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Integrative array-based approach identifies MZB1 as a frequently methylated putative tumor-suppressor in hepatocellular carcinoma (expression)

ABSTRACT: Gene expression was profiled using a 4x44K Human Whole Genome Ver. 2.0 gene expression array (Agilent Technologies) according to the manufacturer's instructions (Microarray-based gene expression analysis protocol ver. 5.0.1, Agilent Technologies)

ORGANISM(S): Homo sapiens

PROVIDER: GSE35311 | GEO | 2012/03/31

SECONDARY ACCESSION(S): PRJNA156017

REPOSITORIES: GEO

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Integrative array-based approach identifies MZB1 as a frequently methylated putative tumor-suppressor in hepatocellular carcinoma (expression)

Project description:Gene expression was profiled using a 4x44K Human Whole Genome Ver. 2.0 gene expression array (Agilent Technologies) according to the manufacturer's instructions (Microarray-based gene expression analysis protocol ver. 5.0.1, Agilent Technologies) Total RNAs extracted from Hep3B, HepG2, and HuH-7 cell lines and from these cell lines treated with 10 ?M 5-aza-dCyd for 5 days were used for conventional and pharmacological unmasking analyses, respectively. Total RNAs from two normal livers (C20 and C40) were used as controls.

2012-03-30 | E-GEOD-35311 | biostudies-arrayexpress

Integrative array-based approach identifies MZB1 as a frequently methylated putative tumor-suppressor in hepatocellular carcinoma (MeDIP)

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Integrative array-based approach identifies MZB1 as a frequently methylated putative tumor-suppressor in hepatocellular carcinoma (MeDIP)

Project description:The analysis of DNA methylation profiles was performed by methylated DNA immunoprecipitation (MeDIP) using anti-5-methylcytidine antibody (Eurogentec, Seraing, Belgium) followed by the Human 244K Agilent CpG island microarray (Agilent, Santa Clara, CA) Genomic DNAs from Hep3B, HepG2 and HuH-7 cells were used for cancer samples and that from a normal liver tissue from surgical sample of colon cancer metastasis, as a control sample (C20)

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Integrative array-based approach identifies MZB1 as a frequently methylated putative tumor-suppressor in hepatocellular carcinoma

Project description:This SuperSeries is composed of the SubSeries listed below.

2012-03-31 | GSE35313 | GEO

Integrative array-based approach identifies MZB1 as a frequently methylated putative tumor-suppressor in hepatocellular carcinoma

Project description:This SuperSeries is composed of the following subset Series: GSE35311: Integrative array-based approach identifies MZB1 as a frequently methylated putative tumor-suppressor in hepatocellular carcinoma (expression) GSE35312: Integrative array-based approach identifies MZB1 as a frequently methylated putative tumor-suppressor in hepatocellular carcinoma (MeDIP) Refer to individual Series

2012-03-30 | E-GEOD-35313 | biostudies-arrayexpress

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Comparison of the RNA expression profiles of CD14+ monocytes from human peripheral blood with derived dendritic cells (DCs) and myeloid-derived suppressor cells (MDSCs) obtained by exposure with GM-CSF/IL4 and GM-CSF/IL4/PGE2, respectively, during 6 days

Project description:The expression profiles of RNA of human CD14+ monocytes were compared with derived dendritic cells (DCs) and myeloid-derived suppressor cells (MDSCs) following GM-CSF/IL4 and GM-CSF/IL4/PGE2 incubation for 6 days using the Agilent Human GE v3 8x60K array (Agilent Technologies, CA, USA). The samples were hybridized in the array following the manufacturer’s instructions.

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Tumor suppressor genes are frequently methylated in lymph node metastases of breast cancers.

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Agilent SurePrint G3 Mouse GE V2.0 Microarray(8*60K,Design ID:074809)

Project description:Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies). The sample labeling, microarray hybridization and washing were performed based on the manufacturer's standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray. After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

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Atra effect on ERBB2 and RARA-coamplified SKBR-3 cells.

Project description:RNA was extracted with Rneasy Micro Kit (Qiagen, France) from SKBR3 cells treated with 1 uM ATRA. The quantity and purity of the extracted RNA was evaluated using a NanoDropTM spectrophotometer and its integrity measured using an Agilent BioanalyzerTM. For microarray hybridizations, 500 ng of total RNA from each RNA sample was amplified and labeled with two fluorescents dye (Cy5 and Cy3) using the Quick Amplification Labeling kit (Agilent Technologies, Palo Alto, CA, USA) following the manufacturer's protocol. Cy3-labeled and Cy5-labelled cRNA were hybridized to the Agilent Human Whole Genome Oligo Microarray format 4x44K (Agilent Technologies), prior to washing and scanning.

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