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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Heme oxygenase-1 knocked down rat mesangial cells treated with hydrogen peroxide

ABSTRACT: HO-1 cells denote the cultured rat mesangial cells with heme oxygenase-1 knocked down by RNA interference (using lentiviral vector). GFP cells denote the cultured rat mesangial cells that are transfected with empty lentiviral vector containing GFP cassette. Cells are treated with hydrogen peroxide 100 micromolar for 2 hours, or without. RNA are then harvested for array analysis. Biological replicates are performed (two independent experiment sets). GFP cell and HO-1 cell are untreated, or treated with hydrogen peroxide (100 micromolar for 2 hours).

ORGANISM(S): Rattus norvegicus

SUBMITTER: Hui-Teng Cheng

PROVIDER: E-GEOD-53953 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Heme oxygenase-1 knocked down rat mesangial cells treated with hydrogen peroxide

Project description:HO-1 cells denote the cultured rat mesangial cells with heme oxygenase-1 knocked down by RNA interference (using lentiviral vector). GFP cells denote the cultured rat mesangial cells that are transfected with empty lentiviral vector containing GFP cassette. Cells are treated with hydrogen peroxide 100 micromolar for 2 hours, or without. RNA are then harvested for array analysis. Biological replicates are performed (two independent experiment sets).

2014-01-10 | GSE53953 | GEO

Gene expression profiling of pancreatic cancer cell line BxPC-3 induced by PAR-2 AP

Project description:Protease-activated receptor-2 (PAR-2), a G protein-coupled receptor activated by trypsin and coagulant factors, plays broad spectrum of physiological and pathological roles especially in cancer development. In this study, we used PAR-2 activating peptide to mimic the action of trypsin to trigger PAR-2 signaling pathway and effects of PAR-2 activation on gene expression in human pancreatic cancer cell line BxPC-3 investigated by microarray analysis. Through DAVID bioinformatic resources, we observed that activated PAR-2-mediated genes are summarized to two different pathways, renal cell carcinoma and NFkB pathway. In renal cell carcinoma pathway, activated PAR-2 dysregulated hypoxia-inducible factors and its target genes, including glucose transporter 1 (GLUT1), transforming growth factor-b (TGF-b) and vascular endothelial growth factor-A (VEGF-A). In addition, activated PAR-2 induced MAPK signaling and transcriptional factors, such as JUN, MAP2K1 and ETS1. The regulation of these genes by PAR-2 assumed that PAR-2 signaling was associated with cancer progression. On the other hand, activated PAR-2 upregulated interleukin-1b (IL-1b) and toll-like receptor 4 (TLR4) related with NFkB activation, which indicated that PAR-2 signaling may cause cancer-related inflammation. In conclusion, PAR-2 may be a factor to regulate cancer progression and inflammation. Two-condition experiment, control cells vs PAR-2 AP-treated cells.

2013-04-30 | E-GEOD-44827 | biostudies-arrayexpress

Rat intervertebral disc cell was stimulated by NGF

Project description:The rat-tail intervertbral disc cells was incubated with NGF at a concentration of 100 ng/ml/day for a total of five days. Primary culture of 8 weeks rat-tail interverbral disc cells. The control group was incubated with PBS and the experimental group was incubated with NGF at a concentration of 100 ng/ml/day for a total of five days.

2013-10-01 | E-GEOD-49560 | biostudies-arrayexpress

Ectopical expression of miR-125b by lentiviral-vector in neuroblastoma cell line SKNDZ

Project description:Differential expression of mRNA were conducted in neuroblastoma cell line SKNDZ, which successfully transduced human miR-125b MYCN-amplification SKNDZ neuroblastoma cell line was transduced with MIRN125B2 gene with lentiviral vector (pLKO.1-puro), and selected by puromycin for 48 hours. Then the total RNA was extracted and analyzed the differential expression of a total of 29,187 genes by Oligonucleotide DNA microarray.

2013-12-01 | E-GEOD-48468 | biostudies-arrayexpress

The effect of vitamin D supplementation on tumorigenesis in a thioacetamide (TAA)-induced rat intrahepatic cholangiocarcinoma model

Project description:In this study, we investigated the effect of vitamin D supplementation on tumorigenesis in a thioacetamide (TAA)-induced rat intrahepatic cholangiocarcinoma model as vitamin D is known to have a spectrum of anticancer activities. Using PET, we found that tumor formation and progression were suppressed in rats fed a diet supplemented with 6 IU/g vitamin D3(+6D) as compared to the group fed a 2 IU/g vitamin D3 diet (+2D) or controls. Microarray analysis of the tumors that arose revealed that vitamin D supplementation caused significant up- and down regulation in 21 and 16 genes, respectively. There are 9 tissue samples (3 rats in each group labeled as (+6), (+2) and control). Duplicate analysis were used for each sample.

2015-08-01 | E-GEOD-48961 | biostudies-arrayexpress

Transcriptional profiling of shoots and roots in japonica and indica rice seedlings under salt stress and recovery stage

Project description:Rice seedlings at 3-leaf stage were used for expression analysis in control and salt stressed (incloudling salt treatment for 3, 24hrs and recovery from cold stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArrayï¼ v1. Control and treated biological replicates of salt-tolerant cultivar TNG67 (japonica) and salt-sensitive cultivar TCN1 (indica) were analyzed

2016-06-30 | E-GEOD-76613 | biostudies-arrayexpress

miRNA profiling in camptothecin-treated or untreated hepatoma-derived exosomes

Project description:Totally 1,308 miRNAs were examined. Three miRNAs (hsa-miR-1976, 4728-3p, and 877-3p) were upregulated with fold change excess 0.8 and six miRNAs (hsa-miR-4497, -204-3p, -6126, -5787, -1273e, and -1908-3p) were downregulated in the exosome released from camptothecin-treated hepatoma. Comparing between results of these two samples revealed novel miRNA regulation upon anti-cancer drug treatments exosomal miRNAs from CPT-treated hepatoma and unrteated

2015-11-10 | E-GEOD-74829 | biostudies-arrayexpress

Microarray analysis of gene expression profiles in PBHA-treated THP-1 cells after LPS stimulation

Project description:Using microarray analysis, 219 differentially expressed genes were isolated between the LPS group and LPS/PBHA treatment-group (fold change > or < 1.5). These genes were analyzed by KEGG system to reveal the important issues. The analyses of gene ontology were shown that the genes of the specific classes M-bM-^@M-^\Chemokine signaling pathwayM-bM-^@M-^], M-bM-^@M-^]Cytokine-cytokine receptor interactionM-bM-^@M-^], M-bM-^@M-^]RIG-I-like receptor signaling pathwayM-bM-^@M-^], M-bM-^@M-^]Leukocyte transendothelial migrationM-bM-^@M-^], and M-bM-^@M-^\MAPK signaling pathwayM-bM-^@M-^] showed markedly different patterns between both groups by KEGG analysis system. In this study presented here, human THP-1 cells were pretreated with only vehicle (resting group), vehicle and LPS (50 ng/ml), or PBHA (10 M-NM-<M) and LPS (50 ng/ml). After stimulation, the total cellular RNAs were manipulated for analyses of gene expression.

2014-11-17 | E-GEOD-52365 | biostudies-arrayexpress

Expression of miR-196a in Huntington's disease transgenic (HD) mice

Project description:We intend to screen altered genes after overexpression of miR-196a in HD transgenic mice. Two transgenic mouse lines were used in this study, including HD transgenic mice and HD transgenic mice overexpressing miR-196a. The mice were all at approximate 12 months of age. At this point, HD transgenic mice showed severve motor dysfunctions, whereas HD transgenic mice overexpressing miR-196a displayed mild motor dysfunctions. We used the striatum tissues from 2 HD transgenic mice and 3 HD transgenic mice overexpressing miR-196a. The mice were all at approximate 12 months of age. Two technique repeats were performed for each sample.

2013-05-30 | E-GEOD-47500 | biostudies-arrayexpress

Transcription profiling of mouse primary mesangial cells stimulated with DNA and RNA ligands

Project description:Extrarenal viral infections commonly trigger glomerulonephritis mostly in association with immune complex disease. The immunoglobulin component of immune complexes can activate glomerular cell Fc receptors but whether complexed viral nucleic acids contribute to glomerular inflammation remains unknown. Glomerular mesangial cells express TLR3 but lack TLR7-9, hence, it is unclear whether mesangial cells can recognize and respond to viral ssRNA or DNA. Here we studied the immune responses activated by 3P-RNA (5'Triphosphate RNA) and Non-CpG DNA (Double stranded DNA) in primary mesangial cells (PMC). We used microarrays to detail the global programme of gene expression that induced by 3P-RNA and Non-CpG DNA. Experiment Overall Design: PMC were stimulated with 3P-RNA and Non-CpG DNA for 6 hours and then total RNA was isolated for hybridization to MOE430_2 arrays.

2008-10-21 | E-GEOD-11898 | biostudies-arrayexpress

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