ArrayCGH study to investigate duplication of T locus in chordoma
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Nischalan Pillay
PROVIDER: E-MEXP-3753 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:To gain mechanistic insights on OsMADS2 functions in rice spikelet development, we have employed global expression profilling to identify the genes regulated by OsMADS2. Transgenic rice panicle RNAs were compared with the wild type panicle RNA of similar developmental stage. Genes downregulated in transgenic lines will be those which expression requires functional OsMADS2 whereas upregulated genes will need OsMADS2 for their repression. Experiment Overall Design: Two independent biological RNA pools of dsRNAiOsMADS2 transgenic panicles were compared with a single wild type RNA pool in two different hybridizations. A third hybridization was performed with reciprocally dye-lebeled wild type RNA and one of the mutant RNA.
2008-06-15 | E-GEOD-7192 | biostudies-arrayexpress
Project description:Adipose tissue abundance relies partly on the factors that regulate adipogenesis, i.e. proliferation and differentiation of adipocytes. While the transcriptional program that initiates adipogenesis is well-known, the importance of microRNAs in adipogenesis is less well studied. We thus set out to investigate whether miRNAs would be actively modulated during adipogenesis and obesity. Several models exist to study adipogenesis in vitro, of which the cell line 3T3-L1 is probably the most well known, albeit not the most physiologically appropriate. We used a microarray strategy to provide a global profile of miRNAs in brown and white primary murine adipocytes (prior to and following differentiation) and evaluated the similarity of the responses to non-primary cell models, through literature data-mining. We found 65 miRNAs regulated during in vitro adipogenesis in primary adipocytes. When we compared our primary adipocyte profiles with those of cell lines reported in the literature, we found a high degree of difference in adipogenesis-regulated miRNAs. We evaluated the expression of 10 of our adipogenesis-regulated miRNAs using real-time qPCR and then selected 5 miRNAs that showed robust expression levels and profiled these by qPCR in subcutaneous adipose tissue of 20 humans with a range of body mass indices (BMI, range=21-48). Of the miRNAs tested, mir-21 was both highly expressed in human adipose tissue and positively correlated with BMI (R2=0.49, p<0.001). In conclusion, we provide the preliminary analysis of miRNAs important for primary cell in vitro adipogenesis and find that the inflammation-associated miRNA, mir-21, is up-regulated in subcutaneous adipose tissue in human obesity. 3 samples of pre adipocytes isolated from brown adipose tissue examined pre and post differentiation to brown adipocytes. 3 samples of pre-adipocytes isolated from white adipose tissue and examined pre and post differentiation to adipocytes.
2011-05-31 | E-GEOD-27912 | biostudies-arrayexpress
Project description:To gain mechanistic insights on RFL functions in rice architecture, we have employed global expression profilling to identify the genes regulated by RFL. Transgenic rice panicle RNAs down-regulated for RFL were compared with the wild type panicle RNA of similar developmental stage. Genes downregulated in transgenic lines will be those which expression requires functional RFL whereas upregulated genes will need RFL for their repression. Experiment Overall Design: Two independent biological RNA pools of dsRNAiRFL and RFL antisense transgenic panicles were compared with two independent wild type RNA pool in two different hybridizations. Two hybridizations were performed with reciprocally dye-labeled wild type RNA and respective mutant RNA.
2008-06-11 | E-GEOD-10098 | biostudies-arrayexpress
Project description:CD4+CD25+FOXP3+ regulatory T cells (Treg) are pivotal for peripheral self-tolerance. They prevent immune responses to auto- and alloantigens and are thus under close scrutiny as cellular therapeutics for autoimmune diseases and the prevention or treatment of alloresponses after organ or stem cell transplantation. We previously showed that human Treg cells with a memory cell phenotype, but not those with a naïve phenotype, rapidly down-regulate expression of the lineage-defining transcription factor forkhead box P3 (FOXP3) upon in vitro expansion. We now compared the transcriptomes of stable FOXP3+ Treg and converted FOXP3- 'ex-Treg' cells by applying a newly developed intranuclear staining protocol that permits the isolation of intact mRNA from fixed, permeabilized and FACS-purified cell populations. Whole genome microarray analysis revealed strong and selective upregulation of Th2 signature genes, including GATA-3, IL-4, IL-5 and IL-13, upon downregulation of FOXP3. Th2 differentiation of converted, FOXP3- ex-Treg cells occurred even under non-polarizing conditions and could not be prevented by IL-4 signaling blockade. Thus, our studies identify Th2 differentiation as the default developmental program of human Treg cells after downregulation of FOXP3. RNA preparations from FOXP3 stained in vitro expanded CD4+CD25highCD45RA- “memory” Treg cells from five independent donors were analyzed using Whole Human Genome Oligo Microarrays (Agilent). An adapted FOXP3 staining procedure to stain FOXP3 in human regulatory T cells to isolate intact RNA for microarray hybridization was developed (see extract protocol).
2011-12-14 | E-GEOD-26190 | biostudies-arrayexpress
Project description:Using high-resolution array-CGH, we identified unique duplications of a region on 6q27 in four multiplex (≥ with ≥ 3 cases) families of chordoma, a cancer of presumed notochordal origin. comparison of test samples from chordoma families to a reference DNA sample
2009-10-04 | E-GEOD-17668 | biostudies-arrayexpress
Project description:Transcription profiling of Physcomitrella patens Gransden strain
2014-05-07 | E-MTAB-917 | biostudies-arrayexpress
Project description:Transcriptional responses of two strain types of Mycobacterium avium subsp. paratuberculosis (MAP, cattle and sheep Strain) under in vitro iron limiting or iron sufficient growth conditions. Background: In MAP, the transcriptional role and essentiality of MAP2827 (IdeR) as an iron dependent regulator has been well established (Janagama et al. 2009). Therefore, in the absence of an ideR deletion mutant of MAP, to understand the genome-wide iron dependent transcriptional variations between the cattle and sheep MAP IdeR we used a heterologous expression of MAP IdeR in Mycobacterium smegmatis ideR deletion mutant.
2010-10-31 | E-MEXP-2865 | biostudies-arrayexpress
Project description:Macrophage activation must be tightly controlled to prevent overzealous responses that cause self-damage. MicroRNAs have been shown to promote classical macrophage activation by blocking concomitant anti-inflammatory signals and transcription factors, but can also place restraints on activation by preventing excessive TLR-signalling. In contrast, the microRNA profile associated with alternatively activated macrophages and their role in regulating wound-healing or anti-helminthic responses has not yet been described. Utilizing an in vivo model of alternative activation, in which adult Brugia malayi nematodes are surgically implanted in the peritoneal cavity of mice, we examined the profile of microRNA expression in these alternatively activated macrophages and compared this to alternatively activated IL-4 receptor knockout macrophages and thioglycollate elicited macrophages. Peritoneal macrophages from BALB/c wild type or IL-4 receptor knockout mice were elicited with thioglycollate or using nemtodes (peritoneal implant of Brugia malayi). The latter leads to a population of alternatively activated macrophages. Microarray analysis was used to examine the microRNA profile of WT alternatively activated macrophages (n = 4), IL-4 receptor knockout alternatively activated macrophages (n = 4), WT thioglycollate elicited macrophages (n = 3) and IL-4 receptor knockout thioglycollate elicited macrophages (n = 3).
2012-08-07 | E-GEOD-35047 | biostudies-arrayexpress
Project description:In this study, the distribution and regulation of periplasmic and cytoplasmic carbon fluxes in Gluconobacter oxydans 621H with glucose were studied by 13C-based metabolic flux analysis (13C-MFA) in combination with transcriptomics and enzyme assays. For 13C-MFA, cells were cultivated with specifically 13C-labeled glucose and intracellular metabolites were analyzed for their labeling pattern by LC-MS. In growth phase I, 90% of the glucose was oxidized periplasmatically to gluconate and partially further oxidized to 2-ketogluconate. Of the glucose taken up by the cells, 9% was phosphorylated to glucose 6-phosphate, whereas 91% was oxidized by cytoplasmic glucose dehydrogenase to gluconate. Additional gluconate was taken up into the cells by transport. Of the cytoplasmic gluconate, 70% was oxidized to 5-ketogluconate and 30% was phosphorylated to 6-phosphogluconate. In growth phase II, 87% of gluconate was oxidized to 2-ketogluconate in the periplasm and 13% was taken up by the cells and almost completely converted to 6-phosphogluconate. Since G. oxydans lacks phosphofructokinase, glucose 6-phosphate can only be metabolized via the oxidative pentose phosphate pathway (PPP) or the Entner-Doudoroff pathway (EDP). 13C-MFA showed that 6-phosphogluconate is catabolized primarily via the oxidative PPP in both phase I and II (62% and 93%) and demonstrated a cyclic carbon flux through the oxidative PPP. The transcriptome comparison revealed an increased expression of PPP genes in growth phase II, which was supported by enzyme activity measurements and correlated with the increased PPP flux in phase II. Moreover, genes possibly related to a general stress response displayed increased expression in growth phase II. The transcriptome comparisons of G. oxydans growth phase II vs. growth phase I were repeated independently three times in biological replicates resulting in 3 hybridizations as termed by sample 1 to 3.
2013-02-13 | E-GEOD-42223 | biostudies-arrayexpress
Project description:The obligatory aerobic acetic acid bacterium Gluconobacter oxydans 621H oxidizes sugars and sugar alcohols primarily in the periplasm and only a small fraction is metabolized in the cytoplasm. The latter can occur either via the Entner-Doudoroff pathway (EDP) or via the pentose phosphate pathway (PPP). The Embden-Meyerhof pathway is non-functional and a cyclic operation of the tricarboxylic acid cycle is prevented by the absence of succinate dehydrogenase. In this work, the cytoplasmic catabolism of fructose formed by oxidation of mannitol was analyzed with a M-NM-^Tgnd mutant lacking the oxidative PPP and a M-NM-^Tedd-eda mutant devoid of the EDP. The growth characteristics of the two mutants under controlled conditions with mannitol as carbon source and enzyme activities showed that the PPP is the main route for cytoplasmic fructose catabolism, whereas the EDP is dispensable and even unfavorable. The M-NM-^Tedd-eda mutant (lacking 6-phosphogluconate dehydratase and 2-keto-3-deoxy-6-phosphogluconate aldolase) formed 24% more cell mass than the reference strain. In contrast, deletion of gnd (6-phosphogluconate dehydrogenase) severely inhibited growth and caused a strong selection pressure for secondary mutations inactivating glucose-6-phosphate dehydrogenase, thus preventing fructose catabolism via the EDP, too. These M-NM-^Tgnd zwf* mutants were almost totally disabled in fructose catabolism, but still produced about 14% of the carbon dioxide of the reference strain, possibly by catabolizing substrates from the yeast extract. Overexpression of gnd in the reference strain improved biomass formation in a similar manner as deletion of edd-eda, further confirming the importance of the PPP for cytoplasmic fructose catabolism. The three transcriptome comparisons of M-NM-^Tupp M-NM-^Tgnd zwf* vs. M-NM-^Tupp and of M-NM-^Tupp M-NM-^Tedd-eda vs. M-NM-^Tupp, and of M-NM-^Tupp M-NM-^Tgnd versus M-NM-^Tupp, were repeated independently three times in biological replicates resulting in 3 x 3 hybridizations as termed by sample 1 to 9.
2012-07-31 | E-GEOD-38933 | biostudies-arrayexpress