Comment[ArrayExpressAccession]	E-GEOD-45332
MAGE-TAB Version	1.1									
Public Release Date	2013-10-01
Investigation Title	Genome-wide total RNA and MBD-sequencing in HCT116 and DKO cells as a global re-expression model [RNA-Seq]									
Comment[Submitted Name]	Genome-wide total RNA and MBD-sequencing in HCT116 and DKO cells as a global re-expression model [RNA-Seq]
Experiment Description	Genome-wide view of the interplay between methylation and RNA expression in this colorectal cancer model was obtained. RNA-sequencing of HCT116 cell line, the DNMT1 and DNMT3B double knock-out HCT116 cell line (DKO), and 7 additional colorectal cell lines.									
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl								
Person Last Name	De Schrijver	De Schrijver	Trooskens	Bosch	Dehan	Carvalho	Van Neste	Meijer	Baylin	Van Criekinge
Person First Name	Joachim	Joachim	Geert	Linda-J	Pierre	Beatriz	Leander	Gerrit	Steve	Wim
Person Mid Initials				W				A		
Person Email	geo@ncbi.nlm.nih.gov									
Person Affiliation	Universiteit Gent									
Person Address	Universiteit Gent, Coupure Links 653, Gent, Belgium									
Person Roles	submitter									
Protocol Name	P-GSE45332-2	P-GSE45332-1								
Protocol Description	Basecalling performed using CASAVA Transcription data is calculated as the average number of bases mapping in the exons of a transcript (i.e. Normalized over transcript length). Intra sample normalization can be done using the matrix in the GEO_RNA_normalization.txt file. Genome_build: NCBI 37 Supplementary_files_format_and_content: RNA data: Average exon coverage per base.	Total RNA was isolated using TRIzol reagent and subjected to purification using RNeasy Mini Kit. PolyA RNA was extracted using the standard Illumina protocol. Single-end standard illumina kit.								
Protocol Type	normalization data transformation protocol	nucleic acid library construction protocol								
Experimental Factor Name	CELL LINE	DSN TIME								
Experimental Factor Type	cell line	dsn time								
Comment[SecondaryAccession]	GSE45332									
Comment[GEOReleaseDate]	2013-10-01									
Comment[ArrayExpressSubmissionDate]	2013-03-20									
Comment[GEOLastUpdateDate]	2013-11-11									
Comment[AEExperimentType]	RNA-seq of coding RNA									
Comment[AdditionalFile:Data1]	GSE45332_GEO_RNA_normalization.txt									
Comment[AdditionalFile:Data2]	GSE45332_GEO_transcription_data.txt									
Comment[SecondaryAccession]	SRP019810									
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR787296-SRR787312									
SDRF File	E-GEOD-45332.sdrf.txt