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The molecular mechanisms by which individuals subjected to environmental heat stress either adapt or develop heat-related complications are not well understood. We analysed the changes in blood mononuclear gene expression patterns in human volunteers exposed to an extreme heat in a sauna (temperature of 78 ± 6 °C).
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DNA methylation of gene promoter regions represses transcription and is a mechanism via which environmental risk factors could affect cells during development in individuals at risk for schizophrenia. We investigated DNA methylation in patient-derived cells that might shed light on early development in schizophrenia. Induced pluripotent stem cells (iPS cells) may reflect a “ground state” upon which developmental and environmental influences would be minimal. Olfactory neurosphere-derived cells (ONS cells) are an adult-derived neuro-ectodermal stem cell modified by developmental and environmental influences. Fibroblasts provide a non-neural control for life-long developmental and environmental influences. Genome-wide profiling of DNA methylation and gene expression was done in these three cell types from the same individuals. All cell types had distinct, statistically significant schizophrenia-associated differences in DNA methylation and linked gene expression, with Gene Ontology analysis showing that the differentially affected genes clustered in networks associated with cell growth, proliferation and movement, functions known to be affected in schizophrenia patient-derived cells. Only 5 gene loci were differentially methylated in all three cell types. These findings suggest that schizophrenia-associated DNA methylation may be a response to the homeostatic demands of different cell types in their local environments. Understanding the role of epigenetics in cell function in the brain in schizophrenia is likely to be complicated by similar cell type differences in intrinsic and environmentally-induced epigenetic regulation. This dataset represents the gene expression part of the study. The DNA methylation data is deposited under accession E-MTAB-2154.
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HCC70 xenografts treated with 11 doses of AZD8186 (100mg/kg BID) were compared to DMSO-treated control xenografts
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Heads and trunk tissues were isolated from zebrafish embryos either wildtype or deficient for b3glct to identify differentially regulated genes which may explain lack of phenotype. Heads and trunks were dissected, solublized in trizol and purified RNA was sent to OakLabs for transcriptional profiling. The expression of mutant to normal tissues was compared to identify differentially regulated genes shared by both head and trunk tissue in mutant embryos.
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The study aims to show that Sox9+ Chd1+ mouse embryonic lung progenitors can be isolated and expanded long-term in 3D culture while maintaining their multipotency. in vitro cultured Sox9+ Chd1+ lung progenitors transcriptionally resemble their in vivo counterparts and show significant difference from adult lung epithelial (Cdh1+ and EpCAM+) and non-epithelial (Cdh1- and EpCAM-) cells
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Infectious bursal disease virus (IBDV) belongs to the family Birnaviridae and is economically important to the poultry industry worldwide. IBDV infects B cells in the bursa of Fabricius (BF), which can cause severe immunosuppression and mortality in young chickens. Earlier studies have shown that strains of IBDV lose their virulence potential after serial passage in non-B lymphoid cells, for reasons that are poorly understood. This study aimed to investigate the gene expression profiles of one cell-culture adapted attenuated IBDV strain (D78) and one very virulent IBDV strain (UK661) in chicken primary B cells cultured ex vivo from the bursa of Fabricius. The viruses were studied in B cells over 48h and their gene expression was initially evaluated with qPCR. The mRNA was isolated from the cells at 18 hours post-infection and screened with Affymetrix microarrays in triplicate. The study included mock controls which were conducted in triplicate.
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The dimerization and binding of DNA by BldD is affected by its interaction with cyclic di-GMP. The D116A mutant of BldD is partially impaired in its biding of cyclic di-GMP. ChIP-Seq was carried out to determine the difference in the degree of DNA binding by the wild type and D116A mutated BldD in Streptomyces venezuelae.
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BldC is a transcriptional regulator essential for morphological development Streptomyces venezuelae. Although bldC deletion strain is unable to produce aerial hyphae, electron microscopy reveals that almost all of the colony biomass is in the form of spores rather than undifferentiated vegetative hyphae. This ChIP-chip experiment was carried out to determine the binding sites, and thence the regulon, of BldC in Streptomyces venezuelae. Cy3(IP):Cy5(Total) signal ratios in the wild type were compared to those in a bldC knockout strain.
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Human intestinal epithelial organoids (IEO) culture models are rapidly emerging as novel experimental tools to investigate fundamental aspects of intestinal epithelial (patho)physiology. Cellular source and culture protocols vary between different IEO models and reliable markers for their characterization/validation are currently limited. DNA methylation has been demonstrated to play a key role in regulating gene expression and cellular function. This epigenetic mark is comparably stable and has been shown to reflect cellular identity such as tissue origin, developmental stage and age. Our genome wide DNA methylation datasets of purified human epithelium represent a unique resource, which can be used by other researchers to validate their model systems We provide the following datasets of genome-wide DNA methylation profiling by Infinium HumanMethylation450 BeadChip: Purified intestinal epithelial cells (EpCAM+) from paediatric ileum and colon, Non-epithelial mucosal cells (EpCAM-), Whole colonic mucosal biopsies, Intestinal organoid cultures from paediatric ileum and colon, Purified intestinal epithelial cells (EpCAM+) from foetal small intestine and foetal large intestine, Intestinal organoid cultures from foetal small intestine and foetal large intestine, Intestinal organoid cultures derived from induced pluripotent stem cells. Note: Some samples in this data set were previously submitted to ArrayExpress under accession number E-MTAB-3709. They're clearly marked in the “Description” field in sample annotations. Information about batch effect during sample handling is included in the experimental variable “block”. Batch effect is not massive but present, so it is recommended that batch correction is carried out in data analysis. Complementary RNA-seq data on the purified cells and organoids can be found in ArrayExpress at E-MTAB-5015 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5015/ ).
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Ewings Sarcoma (ES) belongs to the group of bone cancers defined by the existence of a certain EWS-ETS fusion gene. In this study we use the model cell line CADO-ES1 (EWSR1-ERG fusion gene) to characterize the tumor biology of a versatile ES side-population (SP). We aim to compare SP- and non-SP-cells to identify specific characteristics of the SP which points towards a tumor driving functionality of the SP. Due to some stem cell like properties of the SP fraction a comparison to MSCs and normal fibroblasts as a control are also performed.
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