MAGE-TAB Version 1.1 Investigation Title Genome-wide expression analysis in normal and immortalised and transformed human cell lines Experimental Design reference design genetic modification design development or differentiation design genotyping design Experimental Design Term Source REF Experimental Design Term Accession Number Experimental Factor Name genotype sampling time Experimental Factor Type genotype sampling time Experimental Factor Term Source REF Experimental Factor Term Accession Number Person Last Name de las Heras Person First Name Jose Person Mid Initials I Person Email j.delasheras@ed.ac.uk Person Phone Person Fax Person Affiliation University of Edinburgh Person Address Wellcome Trust Centre Person Roles submitter Person Roles Term Source REF Person Roles Term Accession Number Quality Control Type technical replicate Quality Control Term Source REF EFO Quality Control Term Accession Number Replicate Type Replicate Term Source REF Replicate Term Accession Number Normalization Type Normalization Term Source REF Normalization Term Accession Number Date of Experiment Public Release Date 2013-11-11 PubMed ID 24371281 Publication DOI 10.1093/nar/gkt1351 Publication Author List Gordon, Katrina; Clouaire, Thomas; Bao, Xun; Kemp, Sadie; Xenophontos, Maria; de las Heras, Jose; Stancheva, Irina Gordon K, Clouaire T, Bao XX, Kemp SE, Xenophontos M, de Las Heras JI, Stancheva I. Publication Title Immortality, but not oncogenic transformation, of primary human cells leads to epigenetic reprogramming of DNA methylation and gene expression Immortality, but not oncogenic transformation, of primary human cells leads to epigenetic reprogramming of DNA methylation and gene expression. Publication Status submitted Publication Status Term Source REF Publication Status Term Accession Number Experiment Description Analysis of expression changes in the fetal human lung fibroblast cell line MRC5 over time (two time points: 50 and 100 population doublings) during immortalisation with the catalytic component of telomerase (hTERT) and in vitro transformation with SV40 Large T antigen and oncogenic H-RAS Protocol Name P-MTAB-35603 P-MTAB-35599 P-MTAB-35600 P-NGEN-5 P-NGEN-13 P-MTAB-35602 P-MTAB-35601 P-NGEN-9 Protocol Type nucleic acid extraction protocol treatment protocol treatment protocol labeling image_acquisition treatment protocol treatment protocol hybridization Protocol Term Source REF ArrayExpress ArrayExpress ArrayExpress Protocol Term Accession Number Protocol Description Total RNA was extracted using Invitrogen's Trizol reagent. Quality was assessed by gel electrophoresis and spectrophotometry (using a Nanodrop spectrophotometer). cDNA was synthesised using an anchored poly(dT) primer (20mer) and INvitrogen's SuperscriptII reverse transcriptase. RNA was hydrolysed in basic conditions, and cDNA measured using a Nanodrop sprectrophotometer. About 2.5ug of cDNA were sent to Nimblegen for labelling (Cy3) and hybridisation using their own protocols. Retroviral transduction with a pBabe vector to express hTERT, maintained for 50 population doublings Retroviral transduction with a pBabe vector to express hTERT, maintained for 100 population doublings Title: NimbleGen Sample Labeling (Expression) v1.0. Title: NimbleGen One-Color Array Scanning (Expression) v1.0. Retroviral transduction with a pBabe vector to express hTERT, SV40 large T antigen and oncogenic H-ras, maintained for 100 population doublings Retroviral transduction with a pBabe vector to express hTERT, SV40 large T antigen and oncogenic H-ras, maintained for 50 population doublings Title: NimbleGen Hybridization & Washing (Expression) v1.0. Protocol Parameters Protocol Hardware Protocol Software Protocol Contact Term Source Name ArrayExpress EFO ArrayExpress Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/ http://www.ebi.ac.uk/arrayexpress/ Term Source Version 1.1 2.38 SDRF File E-MTAB-2003.sdrf.txt Comment [Submitted Name] Genome-wide expression analysis in normal and immortalised and transformed human cell lines Comment [AEExperimentType] transcription profiling by array Comment[ArrayExpressAccession] E-MTAB-2003 Comment [AEExperimentDisplayName] Transcription profiling by array of fetal human lung fibroblast cell line MRC5 over time during immortalisation with the catalytic component of telomerase (hTERT) and in vitro transformation with SV40 Large T antigen and oncogenic H-RAS