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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of mouse control 25-dpc embryos from control vs. valproic acid (VPA) treated dams and control P19 mouse EC cells vs 1 mM sodium valproate for 24 h

ABSTRACT: Valproic acid (VPA) is a potent inducer of neural tube defects (NTDs), but its mechanism of teratogenicity is not known. To study the transcriptional response of VPA during the susceptible period, i.e. when VPA is likely to exert most of its teratogenic effect, RNA was extracted from 8.25-dpc embryos (6 h post treatment) from control and VPA-treated dams, and subjected to microarray analysis (four arrays). To be more useful for risk assessment, in vitro models, using cells, may bridge biomarkers discovered by gene expression profiling in an animal in vivo model. Since pluripotent embryocarcinoma (EC) cell lines may be relevant models for early embryonic cells, P19 mouse EC cells were treated with or without 1 mM sodium valproate for 24 h and alos subjected to microarray analysis (four arrays).

ORGANISM(S): Mus musculus

SUBMITTER: Kim Kultima

PROVIDER: E-MEXP-45 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Valproic acid teratogenicity: a toxicogenomics approach.

Kultima Kim K Nyström Anna-Maja AM Scholz Birger B Gustafson Anne-Lee AL Dencker Lennart L Stigson Michael M

Environmental health perspectives 20040801 12

Embryonic development is a highly coordinated set of processes that depend on hierarchies of signaling and gene regulatory networks, and the disruption of such networks may underlie many cases of chemically induced birth defects. The antiepileptic drug valproic acid (VPA) is a potent inducer of neural tube defects (NTDs) in human and mouse embryos. As with many other developmental toxicants however, the mechanism of VPA teratogenicity is unknown. Using microarray analysis, we compared the global ...[more]

PMID: 15345369

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Transcription profiling of mouse embryos 1.5, 3 and 6 hr after maternal treatment with the teratogen sodium valproate

Project description:The antiepileptic drug valproic acid (vpa) is known teratogen giving neural tube defects (ntd:s). Administration of vpa to female NMRI on gestation day 8 induces a high incidence of ntd. In this study we investigate the time dependent gene expression changes induced in the embryo 1.5, 3 respectively 6 hr after maternal sodium valproate treatment.

2008-03-28 | E-MEXP-1062 | biostudies-arrayexpress

Comparative genomic hybridization in traditional fermentative Saccharomyces cerevisiae yeasts

Project description:We study the genetics, including microarray karyotyping using comparative genomic hybridization, to explore global changes in the genomic DNA of seven S. cerevisiae strains related to traditional fermentations of very different sources comparing to the sequenced S. cerevisiae laboratory strain (S288C). Our final goal is to determine the adaptive evolution of properties of biotechnological interest in Saccharomyces yeasts. Many copy number variations (CNVs) were observed, especially in genes associated to subtelomeric regions and transposon elements. Among the fermentation strains, differential CNV was observed in genes related to sugar transport and metabolism. An outstanding example of diverse CNV is the gen PUT1, involved in proline assimilation, which correlated with the adaptation of the strains to the presence of this nitrogen source in the media. Seven S. cerevisiae strains were obtained from natural environments and different fermentation processes. The S. cerevisiae strain S288C was used as a control for microarray hybridizations. All experiments were performed using duplicate arrays, and Cy5-dCTP and Cy3-dCTP dye-swap assays were performed to reduce dye-specific bias.

2013-12-15 | E-GEOD-46165 | biostudies-arrayexpress

Comparative analysis of Tsaiya duck (Anas platyrhynchos) transcriptional profiling between high and low hatchability

Project description:Hatchability is one of the important reproductive traits of poulty, however, molecular biological study related to hatchability of poultry is very limited. The magnum is where the egg white components are produced. During embryo development, egg white secreted by the magnum is gradually transferred into the amniotic fluid, and albumen finally migrates to the embryo. Egg white proteins are composed of ovalbumin, conalbumin, lysozyme, ovomucoid, riboflavin binding protein (RfBP), and other less abundant proteins. Mutation of ovalbumin and RfBP genes increases the mortality of embryos; therefore, egg white might be closely related to poultry hatchability. Tsaiya duck (Anas platyrhynchos) is the major egg-laying duck in Taiwan. In this study, gene expression profiling by cDNA microarray chip technology was performed using mRNA prepared from the magnum epithelium of Tsaiya ducks, and a number of differentially expressed transcripts were found. Keywords = Tsaiya duck (Anas platyrhynchos), magnum, hachability, cDNA microarray, transcriptional profiling. Analysis used low hachability RNA as control samples for comparison to the experimental samples taken from high hachability group. Total RNA was isolated by the RareRNA reagent (GenePure). The MicroMax direct labeling kit (PerkinElmer) was used to prepare the labeled cDNA and further process the hybridization on the arrays. Dye swap was design with four arrays. Arrays were scanned using a GenePix 4000B microarray scanner (Axon Instruments). GenePix Pro 4.1 software was then used to acquire the raw data. The data was analyzed by Avadis software (Strand Life Science).

2010-11-16 | E-GEOD-23100 | biostudies-arrayexpress

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Project description:To define short and long-term changes in the phospho-proteome of the cells following Rho-kinase inhibition with H1152 inhibitor, in mouse embryonic fibroblast cells.

2016-01-18 | PXD002515 | Pride

Analysis of total proteome changes upon long-term treatment with Rho kinase inhibitor H1152.

Project description:We quantified protein changes associated with long-term Rho-kinase inhibition, using SILAC proteomics in conjugation with long-termH1152 treatment of mouse embryonic fibroblast cells.

2016-01-18 | PXD002521 | Pride

Israeli acute paralysis virus – what we have learned about the virus since mysterious disappearance of the US honey bees known as Colony Collapse Disorder (CCD) in 2006

Project description:There were important gaps in our knowledge of Israeli acute paralysis virus (IAPV), when IAPV was tightly linked to bee Colony Collapse Disorder (CCD), the mysterious disease that, starting in 2006-2007, has been wiping out honey bees in the US. To fill in these gaps we studied the molecular basis of transmission, pathogenesis, and genetic diversity of IAPV infection in honey bees. We investigated the impact of IAPV infection on colony losses and host transcriptional response to IAPV infections, and exploited the potential of RNAi-based strategies for treating viral diseases in honey bees. Our study clearly shows that IAPV has become established as a persistent infection and is highly prevalent in the honey bee population. The existence of both horizontal and vertical transmission pathways of the virus likely accounts for the high prevalence of IAPV in bees. While IAPV is probably not the only culprit responsible for CCD, its ability to cause increased mortality in honey bees is firmly demonstrated. The phenotypic differences in pathology among different strains of IAPV may be due to their high level of standing genetic variation. The JAK-STAT pathway, along with other signaling events such as mTOR and MAPK pathways, likely involves honey bees’ antiviral immune responses to the IAPV infection. The identification of IAPV-encoded putative suppressor of RNAi and evidence that silencing the RNAi suppressor led to a significant reduction in IAPV replication in infected bees illustrates the therapeutic potential of targeting viral suppressor protein to reduce virus replication. Our study gives direction for developing strategies to reduce colony losses due to viral diseases. Adult worker bees and brood were collected from colonies that were declining and identified with IAPV infections and its control with 6 replications per group.

2014-04-08 | E-GEOD-46278 | biostudies-arrayexpress

A human interactome in three quantitative dimensions organized by stoichiometries and abundances -- auxiliary dataset

Project description:The organization of a cell emerges from the interactions in protein networks. The interactome is critically dependent on the strengths of interactions and the cellular abundances of the connected proteins, both of which span orders of magnitude. However, these aspects have not yet been analyzed globally. Here, we have generated a library of HeLa cell lines expressing 1,125 GFP-tagged proteins under near-endogenous control, which we used as input for a next-generation interaction survey. Using quantitative proteomics, we detect specific interactions, estimate interaction stoichiometries and measures cellular abundances of interacting proteins. These three quantitative dimensions reveal that the protein network is dominated by weak, substoichiometric interactions that play a pivotal role in defining network topology. The minority of stable complexes can be identified by their unique stoichiometry signature. This study provides a rich interaction dataset connecting thousands of proteins, and introduces a framework for quantitative network analysis. -- This is an auxiliary dataset containing follow-up experiments. The main dataset is available under the identifier PXD002815.

2015-10-28 | PXD002829 | Pride

Transcription profiling of rat gastrocneumius muscle following short and long term denervation

Project description:Effect of "Sensory Protection" on the transcriptome of Gastrocnemius muscle denervated by Tibial nerve transection in the rat. Comparison is made between the muscle transcriptome in denervated muscle (D), muscle undergoing surgical repair with a motor nerve (immediate repair, or IR) and muscle undergoing surgical repair with a pure sensory nerve (sensory protection, or SP). There are 6 cohorts of rats with 4 to 6 rats in each cohort:<br><br>1 Month Denervated, 1 Month Immediate Repair, 1 Month Sensory Protection, 3 Month Denervated, 3 Month Immediate Repair, 3 Month Sensory Protection. <br><br>For each animal RNA was extracted from both the experimental operated (right) gastrocnemius muscle and the contralateral control unoperated (left) gastrocnemius. Samples were run in duplicate with fluorophor reversal experiments (i.e experimental limb RNA labelled with Cy3 and control limb RNA labelled with Cy5 and vice versa) to control for possible unequal incorporation of the dyes in the reverse transcription reaction.

2009-04-15 | E-MEXP-1580 | biostudies-arrayexpress

Using tiling arrays to precisely detect DNA targets of THO in yeast

Project description:Crosslinked DNA from wild type cells or from mutant of the THO complex was analyzed by tiling arrays to precisely detect DNA targets of THO in yeast. DNA coming from SDS-washed DCF pellet and the supernatant SN2k of 2 strains were compared in the study, WT (W303) and mft1 delta (DLY224). The DNA of each condition (Pellet or Supernatant) was labeled either with Cy3 or Cy5 fluorescent dyes and competitively hybridized on 244k agilent arrays. For each strain, the experiment was performed on 2 biological replicates, with dye swap.

2014-03-24 | E-GEOD-32980 | biostudies-arrayexpress

Broad epigenetic signature of maternal care in the brain of adult rats (expression)

Project description:Maternal care is associated with long-term effects on behavior and epigenetic programming of the NR3C1 (GLUCOCORTICOID RECEPTOR) gene in the hippocampus of both rats and humans. However, epigenetic changes at a single gene promoter are unlikely to account for the range of responses to the early life environment and the persistent change in expression of hundreds of additional genes in adult rats in response to differences in maternal care. Here we show that natural variations in maternal care are associated with coordinate changes in DNA methylation, chromatin, and gene expression spanning over a hundred kilobase pairs in the hippocampus of adult rats. The offspring of high compared to low maternal care mothers show epigenetic changes in promoters, exons, and gene ends and higher transcriptional activity across many genes, suggesting that a broad epigenetic regulation of gene expression may form part of a coordinated response to early maternal care. We obtained hippocampal samples from adult offspring of rat mothers that differed in the frequency of pup licking/grooming in the first week of life, 4 from high frequency and 4 from low frequency mothers. Using custom-designed microarrays with probes tiling the 7 million base pair region of rat chromosome 18 centered at the NR3C1 gene at 100 bp spacing, we obtained transcription profiles by hybridizing cDNA to microarrays. Each profile was generated in duplicate.

2011-03-09 | E-GEOD-20717 | biostudies-arrayexpress

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