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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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

ABSTRACT: 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)

ORGANISM(S): Homo sapiens

SUBMITTER: satoshi matsumura

PROVIDER: E-GEOD-35312 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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)

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)

2012-03-31 | GSE35312 | 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

Meythlation profiling by array to investigate the effect of hyperoxia on DNA methylation in mouse lung tissue

Project description:Hyperoxia has a potential to alter DNA methylation status. We assessed the effect of long term hyperoxia in mouse lung tissue. A total of 24 mice were randomized to hyperoxia (85% O2; 12 animals) or normoxia (21% O2; 12 animals) for 14 days continued with normoxia conditions for all animals for the subsequent 14 days. All mice had free access to food and water and were kept under standard conditions in A-Chambers (O2 – monitor ProOX110, CO2 – monitor ProCO2 P120, BioSpherix). The animals were sacrificed on day 28. Lung tissue was harvested on day 28 after euthanasia with a zolazepam/tiletamine/xylazine/fentanyl cocktail. Tissues samples were snap-frozen in liquid nitrogen immediately after cessation of circulation for the subsequent analysis. Subsequently, DNA methylation profiles in lung tissue were compared by means of methylation microarrays between both groups. We used the Genomic Workbench software (Agilent) to assess the mean methylation status of each DNA fragment (array probe) in each group. We first calculated the normalised, combined Z-scores, representing summation of the left and right Gaussian Z-scores and reflecting the location of a probe log-ratio value in relation to the Gaussian distribution of probes. A strong positive value of the combined Z-score means that a given probe is methylated and strong negative value means that it is unmethylated. Next, we compared the mean combined Z-scores (average methylation patterns) of the probes between hyperoxia and normoxia groups.

2018-02-17 | E-MTAB-6489 | biostudies-arrayexpress

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Project description:Transcriptional profiling of human hepatocarcinoma comparing Huh-7 and SNU-739. Two-condition experiment, normalized ratio represented by Huh-7/SNU-739. Biological replicates: 2 Huh-7 replicates, 2 SNU-739 replicates.

2014-04-29 | E-GEOD-57106 | biostudies-arrayexpress

OTUD5 complex mass spectrometry

Project description:DUBs are involved in various pathways and signalling networks by pairing with E3 ubiquitin ligases in protein complexes. In order to test whether OTUD5 associates with an E3 ubiquitin ligase to regulate cell proliferation, the stable Flag-OTUD5/Hep3B cell line was established by transfecting Hep3B cells with plasmids expressing pCIN4-Flag-OTUD5. The cellular factors interacting with OTUD5 were purified by anti-Flag antibody-conjugated M2 beads.

2020-09-11 | PXD019907 | Pride

DNMT1 Maintains Progenitor Function in Self-Renewing Somatic Tissue

Project description:Progenitor cells maintain self-renewing tissues throughout life by sustaining their capacity for proliferation while suppressing cell cycle exit and terminal differentiation. DNA methylation provides a potential epigenetic mechanism for the cellular memory needed to preserve the somatic progenitor state through repeated cell divisions. DNA methyltransferase 1 (DNMT1) maintains DNA methylation patterns after cellular replication. Although dispensable for embryonic stem cell maintenance, a clear role for DNMT1 in maintaining the progenitor state in constantly replenished somatic tissues, such as mammalian epidermis, is uncharacterized. Here we show that DNMT1 is essential for supporting epidermal progenitor cell function. DNMT1 protein was found enriched in undifferentiated cells, where it was required to retain proliferative stamina and suppress differentiation. In tissue, DNMT1 depletion led to exit from the progenitor cell compartment, premature differentiation and eventual tissue loss. These effects correlated with DNA methylation as genome-wide analysis revealed that a significant portion of epidermal differentiation gene promoters were methylated in self-renewing conditions but were subsequently demethylated during differentiation. Gene expression analysis: To establish a differentiation signature for primary human keratinocytes, total RNA was isolated in biologic duplicate from cells cultured in growth conditions and high calcium differentiation conditions and hybridized to Affymetrix HG-U133 2.0 Plus arrays. This gene signature was also compared to DNMT1 deficient cells cultured in growth conditions. Methylated DNA profiling: To globally characterize DNA methylation in primary human keratinocytes, genomic DNA was immunoprecipitated using a 5-methylcytidine antibody, amplified, and hybridized to NimbleGen HG18 promoter tiling arrays. Profiling was done using DNA isolated in growth conditions as well as differentiation conditions.

2010-06-23 | E-GEOD-18590 | biostudies-arrayexpress

Genome-wide analysis of CHD8 binding sites

Project description:Genome-wide analysis of CHD8 binding sites as well as sites associated with the activating histone marks 2mk4H3 and 3mK4H3. These analyses have been performed by ChIP-chip using a custom microarray containing promoter regions and CpG islands. ChIP experiments were performed with the C33A human cervix carcinoma cell line. ChIP-chip analysis of CHD8, 2mK4H3 and 3mK4H3 in C33A cells

2013-12-03 | E-GEOD-51564 | biostudies-arrayexpress

Methylation in breast cancer vs. normal tissue

Project description:We applied a combination of Methyl-CpG Immunoprecipitation (MCIp) and Human CpG Island microarrays to identify aberrant DNA methylation in eight low-grade breast invasive carcinomas and two pre-invasive breast tumors against ten normal breast tissues. 10 breast tumor samples (8 invasive, 2 pre-invasive) and 10 normal breast tissues, paired randomly (except Array 10: matched pair)

2012-09-14 | E-GEOD-35263 | biostudies-arrayexpress

DNA methylation analysis of normal and cancer cells

Project description:DNA methylation of prostatic normal cells (PrEC), normal mammary epithelial cells (HMEC), prostate cancer cell line (MDA-PCa-2b), and breast cancer cell lines (BT474 and MDA-MB-231) was analyzed by MeDIP-on-chip analysis. DNA obtained from each cells was immunoprecipitated by anti 5-methylcytidine antibody. IP DNA and input DNA were labeled with Cy5 and Cy3, respectively, and then analyzed by using human CpG island microarray provided by Agilent Technologies.

2011-06-06 | E-GEOD-28284 | biostudies-arrayexpress

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