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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of Salmo salar (Salmon) hepatocytes treated with DMSO (control), nonylphenol and 3,3,4,4-tetrachlorobiphenyl to identify interactions between estrogen and aryl hydrocarbon receptor signalling pathways

ABSTRACT: Gene Expression Profiling of Interactions Between Estrogen- and Aryl hydrocarbon-Receptor Signalling Pathways

INSTRUMENT(S): BAS-1800 [FUJIFILM]

ORGANISM(S): Salmo salar

SUBMITTER: Anne Mortensen

PROVIDER: E-MEXP-946 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Identification and expression regulation of symbiotically activated legume genes.

Küster Helge H Vieweg Martin F MF Manthey Katja K Baier Markus C MC Hohnjec Natalija N Perlick Andreas M AM

Phytochemistry 20061101 1

Legume plants are able to enter two different endosymbioses with soil prokaryotes and soil fungi, leading to nitrogen-fixing root nodules and to arbuscular mycorrhiza (AM), respectively. We applied in silico and microarray-based transcriptome profiling approaches to uncover the transcriptome of developing root nodules and AM roots of the model legume Medicago truncatula. Several hundred genes were found to be activated in different stages of either symbiosis, with almost 100 genes being co-induc ...[more]

PMID: 17081575

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Transcription profiling of Drosophila transformed with two Plasmodium cell surface antigens

Project description:Two Plasmodium cell surface antigens were transformed into Drosophila, un-induced flies were compared to induced flies.

2008-12-31 | E-MEXP-1859 | biostudies-arrayexpress

Species identification of ancient Lithuanian fish remains using collagen fingerprinting

Project description:Morphological identification of ancient bone is often problematic due to heavy fragmentation that generally influences zooarchaeological assemblages. Fish bones are more taphonomically sensitive than those of other vertebrates as they are typically smaller and less biomineralised. Thus, taxonomic identification based on the preservation of morphological features is often extremely limited and can reduce or eliminate the usefulness of an assemblage for inferring taxon information. Currently, one of the most time- and cost-efficient methods of achieving faunal identity from ancient bone is by the collagen fingerprinting technique known as ZooMS (Zooarchaeology by Mass Spectrometry). ZooMS harnesses the potential of preserved collagen, which is the most dominant and time-stable protein in bone. In this research, ZooMS is applied to ancient Baltic region fish assemblages that are between 500 and 6000 years old in order to define species identity and construct assemblage compositions. Alongside inferences into environmental and biological shifts from the Neolithic era to present day in the Baltic region, we demonstrate for the first time the ability to distinguish between recently diverged members of the Salmo (salmon) and Scophthalmus (turbot) genera. ZooMS analysis highlights 7% of the collagen-containing assemblage as having been morphologically identified incorrectly and has facilitated taxonomic refinement of a further 28% of samples, including some of the morphologically indeterminate bone fragments. This research emphasises the great potential of ZooMS in identifying ichthyoarchaeological bone remains to species-level, and provides a case for the use of collagen fingerprinting in contributing to baseline fisheries and ecological data, to inform modern management.

2018-08-29 | PXD010041 | Pride

Dissecting modes of action of non-genotoxic carcinogens in primary mouse hepatocytes.

Project description:Under REACH, the European Community Regulation on chemicals, the testing strategy for carcinogenicity is generally based on in vitro and in vivo genotoxicity assays. Given that non-genotoxic carcinogens are negative for genotoxicity, this class of carcinogens will not be detected. Therefore, alternative test are urgently needed. Non-genotoxic carcinogens, however, act through different modes of action, which complicates the development of such an assay. The aim of this study was to investigate whether gene expression profiling in primary mouse hepatocytes can be used to distinguish different modes of action of non-genotoxic carcinogens. Primary mouse hepatocytes were exposed to 16 non-genotoxic carcinogens with diverse modes of action. Upon profiling, pathway analysis was performed to obtain insight into the biological relevance of the observed changes in gene expression. To recognize similarities in mode of action at the transcriptomic level, both a supervised and an unsupervised comparison approach was applied.

2012-06-25 | E-GEOD-35058 | biostudies-arrayexpress

Gene expression profiling to recognize specific features of non-genotoxic carcinogens

Project description:The current test strategy for carcinogenicity is generally based on in vitro and in vivo genotoxicity assays. Non-genotoxic carcinogens (NGTXC) are negative for genotoxicity and go undetected. Therefore, alternative tests to detect these chemicals are urgently needed. NGTXC act through different modes of action, which complicates the development of such assays. We have demonstrated recently in primary mouse hepatocytes that some, but certainly not all, NGTXC can be categorized according to their mode of action based on feature detection at a gene expression level (Schaap et al. 2012 (PMID 22710402)). Identification of a wider range of chemicals probably requires multiple in vitro systems. In the current study, we describe the added value of using mouse embryonic stem cells. In this study, the focus is on NGTXC, but we also included genotoxic carcinogens and non-carcinogens. This approach enables us to assess the robustness of this method and to evaluate the system for recognizing features of chemicals in general, which is important for application in future risk assessment. Primary mouse hepatocytes and mouse embryonic stem cells were exposed to 26 chemicals (non-genotoxic carcinogens and non-carcinogens) representing diverse modes of action. Upon profiling, an unsupervised comparison approach was applied to recognize similar features at the transcriptomic level. This Series consists of the gene expression data of the primary mouse hepatocytes. The expression data of the mouse embryonic stem cells is submitted separately under another accession number. In this study we tested 26 chemicals of which 16 non-genotoxic carcinogens, 4 genotoxic carcinogens, 2 genotoxic non-carcinogens and 4 non-carcinogens. Specification of the chemicals can be found in the readme file.

2014-10-23 | E-GEOD-44088 | biostudies-arrayexpress

Benzo[a]pyrene response in primary mouse hepatocytes

Project description:Gene expression changes to several concentrations of benzo[a]pyrene in primary hepatocytes of wildtype and Xpa-/-p53+/- mice

2011-08-11 | E-TABM-1139 | biostudies-arrayexpress

Adaption of oxidative phosphorylation machinery compensates hepatic lipotoxicity in early stages of MAFLD; PMID:35743314

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2022-08-02 | PXD032214 | Pride

Genotoxic Carcinogen response in primary mouse hepatocytes

Project description:Gene expression changes to several compounds in primary hepatocytes of wildtype and Xpa-/-p53+/- mice

2018-04-06 | E-MTAB-665 | biostudies-arrayexpress

Expression data from control and heat shocked mouse spermatocytes and hepatocytes

Project description:In somatic cells elevated temperature induces activation of the heat shock transcription factor 1 (HSF1) what leads to heat shock proteins synthesis and cytoprotection. However, in the male germ cells (spermatocytes) upon HSF1 activation, caspase-3 dependent apoptosis is induced and spermatogenic cells are actively eliminated. To elucidate a mechanism of such diverse HSF1 activity we carried out genome-wide transcriptional analysis in control and heat-shocked cells, either spermatogenic or somatic. As model somatic cells we used hepatocytes that respond to hyperthermia in a classical way by induction of heat shock genes transcription. As spermatogenic cells we used a fraction of cells enriched with spermatocytes, which are the most sensitive to damage in elevated temperatures. Using isolated spermatocytes we avoided the influence of the somatic testicular component on the our final results. Genes that are differently regulated during hyperthermia in both types of cells have been identified. On Affymetrix gene chip arrays we analyzed RNA isolated from spermatocytes or hepatocytes, either untreated (control) or after heat shock and 2h of recovery at physiological temperature. Analyses were done in triplicate.

2012-08-22 | E-GEOD-40248 | biostudies-arrayexpress

Cardiac transcriptome response in developing rainbow trout exposed to retene and fluoranthene

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2021-06-18 | E-MTAB-8980 | biostudies-arrayexpress

Comparison of hepatocarcinogen-induced gene expression profiles in conventional primary rat hepatocytes with in vivo rat liver

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2012-04-23 | E-GEOD-36524 | biostudies-arrayexpress

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