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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Microarray analysis of Wild-type vs. Brpf1-deficient P4 mouse brain

ABSTRACT: RNA was isolated from three pairs of wild-type and Brpf1-deficient mouse brains (the dorsal cortex part) at postnatal day 4 for microarray analysis. The cDNA samples were then labeled and mixed for hybridization with one array. The data from three arrays were obtained and used for bioinformatic analysis.

ORGANISM(S): Mus musculus

SUBMITTER: Xiang-Jiao Yang

PROVIDER: E-GEOD-63909 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Deficiency of the chromatin regulator BRPF1 causes abnormal brain development.

You Linya L Zou Jinfeng J Zhao Hong H Bertos Nicholas R NR Park Morag M Wang Edwin E Yang Xiang-Jiao XJ

The Journal of biological chemistry 20150107 11

Epigenetic mechanisms are important in different neurological disorders, and one such mechanism is histone acetylation. The multivalent chromatin regulator BRPF1 (bromodomain- and plant homeodomain-linked (PHD) zinc finger-containing protein 1) recognizes different epigenetic marks and activates three histone acetyltransferases, so it is both a reader and a co-writer of the epigenetic language. The three histone acetyltransferases are MOZ, MORF, and HBO1, which are also known as lysine acetyltra ...[more]

PMID: 25568313

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Microarray analysis of Wild-type vs. Brpf1-deficient E8.75 mouse embryo

Project description:RNA was isolated from three pairs of wild-type and Brpf1-deficient E8.75 mouse embryos for microarray analysis. The cDNA samples were then labeled and mixed for hybridization with one array. The data from three arrays were obtained and used for bioinformatic analysis.

2015-05-15 | E-GEOD-63908 | biostudies-arrayexpress

Inhibition of Met results in concomitant inhibition of Akt and STAT3 signaling pathways, while abrogation of negative feedback permits Erk reactivation

Project description:Amplification and activation of the Met receptor tyrosine kinase occurs up to 23% of gastric cancers, suggesting that Met is a therapeutic target in these cancers. However, the steady-state signaling events that occur during chronic Met activation, and mechanisms for resistance to Met small-molecule inhibitors, are poorly understood. Here we show that multiple gastric cancer cell lines harboring MET amplifications are dependent on Met signaling for proliferation and anchorage-independent growth. In these cells, short-term inhibition of Met leads to coordinated changes in gene expression; these include a rapid loss in expression of immediate-early genes, followed by decreased expression of genes involved in cell cycle and proliferation. Activation of Ras-Erk, PI3K-Akt and STAT3 pathways is attenuated by acute Met inhibition. STAT3 inhibition alone, but not individual inhibition of Mek or Akt, is sufficient to abrogate Met-dependent growth of these cells. However, following chronic Met inhibition, reactivation of Mek-dependent Erk phosphorylation occurs even in the presence of Met inhibitor corresponding with a downregulation of Erk negative regulators DUSP4/6. This provides a mechanism for the emergence of drug resistance. Our findings provide insights into innate resistance to a small-molecule Met inhibitor and highlight rational combination therapies that could be evaluated in clinical trials. Time series experiment, four cell lines, 2 treatments

2014-05-19 | E-GEOD-54532 | biostudies-arrayexpress

Expression data from ethanol and saline exposed mice [mRNA]

Project description:Mouse models of Fetal Alcohol Spectrum Disorder can be used to assess molecular changes underlying the disorder. Neonatal ethanol exposure in mice can be used to model third trimester ethanol exposure in humans. Mice were injected with 2.5 g/kg twice on each of postnatal days 4 and 7. Mice were allowed to reach postnatal day 70, at which time whole-hippocampus was isolated and snap frozen. Tissue was thawed and RNA was isolated. RNA run on affymetrix gene expression array according to standard protocol. Each array was a pool of three mice, for a total n=9 ethanol-exposed and 9 control mice. All mice were male.

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Project description:In this research, Human OneArray Microarray analysis was performed to obtain broad spectrum information about the genes differentially expressed in human bladder cancer cell line RT112 and Gemcitabine Resistant Bladder Cancer cell line RT112-Gr.

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Functional analysis of the TRIB1 associated locus (TRIBAL) linked to plasma triglycerides and coronary artery disease

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-02-14 | E-GEOD-54957 | biostudies-arrayexpress

Comparison of microRNA Profiling Platforms (BeadChip)

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TRIBAL overexpression in HepG2 cells

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Comparison of microRNA Profiling Platforms (NanoString)

2013-10-22 | E-GEOD-51504 | biostudies-arrayexpress

Comparison of microRNA Profiling Platforms

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2013-10-22 | E-GEOD-51508 | biostudies-arrayexpress

Transcription profiling of Saccharomyces cerevisiae pGAL1-MKS1, pGAL1-NNK1, and pGAL1-FMP48 overexpression

Project description:Analysis of the transcriptional effects of pGAL1-MKS1, pGAL1-NNK1, and pGAL1-FMP48 overexpression. BY4700 gal1::NAT ura3delta0 S. cerevisiae cells carrying a [pGAL1-MKS1-HA, URA3, CEN], [pGAL1-NNK1-HA, URA3, CEN], or [pGAL1-FMP48-HA, URA3, CEN] plasmid, or empty vector BG1805, were grown to early log phase, induced with 0.2% galactose, and harvested after 1.5 h and 6 h. RNA from a strain overexpressing MKS1, NNK1, or FMP48 was competitively hybridized with RNA from an identically treated strain carrying empty vector.<br><br>FMP48 = YGR052W. MKS1 = YNL076W. NNK1 = YKL171W.

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