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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Human Wnt signaling pathway (Realtime qPCR array)

ABSTRACT: Human bone marrow mesenchymal stem cells (BMMSC) and human embryonic mesenchymal stem cells (ESMSC)were used. X-ray irradiation (2Gy) or 0Gy was delivered. After 4 hours, equal amount total RNA from each sample was extracted prior to gene expression analysis. After making cDNA, genes associated with Wnt signaling pathway were analyzed. qPCR gene expression profiling. Human bone marrow mesenchymal stem cells and human embryonic mesenchymal stem cells were used. X-ray irradiation (2Gy) or 0Gy was delivered. After 4 hours, equal amount total RNA from each sample was extracted prior to gene expression analysis.

ORGANISM(S): Homo sapiens

SUBMITTER: susanta hui

PROVIDER: E-GEOD-60310 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Human Wnt signaling pathway (Realtime qPCR array)

Project description:Human bone marrow mesenchymal stem cells (BMMSC) and human embryonic mesenchymal stem cells (ESMSC)were used. X-ray irradiation (2Gy) or 0Gy was delivered. After 4 hours, equal amount total RNA from each sample was extracted prior to gene expression analysis. After making cDNA, genes associated with Wnt signaling pathway were analyzed.

2014-08-12 | GSE60310 | GEO

Differentially expressed miRNAs in MDA-MB-231 over-expressing GATA3

Project description:To determine the differentially expressed miRNAs in MDA-MB-231-GATA3 cells vs. MDA-MB-231-Control cells Pooled polyclonal cells from MDA-MB-231 breast cancer cells +/- GATA3 over-expression were analyzed for miRNA expression

2012-11-27 | E-GEOD-42468 | biostudies-arrayexpress

Real-time quantitative PCR analysis of undifferentiated rat embryonic stem cells and induced pluripotent stem cells

Project description:Validation study of a focused microarray for evaluation of undifferentiated rat ESCs.Using a focused microarray, undifferentiated embryonic stem cells (ESCs) can be distinguished from differentiated ESCs and other cells derived from the early embryo since they have a unique gene expression pattern associated with pluripotency and lack of markers of differentiation. To date, however, such an array has not been developed for the rat species and differences in genomes of rat and human or rat and mouse preclude the use of ESC focused human or mouse microarrays for the rat. Here, we developed a focused microarray for screening rat ESCs and provide validation data that this array can distinguish undifferentiated rat ESCs from rat trophoblast stem cells (TS), rat extraembryonic endoderm cells (XEN), mouse embryonic fibroblast feeder cells (MEFs) and rat ESCs that have been differentiated in vitro. We used this tool to compare rat ESCs which have been expanded in a conventional rat ESC medium containing two inhibitors, e.g., GSK3 and MEK inhibitors, and leukemia inhibitory factor (LIF), and found expression of Cdx2, a gene associated with trophoblast determination. The rat ESC focused microarray described in this report has utility for rapid screening rat ESCs. This will enable optimization of culture conditions in the future. qRT-PCR gene expression profiling of undifferentiated ESCs and iPS cells. Equal amounts (1000ng) total RNA from each cell line was used in independent trials conducted by two investigators, these are technical replicates.

2014-09-25 | E-GEOD-61731 | biostudies-arrayexpress

Real-time quantitative PCR analysis of rat diaphragm before and after acute cervical spinal cord injury

Project description:Male Sprague Dawley adult rats were subjected to a cervical hemisection at C2 (C2HS). Costal diaphragm (both ipsilesional and contralesional sides) were assessed under control conditions (sham surgery) and at 1 and 7 days post-C2HS. We used SA Biosciences Rat Skeletal Muscle Development and Disease RT2 Profiler PCR Array to quantitate gene expression of muscle atrophy and regeneration-relevant genes from the uninjured and injured tissues on the indicated sides and at the indicated timepoints post-lesion. qPCR gene expression profiling. Tissue was derived from the costal diaphragm from control animals, and from contralesional and ipsilesional sides at days 1 and 7 post-lesion. RNA was extracted from flash-frozen tissue (TRIzol reagent) and quantitated via spectrophotometry. Equal amount total RNA from each donor was pooled prior to gene expression analysis. N=3 or 4 rats per condition. Four genes in the array study appeared to undergo unphysiologic increases in expression following SCI: Mmp9, Leptin, activin A and alpha actinin. For these genes, expression levels in control tissue were detectable but extremely low, thus fold-increases following SCI are numerically exaggerated. Therefore, we cannot explicitly comment on the physiologic scale of this response

2013-12-18 | E-GEOD-45021 | biostudies-arrayexpress

Real-time quantitative PCR analysis of MDA MB 231 cells

Project description:MDA-MB-231 breast cancer cells were infected with either Ad-GFP, Ad-FLI1, or Ad-PDEF qPCR gene expression profiling of MDA-MB-231 breast cancer cells were infected with either Ad-GFP, Ad-FLI1, or Ad-PDEF.

2012-12-31 | E-GEOD-38499 | biostudies-arrayexpress

Real time quantitative PCR analysis of murine macrophages

Project description:Murine macrophages were isolated from the lungs of mice given a pulmonary challenge with C. neoformans strain H99. Mice were either given a protective (H99γ) or a mock (HKCn) immunization prior to C. neoformans H99 challenge, and macrophages were isolated from the lungs of mice 24 hours, 3 days, or 7 days post-challenge using anti-CD11b microbeads according to the Miltenyi cell sorting system. We used SA Biosciences Toll-like Receptor PCR assay panel to quantitate gene expression of signal transduction factors in total RNA isolated from macrophages derived from immunized mice compared to non-immunized. qPCR gene expression profiling. Macrophages from 5 mice per group were pooled and assayed as indicated in the summary. Each experiment was performed 3 times and the resulting Ct values of each group from each experiment averaged prior to data analysis. TIme points were analyzed separately

2012-08-09 | E-GEOD-39990 | biostudies-arrayexpress

MMP14 knockdown at U87 brain tumor cells.Analyse of the genes responsible for cell division

Project description:Compared to the Scramble U87 cells, MMP14 ablation induces G2M arrest SABioscience Cell cycle platform, human genes. U87 cells were infected separately with eithr lentivirus carry on Scramble or sh RNA against human MMP14 gene.Equla amount of mRNA was isolated prior RT-PCR analyses

2013-03-19 | E-GEOD-45294 | biostudies-arrayexpress

Altered neurotrophin expression profiles in the nucleus of the solitary tract of spontaneously hypertensive rats

Project description:Our previous findings suggest that the nucleus of the solitary tract (NTS), a pivotal region for regulating the set-point of arterial pressure, exhibits abnormal inflammation in pre-hypertensive and spontaneously hypertensive rats (SHRs) together with elevated anti-apoptotic and low apoptotic factor levels compared with that of normotensive Wistar–Kyoto (WKY) rats. Whether this chronic condition affects neuronal growth and plasticity in the NTS remains unknown. To unveil the characteristics of the neurodevelopmental environment in the NTS of hypertensive rats, we investigated the gene expression profile of neurotrophins and their receptors in SHRs compared to that of normotensive rat WKY. The NTS was dissected from the brain of 6 SHRs and 6 WKY rats and the total RNA was extracted. In both groups of rats (SHRs & WKY rats, n = 6 each), a total of 2 ug mRNA extracts from each NTS were pooled together, treated with RNase-free DNAse I (Invitrogen Life technologies) to remove any genomic contamination, and further purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions. Reverse transcription was subsequently performed on 1 ug total RNA using SuperArray’s RT2 First Strand Kit (SABiosciences); the resulting cDNA was submitted for real-time quantitative PCR reactions on RT2 ProfilerTM PCR array plates using Superarray RT2 SYBR Green qPCR Master Mix (SAbiosciences) and iCycler iQ thermal cycler (Bio-rad), following the manufacturer’s instructions. The experiment was performed in duplicate in each group.

2015-04-15 | E-GEOD-67874 | biostudies-arrayexpress

Real-time quantitative PCR analysis reveals high expression of activin A during NK-DC interactions

Project description:The interaction of natural killer (NK) cells with dendritic cells (DC) results in reciprocal cell activation through the interaction of membrane proteins and the release of soluble factors. Here we report that in NK-DC cocultures, among a set of 84 cytokines investigated, activin A was the second highest induced gene, with CXCL8 being the most upregulated one. Activin A is a member of the TGF-M-NM-2 superfamily and was previously shown to possess both pro- and antiinflammatory activities. In NK-DC cocultures, the induction of activin A required cell contact and was dependent on the presence of proinflammatory cytokines (i.e. IFN-M-NM-3, TNF-M-NM-1 and GM-CSF) as well as on NK cell-mediated DC killing. CD1+ DC were the main activin A producer cells among myeloid blood DC subsets. In NK-DC cocultures, inhibition of acitivn A by follistatin, a natural inhibitory protein, or by a specific blocking antibody, resulted in the upregulation of proinflammatory cytokine release (i.e. IL-6, IL-8, TNF-M-NM-1) by DC and in the increase of DC maturation. In conclusion, our study reports that activin A, produced during NK-DC interactions, represents a relevant negative feedback mechanism that might function to prevent excessive immune activation by DC. Human CD14 positive monocytes were differentiated to DC in vitro in the presence of IL-4 (20 ng/ml) and GM-CSF (50 ng/ml) for 6 days. Immature DC were then cocultured with allogeneic IL-15-activated NK cells (at 1:1 NK:DC ratio) for 0, 2 and 6 hrs. RNA was obtained from three independent coculture experiments. Equal amount of total RNA from each experiment was pooled prior to gene expression analysis. The gene expression of common cytokines was quantified using an RT2 Profiler PCR Array (Qiagen).

2013-11-13 | E-GEOD-52306 | biostudies-arrayexpress

Real-time quantitative PCR analysis of mouse total CD4SP thymocytes

Project description:RNA was isolated with the RNeasy kit (Qiagen) from electronically sorted total CD4SP thymocytes. RNA was reverse transcribed into cDNA by oligo(dT) priming with the QuantiTect Reverse transcription kit (Qiagen). The expression of 84 key genes involved in apoptosis, or programmed cell death was performed with mouse apoptosis RT2ProfilerTM PCR array system (PAMM-012 E; SABiosciences). PCR Array data were analyzed by the Ct data analysis method. qPCR gene expression profiling. CD4SP thymocytes from WT and Ik7Tg mice were used.

2013-07-27 | E-GEOD-49264 | biostudies-arrayexpress

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