RelA Nuclear factor-kappaB (NF-kB) Subunit binding Loci in Promoter Regions of PHM1-31 Myometrial Smooth Muscle Cells (expression)
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Neil Chapman
PROVIDER: E-GEOD-65707 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2015-03-31 | E-GEOD-65721 | biostudies-arrayexpress
Project description:A study to define the binding loci of RelA-containing NF-kappaB dimers in a human myometrial smooth muscle cell line after exposure to TNF. Monolayers of PHM1-31 cells were exposed to TNF (10ng/ml) for 1 hour or left unstimulated. The Chromatin immunoprecipitation (ChIP) assay was performed to recover RelA-bound chromatin or non-specifically bound chromatin with IgG. That chromatin was prepared and used to probe Affymetrix GeneChIP 1.0R Human Promoter arrays. Three biological replicates of each experiment were conducted. Datasets were subsequently analysed in Partek Genomics Suite V6.6 where baseline was normalised by subtraction of IgG values from conrresponding RelA-immunoprecipitated samples. Control samples immunoprecipitated with RelA were then compared with TNF-stimulated samples immunoprecipitated with RelA.
2015-03-31 | E-GEOD-65690 | biostudies-arrayexpress
Project description:gene expression analysis of wild type and DelilaRosea overexpressing microtom tomato fruits
2008-12-01 | E-MEXP-1830 | biostudies-arrayexpress
Project description:Alternative pre-mRNA splicing critically contributes to the generation of protein variety in a tissue- and development-specific manner. Alterations in the normal pathways of alternative splicing (AS) have been associated with the growth and maintenance of several tumour types, and have been indicated as candidate bio-markers of tumour progression, metastasis and patient survival. In this study we applied genome-wide exon array technology to investigate AS events that may distinguish between human medulloblastoma and normal cerebellum. We initially investigated gene-level expression profiles to identify samples expressing gene signatures characteristic of previously described MB molecular subgroups. 3 medulloblastomas significantly over-expressed genes typically belonging to the Shh signalling pathway or associated with a granule cell progenitor status and were therefore classified as Shh-activated tumours (MB1). The remaining tumour samples were grouped together as medulloblastoma subset 2 (MB2). We then applied the Splicing Index algorithm and identified 1260 unique genes containing at least one candidate exon whose inclusion rate differed between different sample subgroups. Following the analysis of candidate event expression plots and gene structure annotation, we selected 14 examples of differential splicing of cassette exons and successfully validated 11 of them by semi-quantitative RT-PCR in a selection of the initial sample-set and subsequently in an independent set of 10 normal cerebellum and 20 medulloblastoma samples. Through the analysis of AS pathway in in vitro cultures of cerebellar granule cell progenitors (the putative cell of origin of least a subset of medulloblastomas), we showed that medulloblastoma-associated AS patterns could be indicative of a normal cerebellar undifferentiated phenotype and suggested that activation of oncogenic pathways during the development of the cerebellum may lead to a failure of neuronal differentiation also through the disruption of AS programs.
2011-01-01 | E-MTAB-292 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE30495: Detailed transcriptomics analysis of the effect of dietary fatty acids on gene regulation in the murine heart. GSE30553: Detailed transcriptomics analysis of the effect of the PPARalpha agonist Wy14,643 on gene regulation in the murine heart Refer to individual Series
2012-02-21 | E-GEOD-30649 | biostudies-arrayexpress
Project description:Persisters are cells which evade stresses like antibiotics and which are characterized by reduced metabolism and a lack of genetic alterations required to achieve this state. We showed previously that MqsR and MqsA of Escherichia coli are a toxin-antitoxin pair that influence cell physiology (e.g., biofilm formation and motility) via RNase activity as well as through regulation of toxin CspD. Here, we show that deletion of the mqsRA locus decreases persister cell formation and, consistent with this result, overexpression of MqsR increases persister cell formation. Furthermore, toxins Hha, CspD, and HokA increase persister cell formation. In addition, by overproducing MqsR in a series of isogenic mutants, we show that Hha and CspD are necessary for persister cell formation via MqsR overexpression. Surprisingly, Hfq, a small RNA chaperone, decreases persistence. A whole-transcriptome study shows that Hfq induces transport-related genes (oppA, oppB, oppC, oppD, oppF, and dppA), outer membrane protein-related genes (ybfM and ybfN), toxins (hha), and proteases (clpX, clpP, and lon). Taken together, these results indicate that toxins CspD and Hha influence persister cell formation via MqsR and that Hfq plays an important role in the regulation of persister cell formation via regulation of transport or outer membrane proteins. Strains: E. coli BW25113 K-12 hfq deleted mutant vs. wild-type Medium: LB Culture: Planktonic cell grown OD=0.5, adjusted OD=1.0, and then exposed to 100 ug/mL ampicillin for 2 h.
2009-11-07 | E-GEOD-18852 | biostudies-arrayexpress
Project description:Background: Mycobacterium avium subspecies paratuberculosis (MPTb) is the causative agent of Johne’s disease, an intestinal disease of ruminants with major economic consequences. MPTb bacilli are phagocytosed by host macrophages upon exposure where they persist, resulting in lengthy subclinical phases of infection that can lead to immunopathology and disease dissemination. Consequently, analysis of the macrophage transcriptome in response to MPTb infection can provide valuable insights into the molecular mechanisms that underlie Johne’s disease. Here, we investigate pan-genomic gene expression in bovine monocyte-derived macrophages (MDM) purified from seven age-matched non-related females, in response to in vitro infection with MPTb (multiplicity of infection 2:1) at intervals of 2 hours, 6 hours and 24 hours post-infection. Results: Differentially expressed genes were identified by comparing the transcriptomes of the infected MDM to the control MDM at each time point (adjusted P-value threshold ≤ 0.10). 1,050 differentially expressed unique genes were identified 2 hours post-infection, with 974 and 84 differentially expressed unique genes detected 6 hours and 24 hours post-infection, respectively. Furthermore, in the infected MDM the number of upregulated genes exceeded the number of downregulated genes at each time point, with the fold-change in expression for the upregulated genes markedly higher than that for the downregulated genes. Conclusions: Inspection and systems analysis of the differentially expressed genes revealed changes in the expression profiles of genes involved in the inflammatory response, cell signalling pathways and apoptosis. The transcriptional changes associated with cellular signalling and the inflammatory response may reflect different immuno-modulatory mechanisms that underlie host-pathogen interactions during infection. Affymetrix GeneChip® Bovine Genome Arrays were used to examine gene expression of bovine monocyte-derived macrophages (MDM) after in vitro challenge with Mycobacterium avium subspecies paratuberculosis across a time series of 2 hr, 6 hr and 24 hr post-challenge. A 0 hr control treatment was also generated and seven different age-matched female Holstein-Friesian cattle were used for each time-point/treatment combination for a total of 49 microarrays, one of which was excluded from analysis since it did not pass quality control.
2012-01-31 | E-GEOD-35185 | biostudies-arrayexpress
Project description:An antivirulence approach targets bacterial virulence rather than cell viability in the antibiotic approach that can readily lead to drug resistance. Opportunistic human pathogen Pseudomonas aeruginosa produces a variety of virulence factors, and biofilm cells of this bacterium are much more resistant to antibiotics than planktonic cells. To identify novel inorganic antivirulence compounds, the dual screenings of thirty-six metal ions were performed to identify that zinc ions and ZnO nanoparticle inhibited the pyocyanin production and biofilm formation in P. aeruginosa without affecting the growth of planktonic cells. Moreover, zinc ion and ZnO nanoparticle markedly reduced the production of 2-heptyl-3-hydroxy-4(1H)-quinolone and siderophore pyochelin, while increased the production of another sideropore pyoverdine and swarming motility. Further, zinc ion and ZnO nanoparticle clearly suppressed hemolytic activity in P. aeruginosa. Transcriptome analyses showed that ZnO nanoparticle induced zinc cation efflux pump czc operon, porin genes (oprD and opdT), and Pseudomonas type III repressor A ptrA, while repressed pyocyanin-related phz operon, which partially explains the phenotypic changes. Overall, ZnO nanoparticle is a potential candidate for use in an antivirulence approach against persistent P. aeruginosa infection. P. aeruginosa Genechip Genome Array (Affymetrix, P/N 900339) was used in order to study the cells after the addition of ZnO nanoparticles. DNA microarray analysis with one biological replicate was performed with an Affymetrix system. P. aeruginosa was inoculated in 25 ml of LB medium in 250 ml shaker flasks with overnight cultures (1 : 100 dilution). Cells were cultured for 5 h with shaking at 250 rpm with and without ZnO nanoparticles (1 mM). Before sample collection, RNase inhibitor (RNAlater, Ambion, TX, USA) was added, and the cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 s before centrifugation at 16,000 g for 2 min. The cell pellets were immediately frozen with dry ice and stored at –80°C. Total RNA was isolated using a Qiagen RNeasy mini Kit (Valencia, CA, USA).
2015-05-25 | E-GEOD-46947 | biostudies-arrayexpress
Project description:Contamination with enterohemorrhagic Escherichia coli O157:H7 (EHEC) is a worldwide problem but there is no effective therapy available for EHEC infection. Biofilm formation is closely related with EHEC infection and is one of the mechanisms of antimicrobial resistance. Antibiofilm screening of 560 plant secondary metabolites against EHEC shows that ginkgolic acids C15:1 and C17:1 at 5 μg/ml and Ginko biloba extract at 100 μg/ml significantly inhibited EHEC biofilm formation on the surface of polystyrene, nylon membrane, and glass. Importantly, the working concentration of ginkgolic acids and G. biloba extract did not affect bacterial growth and has been known to be non-toxic to human. Transcriptional analyses showed that ginkgolic acid C15:1 repressed curli genes and prophage genes in EHEC, which were corroborated by reduced fimbriae production and biofilm reduction in EHEC. Interestingly, ginkgolic acids and G. biloba extract did not inhibit the biofilm formation of commensal E. coli K-12 strain. The current study suggests that plant secondary metabolites are important resource of biofilm inhibitors, as well as other bioactive compounds. E. coli GeneChip Genome 2.0 Array (Affymetrix, P/N 900551, Santa Clara, USA) was used to study the differential gene expression of the E. coli O157:H7 cells after the treatment with ginkgolic acid C15:1 (0.005 mg/ml). Cells were inoculated into 25 ml LB medium in 250 mL shake flasks with a starting OD600 of 0.05, and cultured at 37oC for 8 h without shaking in the presence or absence of ginkgolic acid C15:1 (5 μg/ml). To prevent RNA degradation, RNase inhibitor (RNAlater, Ambion, TX, USA) was added, and the EHEC cells were collected by centrifugation at 10,000 rpm for 1 min. The cell pellets obtained were immediately frozen with dry ice and stored at -80°C. Total RNA was isolated using a Qiagen RNeasy mini Kit (Valencia, CA, USA).
2015-07-29 | E-GEOD-49367 | biostudies-arrayexpress
Project description:Stomataless Arabidopsis thaliana mutants spch-3 and mute-3 are extreme dwarfs but can produce cotyledons and tiny leaves, providing a system to interrogate plant life in the absence of stomata. To this end, we compared the transcriptomes of mutant cotyledons lacking SPCH or MUTE functions, and therefore lacking stomata, with those of wild-type, stomata-bearing Col-0 accession. RNA was obtained from 21 days old cotyledons collected from 9 independent biological replicates per genotype. These were pooled in 3x3 replicates and used to hybridize Affymetrix ATH1 microarrays.
2015-07-02 | E-MTAB-3416 | biostudies-arrayexpress