation, are important parts of the epigenome that may be affected by environmental exposures. However, most studies do not differentiate between these two DNA modifications, possibly masking significant effects. To investigate the relationship between DNA hydroxymethylation and developmental exposure to common contaminants, a collaborative, NIEHS-sponsored consortium, TaRGET II, initiated longitudinal mouse studies of developmental exposure to human-relevant levels of the phthalate plasticizer di(2-ethylhexyl) phthalate (DEHP), and the metal lead (Pb). Exposures to 25 mg DEHP/kg of food (approximately 5 mg DEHP/kg body weight) or 32 ppm Pb-acetate in drinking water were administered to nulliparous adult female mice. Exposure began 2 weeks before breeding, and continued throughout pregnancy and lactation, until offspring were 21 days old. At 5 months, perinatally exposed offspring blood and cortex tissue were collected, for a total of 25 male mice and 17 female mice (n=5-7 per tissue and exposure). DNA was extracted and hydroxymethylation was measured using hydroxymethylated DNA immunoprecipitation sequencing (hMeDIP-seq). Differential peak and pathway analysis was conducted comparing across exposure groups, tissue types, and animal sex, using an FDR cutoff of 0.15. DEHP-exposed females had two genomic regions with lower hydroxymethylation in blood and no differences in cortex hydroxymethylation. For DEHP-exposed males, ten regions in blood (six higher and four lower) and 246 regions (242 higher and four lower) and four pathways in cortex were identified. Pb-exposed females had no statistically significant differences in blood or cortex hydroxymethylation compared to controls. Pb-exposed males, however, had 385 regions (all higher) and six pathways altered in cortex, but no differential hydroxymethylation was identified in blood. Overall, perinatal exposure to human-relevant levels of two common toxicants showed differences in DNA hydroxymethylation specific to sex, exposure type, and tissue, but male cortex was most susceptible to hydroxymethylation differences by exposure. Future assessments should focus on understanding if these findings indicate potential biomarkers of exposure or are related to functional long-term health effects.
2023-04-28 | GSE229717 | GEO