MCAM MPM cell line
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
DISEASE(S): malignant mesothelioma
SUBMITTER: Keiko Shinjo
PROVIDER: E-TABM-808 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Compare the global methylation profile of 20 malignant pleural mesotheliomas and lung adenocarcinomas. A DNA mixture of two normal mesothelium tissues was used as a reference for the mesotheliomas and a mixture of five normal lung tissues used as the reference for the lung adenocarcinomas
2009-12-01 | E-TABM-813 | biostudies-arrayexpress
Project description:To examine methylation profile of the CpG promoters in glioma stem cells
2012-02-18 | E-TABM-1122 | biostudies-arrayexpress
Project description:Genome wide DNA methylation analysis using 20 human hepatocyte chimeric mice after hepatitis viral infection.
2014-01-03 | E-MTAB-1474 | biostudies-arrayexpress
Project description:We perform genome wide methylation analysis using 33 clinical samples, which were obtained from patients who underwent surgical resection at the Aichi Cancer Center Hospital in accordance with institutional policies. The purpose of this experiment is revealing the methylation status affected by hepatitis viral infection.
2014-01-03 | E-MTAB-1472 | biostudies-arrayexpress
Project description:Genome wide DNA methylation analysis usig two individual huh7.5.1 after HCV-JFH1 infection
2014-01-03 | E-MTAB-1473 | biostudies-arrayexpress
Project description:A large-scale characterization of the methylation states of candidate CpG islands (CGIs) throughout the gastric cancer methylome has not previously been conducted. Genome-wide DNA methylation profiles were compared between 4 metastatic and 4 non-metastatic gastric carcinomas (GCs) and their surgical margins (SMs). The GC genome showed significantly higher proportions of hypomethylation in the promoter and exon-1 regions, as well as increased hypermethylation of intragenic fragments when compared to SMs. Differential methylation was observed in CGIs near transcription start sites of 546 genes between GCs and SMs, and 601 genes between metastatic and non-metastatic GCs. From the list of differentially methylated CGIs, 68 candidate genes and 10 known tumor-related genes were selected for further characterization based on their known molecular function using DHPLC. Significant differential methylation was validated in the CGIs of 15 genes between GCs and SMs (Ps<0.05) and confirmed using bisulfite-sequencing. These genes include BMP3, BNIP3, CDKN2A, ECEL1, ELK1, GFRA1, HOXD10, KCNH1, PSMD10, PTPRT, SIGIRR, SRF, TBX5, TFPI2, and ZNF382. Hypomethylation of CGIs correlated with up-regulation of GFRA1 expression in GCs, while hypermethylation of other genes inactivated their transcription. Most importantly, prevalence of GFRA1, SRF, and ZNF382 methylation alterations were inversely and coordinately associated with GC metastasis and the patients’ overall survival throughout discovery and testing cohorts in China as well as independent validation cohorts in Japan and Korea. In conclusion, methylation changes in the CGIs of 15 genes correlated strongly with GC development. GFRA1 hypomethylation and SRF and ZNF382 hypermethylation are potential synergistic biomarkers for the prediction of GC metastasis. To identify differential methylation of CGIs related to GC development and metastasis, genome-wide DNA methylation changes in 8 pairs of GC and SM samples were analysed using the MCAM assay with a 99K custom-designed Agilent oligonucleotide microarray composed of 99,027 probes targeting 6,177 unique protein-coding genes containing at least two methylation-sensitive/insensitive SmaI/ XmaI restriction sites (CCC|GGG/ C|CmCGGG) as described in Shen et al, PLoS Genet 3, 2023-2036 (2007).
2014-06-02 | E-GEOD-47724 | biostudies-arrayexpress
Project description:Purpose: AURKA plays an important role in breast cancer development. Exploring the gene expression profiles regulated by AURKA will facilitate to understand the mechanism which is responsible for AURKA induced breast cancer development. Results: We found that 350 genes were significantly up-regulated during AURKA overexpression in MCF-10A cells, 346 genes were significantly down-regulated during AURKA overexpression in MCF-10A cells. Conclusions: Our study indicated that 696 differentially expressed genes might contribute to AURKA induced breast cancer development. MCF-10A cells overexpressed AURKA or the empty vector were subjected to RNA extraction. The resulted RNA samples were performed RNA-sequencing analyses of gene expression profiles.
2015-10-28 | E-GEOD-57931 | biostudies-arrayexpress
Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of transcriptome in mazie plants. The ZmPIS gene coding PtdIns synthase from maize with a maize ubiquitin promoter was transferred into maize. The transgenic ZmPIS maize showed enhanced drought tolerance compared to non-transgenic maize. The differentially expressed genes between wide-type maize and transgenic ZmPIS maize were detected by the assay of digital gene expression profile and real time RT-PCR datas. The results displayed that the overexpression of ZmPIS resulted in the expression levels changes of a large number of genes including genes involved in the phosphatidylinositol (PI) metabolic pathway, photosynthesis metabolism, carbohydrate metabolism, aminoacid metabolism and genes coding transcription factors. Examination of The differences of the transcriptional profile between wide-type maize and transgenic ZmPIS maize and analysis of the network regulated by the ZmPIS gene
2013-09-01 | E-GEOD-31944 | biostudies-arrayexpress
Project description:Next Generation Sequencing of Unmethylated Alu (NSUMA) interrogation of more than 130,000 individual Alus for differential methylation with concomitant analysis of copy number variations applied to the study of hypomethylation in primates. 3 replicates of Gorilla gorilla, Pan troglodytes, Pongo pygmaeus and Homo sapiens were studied.
2015-09-10 | E-GEOD-72877 | biostudies-arrayexpress
Project description:Friable embryogenic callus (FEC) has been considered as the most suitable materials for efficient genetic transformation of cassava. Due to heavy genotype dependence on FEC induction and being amenable to somaclonal variation, the production and maintaining of reliable FEC is a limitation factor for cassava genetic transformation. Identification of key elements involving in biological processes from somatic embryos (SEs) to the FEC at different stages will provide critical insights for FEC improvement. Cytological observation showed the dramatic change of subcellular structures among SEs, fresh FEC (FFEC) and old FEC (OFEC). Decrease of sucrose and increase of fructose and glucose were detected in OFEC. A total of 6871 differentially expressed genes (DEGs) were identified from SEs, FFEC and OFEC by RNA-seq. Analysis of the DEGs showed that FEC induction was accompanied by the process of dedifferentiation, whereas the epigenetics modification occurred during the continuous subculturing process. The cell structure was reconstructed, mainly including the GO terms of "cell periphery" and "external encapsulating structure"; in parallel, the internal mechanisms were changed correspondingly, including the metabolisms of process (glycolysis) and compounds(alanine, aspartate, and glutamate). The significant reduction of genomic DNA methylation in OFEC indicates altered gene expression via chromatin modification. These results indicate that the induction and long-term subculture of FEC is a complicated biological process involving changes of genome modification, gene expression and subcellular reconstruction. The findings will be useful for improving FEC induction and maintenance from farmer-preferred cassava cultivars that are recalcitrant to genetic transformation, hence improving cassava through genetic engineering. Two-week-old SEs cultured on GD, FFEC emerging from SEs, and 9-month-old OFEC were used for analysis. Each sample was mixtured from six indepedent replicates and were collected for RNA extraction respectively.
2015-09-05 | E-GEOD-72717 | biostudies-arrayexpress