Human Breast Tumor Cored Sample mRNA Array
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Kevin Claffey
PROVIDER: E-GEOD-38708 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2013-12-31 | E-GEOD-24590 | biostudies-arrayexpress
Project description:Ovarian cancer cells treated with CDDP showed up-regulation of IRF-1 and IRF-7. The expression of putative IRF-1 target genes was modulated. CDDP triggered nuclear translocation of IRF-1 and IRF-1 silencing re-orchestrated the expression profiles of CDDP treated cells. Using microarrays, we evaluated the expression profiles of IRF-1 silenced SK-OV-3.
2013-12-31 | E-GEOD-38551 | biostudies-arrayexpress
Project description:Here, we report synergistic inhibition of glycogen synthase kinase 3 (GSK3), transforming growth factor β (TGF β), and Notch signaling pathways by small molecules can efficiently convert monolayer cultured hESCs into homogenous primitive neuroepithelium within one week under chemically defined condition. These primitive neuroepithelia can stably self-renew in the presence of leukemia inhibitory factor, GSK3 inhibitor (CHIR99021) and TGF β receptor inhibitor (SB431542); retain high neurogenic potential and responsiveness to instructive neural patterning cues toward midbrain and hindbrain neuronal subtypes; and exhibit in vivo integration. hESCs at about 20% confluence were treated with 3 μM CHIR99021, 2 μM SB431542, 0.1 μM Compound E (γ-Secretase Inhibitor XXI) in neural induction media containing Advanced DMEM/F12:Neurobasal (1:1), 1xN2, 1xB27, 1% Glutmax, 5 μg/ml BSA and 10 ng/ml hLIF, for 7 days. The culture was then split 1:3 for the next six passages using Accutase and cultured in neural induction media supplemented with 3 μM CHIR99021 and 2 μM SB431542 on X-ray inactivated MEF feeders or Matrigel-coated plates. After six passages, the cells were split 1:10 regularly. Global gene expression analysis of primitive neural stem cells
2011-04-28 | E-GEOD-28595 | biostudies-arrayexpress
Project description:Purpose: Discovery of curative therapies for renal cell carcinoma (RCC) is hampered by lack of authentic preclinical models. Tumorgrafts, generated by direct implantation of patient-derived tissues into mice, have demonstrated superior ability to predict therapeutic response. We evaluated âtissue slice graftsâ (TSGs) as an improved tumorgraft model of RCC. Experimental Design: Cores of fresh RCC were precision-cut at 300-μm and implanted under the renal capsule of RAG2-/-γC-/- mice. Engraftment rate, histology, biomarker expression, genetic fidelity and metastatic potential were evaluated. Magnetic resonance imaging (MRI) was tested as a non-invasive method to measure tumor volume, and response to a targeted therapy was determined. Results: All 13 cases of RCC engrafted and displayed characteristic histology and biomarkers. TSG volume quantified non-invasively by MRI highly correlated with graft weights, providing a unique tool for monitoring orthotopic growth. Moreover, in 2 cases, cancer cells from TSGs metastasized to clinically relevant sites, including bone. Microarray analysis and DNA sequencing demonstrated a high degree of correlation of global gene expression and VHL status between TSGs and parental tumors. Treatment of TSGs with sunitinib significantly decreased graft weight and mean vessel density compared to controls. Conclusions: The TSG model of RCC faithfully recapitulates tumor pathology, gene expression, genetic mutation and drug response. The high engraftment rate and metastatic potential of this authentic model, in conjunction with the ability to generate large first-generation animal cohorts and to quantitate tumor volume at the orthotopic site by MRI, proffer significant advantages compared to other preclinical platforms. Three pairs of tissue slice graftes and parent tumors were included in the study. Tissue slice grafts and parent tumors were preserved in Allprotect tissue reagent (Qiagen, Valencia, CA) at -20°C prior to RNA extraction using an AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Valencia, CA). The quality of RNA was determined using an Agilent 2100 Bioanalyzer (Agilent Biotechnologies, Santa Clara, CA). Microarray hybridization was performed using Illumina Human HT-12 v4 Beadchips (Illumina Inc., San Diego, CA) according to the manufacturerâs directions. Expression data was rank invariant normalized using BeadStudio software (Illumina Inc.).
2016-07-03 | E-GEOD-44548 | biostudies-arrayexpress
Project description:Mutations in KDM5C, (previously named SMCX or JARID1C) a gene that encodes a transcriptional regulator with histone-demethylase activity specific for di- and tri-methylated H3K4, are a comparatively frequent cause of non-syndromic X-linked mental retardation (NS-XLMR). Specific transcriptional targets of KDM5C, however, are still unknown and the effects of KDM5C deficiency on gene expression have not yet been investigated. Here we present the results of gene expression profiling performed on lymphoblastoid cell lines as well as blood from patients with mutations in KDM5C. Using whole genome expression arrays and QRT-PCR we identified several genes, including CMKOR1, JARID1B and KIAA0469 that were consistently deregulated in both tissues. These findings shed light on the patho-mechanisms underlying mental retardation and may have implications for future diagnostics of this heterogeneous disorder. We compared the mRNA expression of a patient lymphoblastoid cell line deficient for KDM5C with that of three controls to identify genes that are deregulated in the patient cell line.
2010-08-19 | E-GEOD-17369 | biostudies-arrayexpress
Project description:Analysis of S100A4+ stromal cells at the gene expression level in physiological setting versus metastatic setting. Total RNA was isolated from FACS-sorted S100A4+ stromal cells from normal lung of S100A4-GFP transgenic mice compared to FACS-sorted S100A4+ stromal cells from metastatic lung of 4T1 tumor-bearing S100A4-GFP transgenic mice.
2011-08-29 | E-GEOD-31711 | biostudies-arrayexpress
Project description:HGF sensitizes ovarian cancer cells to chemotherapeutics, e.g. cisplatin (CDDP), through a signaling cascade activated by its MET oncogene encoded receptor and transduced by the p38MAPK. This cascade results in the regulation of a common set of transcripts in three ovarian cancer cell lines, with different genetic profiles and susceptibility to drugs. In order to elucidate the mechanism of HGF dependent cell sensitization to drugs, the transcriptional response of the three ovarian cancer cell lines to HGF and CDDP were studied by microarray based transcription profiling
2013-12-31 | E-GEOD-24589 | biostudies-arrayexpress
Project description:Expression analysis of genes potentially regulated by BMPRII and beta-catenin. BMPRII has been linked as a genetic factor to the disease pulmonary arterial hypertension. Comparison of total mRNA obtained from human pulmonary artery endothelial cells treated with control, bone morphogentic protein receptor II, or beta-catenin siRNA
2010-11-06 | E-GEOD-18956 | biostudies-arrayexpress
Project description:Low-grade chronic inflammation plays an important role in the development of obesity and obesity-associated disorders such as insulin resistance, type 2 diabetes, the metabolic syndrome and atherosclerosis. One possible link between obesity and inflammation is the enhanced activation of circulating monocytes making them more prone to infiltration into the adipose and vascular tissues of obese persons. Furthermore, weight loss after bariatric surgery is associated with less inflammation. Transcriptome analysis of circulating monocytes from control and obese patients before and after bariatric surgery will potentially provide insights into the pathophysiology of obesity and associated disorders and supply biomarkers for diagnostic purpose. The cohort comprised 6 lean age-matched controls (BMI: 20.3±0.5 kg/m2, mean±SEM) and 18 obese individuals without clinical symptoms of cardiovascular disease (BMI: 45.1±1.4 kg/m2, P<0.001 compared with lean controls). These 18 morbidly obese subjects were referred to our hospital for bariatric surgery. Before they were included, individuals were evaluated by an endocrinologist, an abdominal surgeon, a psychologist and a dietician. Only after multidisciplinary deliberation, the selected patients received a laparoscopic Roux-en-Y gastric bypass. CD14+ monocytes were collected before and three months after bariatric surgery (BMI: 37.5±1.3 kg/m2, P<0.001 compared with before weight loss), total RNA was extracted and subjected to genome-wide expression analysis. Samples consisted of CD14+ monocytes from 6 lean controls and 18 morbidly obese patients before and three months after bariatric surgery. The 6 lean controls were also used to make 6 control pools.
2012-05-23 | E-GEOD-32575 | biostudies-arrayexpress
Project description:To determine the effect of Sox17 overexpression in mouse embryonic stem (ES) cells, we performed gain-of-function analysis by generating ES cell lines carrying a doxycycline inducible FLAG-tagged Sox17 transgene. We treated Sox17-inducible ES cells with doxycycline, collected RNA and performed genome-wide transcriptional analysis. We found that genes invovled in adhesion function and basement membrane establishment were transcriptionally upregulated in ES cells upon induction of Sox17. We also observed downregulation in the transcription of genes involved in pathways known to be functionally important for ES cell pluripotency and self-renewal. However, Sox17 expression was not sufficient to rapidly down-regulate Sox2, Nanog, and Oct4. Two independent doxycycline inducible Sox17-overexpressing mouse embryonic stem cells were derived. The genes expression changes in the Sox17-induced cells were compared to untreated (no doxycycline) controls and to control cells treated with or without doxycycline. The total RNA from these samples were amplified using Ambion Illumina TotalPrep RNA Amplification kit and arrayed on Illumina MouseRef8 v2 chips.
2010-03-31 | E-GEOD-19028 | biostudies-arrayexpress