Transcription profiling of human cancer cell lines
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
DISEASE(S): carcinoma
SUBMITTER: Anita Grigoriadis
PROVIDER: E-TABM-610 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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2010-01-06 | E-MEXP-2495 | biostudies-arrayexpress
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2010-12-01 | E-MEXP-2783 | biostudies-arrayexpress
Project description:Four experimental groups with five pools of six control samples prepared from seven-week-old C57BL/6 female mice injected with PBS and five pools of six mice vaccinated with GVO43, a recombinant adenovirus (rAd) vector derived from human rAd5 deleted in early regions 1 and 3 (Desjardins et al., 2009). For each experimental group, total splenocytes were prepared in order to sort Tregs.
2010-12-01 | E-MEXP-2781 | biostudies-arrayexpress
Project description:Background: The Medicago truncatula 2HA seed line is highly embryogenic while the parental line Jemalong rarely produces embryos. The 2HA line was developed from one of the rare Jemalong regenerates and this method for obtaining a highly regenerable genotype in M. truncatula is readily reproducible suggesting an epigenetic mechanism. Microarray transcriptomic analysis showed down regulation of an ETHYLENE INSENSITIVE 3-like gene in 2HA callus which provided an approach to investigating epigenetic regulation of genes related to ethylene signalling and the 2HA phenotype. Ethylene is involved in many developmental processes including somatic embryogenesis (SE) and is associated with stress responses. Results: Microarray transcriptomic analysis showed a significant number of up-regulated transcripts in 2HA tissue culture, including nodule and embryo specific genes and transposon-like genes, while only a few genes were down-regulated, including an EIN3-like gene we called MtEIL1. This reduced expression was associated with ethylene insensitivity of 2HA plants that was further investigated. The weak ethylene insensitivity affected root and nodule development. Sequencing of MtEIL1 found no difference between 2HA and wild-type plants. DNA methylation analysis of MtEIL1 revealed significant difference between 2HA and wild-type plants. Tiling arrays demonstrated an elevated level of miRNA in 2HA plants that hybridised to the antisense strand of the MtEIL1 gene. AFLP-like methylation profiling revealed more differences in DNA methylation between 2HA and wild-type. Segregation analysis demonstrated the recessive nature of the eil1 phenotype and the dominant nature of the SE trait. Conclusions: We have demonstrated that EIL1 of Medicago truncatula (MtEIL1) is epigenetically silenced in the 2HA seed line. The possible cause is an elevated level of miRNA that targets its 3M-bM-^@M-^YUTR leading to DNA methylation. Down regulation of MtEIL1 makes it possible to form nodules in the presence of ethylene and affects root growth under normal conditions. Segregation analysis showed no association between MtEIL1 expression and SE in culture but the role and mechanism of ethylene signalling in the process of plant regeneration through SE requires further investigation. Comparison of transcriptome of WT and highly embryogenic 2HA spontaneous mutant of Medicago truncatula in 4 weeks tissue culture
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Project description:We have demonstrated that fish oil/pectin (FO/P) diets protect against colon cancer compared to corn oil/cellulose (CO/C) by upregulating apoptosis and suppressing proliferation. To elucidate the mechanisms whereby FO/P diets induce apoptosis and suppress proliferation during the tumorigenic process, we analyzed the temporal gene expression profiles from exfoliated rat colonocytes. KEYWORDS: Fish oil/pectin, pectin, exfoliated colonocytes, gene expression, apoptosis, colon cancer, chemoprevention Rats consumed diets containing FO/P or CO/C and were injected with azoxymethane (AOM, 2x, 15 mg/kg BW, s.c.). Feces collected at the initiation, aberrant crypt foci (ACF), and tumor stages of colon cancer (24 h (n=20), 7 wk (n=37), and 28 wk (n=28) after AOM injection, respectively) was used for poly A(+) RNA extraction. Gene expression signatures were determined using Codelink arrays.
2012-02-20 | E-GEOD-27266 | biostudies-arrayexpress
Project description:In this study, we have used transcript profiling with microarrays in bone marrow-derived macrophages (BMDMs) to systematically identify genes transcriptionally regulated by IRF8 during ontogeny and maturation of macrophages, and in response of these cells to combined exposure to IFNgamma and Tlr9 ligand (CpG). For this, we used an experimental strategy based on the co-segregation of IRF8-dependent differential gene expression in macrophages from [BALB/c X BXH2] F2 animals selected for homozygosity for either wild type (wt; IRF8R294) or mutant (IRF8C294) IRF8 alleles. The study of IRF8-associated gene expression differences in individual animals of mixed genetic background, allows one to distinguish true IRF8-dependent effects on gene expression from unrelated differences in gene expression associated with intrinsic differences in genetic background but unrelated to IRF8.
2011-04-27 | E-MEXP-2962 | biostudies-arrayexpress
Project description:Epidemiological studies have shown that the regular use of non-steroidal anti-inflammatory (NSAIDs) drugs is associated with a reduced risk of various cancers. In addition, in vitro and experiments in mouse models have demonstrated that NSAIDs decrease tumor initiation and/or progression of several cancers. However, there are limited preclinical studies investigating the effects of NSAIDs in ovarian cancer. Here, we have studied the effects of two NSAIDs, diclofenac and indomethacin, in ovarian cancer cell lines and in a xenograft mouse model. Diclofenac and indomethacin treatment decreased cell growth by inducing cell cycle arrest and apoptosis. In addition, diclofenac and indomethacin reduced tumor volume in a xenograft model of ovarian cancer. To identify possible molecular pathways mediating the effects of NSAID treatment in ovarian cancer, we performed microarray analysis of ovarian cancer cells treated with indomethacin or diclofenac. Interestingly, several of the genes found downregulated following diclofenac or indomethacin treatment are transcriptional target genes of E2F1. E2F1 was downregulated at the mRNA and protein level upon treatment with diclofenac and indomethacin, and overexpression of E2F1 rescued cells from the growth inhibitory effects of diclofenac and indomethacin. In conclusion, NSAIDs diclofenac and indomethacin exert an anti-proliferative effect in ovarian cancer in vitro and in vivo and the effects of NSAIDs may be mediated, in part, by downregulation of E2F1. The serous ovarian adenocarcinoma cell lines HEY, OVCAR5 and UCI-101 were grown in culture then seeded in 60 mm dishes and treated for 24 hours with 300 mM diclofenac, indomethacin or no treatment (Control). RNA was isolated and one sample from each group was labeled and hybridized to Illumina Sentrix bead arrays.
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Project description:Innate immunity is fundamental to recognition and clearance of bacterial infection. The relevant cells and molecules that orchestrate an effective response, however, remain incompletely understood. Here we describe a previously unknown population of B cells, which we have named innate response activator (IRA) B cells that recognize bacteria directly through TLR-4-MyD88 and protect against polymicrobial sepsis. IRA-B cells have a unique IgM high CD23 low CD43 + CD93+ GM-CSF+ signature, develop and diverge from B1a B cells, require BAFFR, and adhere to tissue via VLA-4 and LFA-1. B cell subsets are sorted from the spleen and peritoneum of C57BL/6 mice that were given intraperitoneal injections of LPS once daily for four days.
2012-02-07 | E-GEOD-32372 | biostudies-arrayexpress
Project description:The hypothalamic paraventricular (PVN) and supraoptic (SON) nuclei are important integrative structures that regulate co-ordinated responses to perturbations in cardiovascular homeostasis. Through descending projections from parvocellular neurons to the brainstem, the PVN acts as an autonomic 'premotor nucleus', regulating reflex changes in sympathetic nerve activity that are involved in blood pressure and blood volume regulation. Endocrine responses are mediated through axonal projections from SON and PVN magnocellular neurons (MCNs) to the capillaries of the posterior pituitary neural lobe. In response to dehydration, a massive release of the antidiuretic peptide hormone vasopressin (VP) into the circulation is accompanied by a dramatic functional remodelling of the HNS. We have used microarrays to comprehensively catalogue the genes expressed in the PVN, the SON and the neurointermediate lobe (NIL) of the pituitary gland. Further, we have identified transcripts that are regulated as a consequence of dehydration, as well as RNAs that are enriched in either the PVN or the SON. We suggest that these differentially expressed genes represent candidate regulators and effectors of HNS activity and remodelling. Experiment Overall Design: In total, 10 Affymetrix Genechip Rat Genome 230 2.0 were used. The experiment compared hypothalamic supraoptic nucleus from 3 day dehydrated and control male Sprague Dawley rats (10-12 weeks). For each chip, tissue from 5 animals was pooled prior to extraction of total RNA and in total 5 chips were used for each condition using independently prepared RNA samples from separate groups of animals.
2008-06-12 | E-GEOD-3110 | biostudies-arrayexpress
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