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Transcription profiling of mouse embryonic stem cells (D3-pOCT-mESC) grown in low concentrations of nitric oxide

ABSTRACT: In order to identify the genes regulated in mouse embryonic stem cells by the effect of low concentrations of nitric oxide (NO), we analysed the transcriptome of cells treated with NO and compared it to those of cells cultured in the absence of leukemia inhibitory factor (LIF), and in the presence of LIF. We used the cell line D3-pOct4, which carries the enhanced Green Fluorescence Protein gene (eGFP) under the control of the Oct-4 promotor. This line is continuously maintained in the undifferentiated state in comparison with the wild type line in the presence of LIF. Experiment Overall Design: D3-pOct4 cells cultured in the presence of 1000 U/ml of LIF, in the absence of LIF, and in the absence of LIF with 2uM of diethylenetriamine nitric oxide adduct (DETA)/NO were grown for 7 days, maintaining the conditions of the treatment everyday. DETA-NO (Sigma) was used as donor of nitric oxide. RNA was extracted and analyzed by Bioanalyzer of Agilent. The cDNA microarray chip used was Mouse Genome 430_2.0 (Affymetrix) and the data were analyzed with GeneChip Operating System v1.4.0.036 using global scaling as the normalization method.

ORGANISM(S): Mus musculus

SUBMITTER: Rafael Tapia Limonchi

PROVIDER: E-GEOD-13235 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression profile of human embryonic stem cells growth in low concentrations of nitric oxide

Project description:Identification of genes regulated in human embryonic stem cells by the effect of low concentrations of nitric oxide. The transcriptome of cells treated with NO were compared with that of cells cultured in abscense of LIF, and undifferentiated ES cells cultured in presence of LIF. The H181 hES cell line was used for the experiments. These data complement a previous study realized in mES cells under the same NO conditions . The aim of the work is to know how NO modify transcriptome of ES cells and how participate in the modulation of self renewal and differentiation. Passages between 72 and 74 of the H181 cell line were cultured on Matrigel-coated tissue culture plates in presence of 8ng/ml of bFGF for maintain them undifferentiated (control). For treatments, cells were cultured in the absence of bFGF to induce differentiation and treat cells with 2uM of DETA/NO. Cells were grown for 6 days mantaining the conditions of the treatment each 19 hours. Dietilentriamine-NO (DETA-NO) (Sigma) was used as donor of nitric oxide. Expression data of cells treated with NO in absence of bFGF were compared with cells cultured in absence of this, in order to observe how the treatment affects the transcriptome, and if there is some similarity with undifferentiated condition in presence of bFGF.

2012-03-20 | E-GEOD-36609 | biostudies-arrayexpress

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Project description:The goal of this study was to measure the effects of nitric oxide exposure (using DETA NONOate as a nitric oxide donor) on transcription in Caulobacter.

2010-06-21 | GSE21139 | GEO

Transcription profiling of human CD3-positive T cells from SLE and controls reveals activation of mTOR controls the loss of TCRI? in lupus T cells through HRES-1/Rab4-regulated lysosomal degradation

Project description:CD3-positive T cells were negatively isolated from 10 SLE patients and 9 healthy controls without SLE. All of the SLE samples and control samples were compared with one another to identify baseline differences in expression due to the disease. Next, T cell preparations from 4 of the control subjects were stimulated with either Nitric Oxide (NOC-18) 600 uM for 24hr or stimulated through CD3/CD28 for 24hr to determine which genes were responsive to these signaling mechanisms. Here, we show that activity of the mammalian target of rapamycin (mTOR), which is a sensor of the mitochondrial transmembrane potential, is increased in SLE T cells. Activation of mTOR was inducible by NO, a key trigger of MHP which in turn enhanced the expression of HRES-1/Rab4, a small GTPase that regulates recycling of surface receptors through early endosomes. Expression of HRES-1/Rab4 was increased in SLE T cells and, in accordance with its dominant impact on the endocytic recycling of CD4, it was inversely correlated with diminished CD4 expression. HRES-1/Rab4 over-expression was also inversely correlated with diminished TCRÎ¶ protein levels. Combined with follow up studies, these results suggest that activation of mTOR causes the loss of TCRÎ¶ in lupus T cells through HRES-1/Rab4-dependent lysosomal degradation. Experiment Overall Design: 10 replicate T cell samples from SLE (Lupus) patients Experiment Overall Design: 9 replicate T cell samples from healthy control (BC) subjects Experiment Overall Design: 4 replicate Nitric Oxide (NOC-18) stimulated T cell samples from 4 of the control subjects Experiment Overall Design: 4 replicate CD3/CD28 stimulated T cell samples from 4 of the control subjects

2009-02-28 | E-GEOD-13887 | biostudies-arrayexpress

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2010-06-20 | E-GEOD-21139 | biostudies-arrayexpress

BCG vaccine strains lack narK2 and narX induction and exhibit altered phenotypes during dormancy

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2008-05-03 | E-GEOD-11315 | biostudies-arrayexpress

Analysis of Fusarium verticillioides gene expression in response to nitric oxide

Project description:Investigation of whole genome gene expression level changes in F. verticillioides M3125 when exposed to 1.5 mM DETA NONOate for 30 minutes. Assessed in reference to unexposed M3125. DETA NONOate is a nitric oxide (NO) donor with a half-life of approximately 56 hours at 27°C, pH 7.4, to liberate 2 moles of NO per mole of parent compound.

2017-11-01 | GSE56827 | GEO

Transcription profiling of human umbilical vein endothelial cells to identify targets of pharmacological histone deacetylase inhibition

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2008-06-14 | E-GEOD-5856 | biostudies-arrayexpress

Mycobacterium bovis transcriptional response to nitric oxide

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2010-05-17 | E-GEOD-15164 | biostudies-arrayexpress

Expression data from fission yeast Schizosaccharomyces pombe under nitrosative stress

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