Comment[ArrayExpressAccession] E-GEOD-35312 Public Release Date 2012-03-30 Investigation Title Integrative array-based approach identifies MZB1 as a frequently methylated putative tumor-suppressor in hepatocellular carcinoma (MeDIP) Comment[Submitted Name] Integrative array-based approach identifies MZB1 as a frequently methylated putative tumor-suppressor in hepatocellular carcinoma (MeDIP) Experiment 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) Date of Experiment Term Source Name EFO Term Source Version Term Source File http://www.ebi.ac.uk/efo/efo.owl Person Last Name matsumura Imoto Kozaki Matsui Muramatsu Furuta Tanaka Sakamoto Arii Inazawa Person First Name satoshi Issei Ken-ichi Takeshi Tomoki Mayuko Shinji Michiie Shigeki Johji Person Mid Initials Person Email s-matsumura@yokohamah.rofuku.go.jp Person Affiliation Inst. of Med. Sci., Tokyo Med. & Dent. Univ. Person Phone +81-3-5803-5821 Person Fax Person Address Dept. of Mol. Cytogenet., Inst. of Med. Sci., Tokyo Med. & Dent. Univ., 1-5-45 Yushima, Bunkyo-ku, Tokyo, Japan Person Roles submitter Person Roles Term Source REF Person Roles Term Accession Number Normalization Type Normalization Term Accession Number Normalization Term Source REF Replicate Type Replicate Term Accession Number Replicate Term Source REF Experimental Design Experimental Design Term Accession Number Experimental Design Term Source REF Quality Control Type Quality Control Term Accession Number Quality Control Term Source REF Protocol Name P-GSE35312-1 P-GSE35312-6 P-GSE35312-5 P-GSE35312-3 P-GSE35312-2 P-GSE35312-4 P-GSE35312-7 Protocol Description ID_REF =
VALUE = normalized log10 ratio Cy5/Cy3 according to the manufacturer's instructions (Agilent microarray analysis of methylated DNA immunoprecipitation protocol version 1.0, Agilent Technologies) according to the manufacturer's instructions (Agilent microarray analysis of methylated DNA immunoprecipitation protocol version 1.0, Agilent Technologies) genomic DNA was extracted using common method prior to MeDIP method DMEM containing 10% FBS according to the manufacturer's instructions (Agilent microarray analysis of methylated DNA immunoprecipitation protocol version 1.0, Agilent Technologies) Data from scanned images (tiff) were extracted using Feature Extraction Software, version 9.0 (Agilent Technologies) Protocol Software Protocol Hardware Protocol Contact Protocol Type bioassay_data_transformation image_aquisition hybridization nucleic_acid_extraction grow labeling feature_extraction Protocol Term Source REF Protocol Term Accession Number Experimental Factor Name CELL LINE ANTIBODY Experimental Factor Type cell line antibody Experimental Factor Term Source REF Experimental Factor Term Accession Number Publication Title Publication Author List PubMed ID Publication DOI Publication Status Publication Status Term Source REF Publication Status Term Accession Number Comment[SecondaryAccession] GSE35312 Comment[GEOLastUpdateDate] 2012-03-30 Comment[AEExperimentType] methylation profiling by array Comment[GEOReleaseDate] 2012-03-29 Comment[ArrayExpressSubmissionDate] 2012-01-24 SDRF File E-GEOD-35312.sdrf.txt