Comment[ArrayExpressAccession]	E-GEOD-41586						
MAGE-TAB Version	1.1						
Public Release Date	2013-09-17						
Investigation Title	Expression data for HT29 cells treated with 5-aza-deoxy-cytidine [RNA-Seq]						
Comment[Submitted Name]	Expression data for HT29 cells treated with 5-aza-deoxy-cytidine [RNA-Seq]						
Experiment Description	The RNA samples from HT-29 (ATCC) colon cancer cell line were reverse transcribed to build cDNA libraries and categorized into 3 groups with different concentrations of 5-aza-deoxy-cytidine (5-Aza); in each group three replicative 150 mm cultures were treated with: 1) dimethyl sulfoxide (vehicle alone, 0 μM 5-Aza); 2) 5μM 5-Aza and 3) 10 μM 5-Aza; for five days. This experiment was also performed parallel on a commercial Affymetrix microarray [GSE41364] and the aim of the study was to compare the two platforms on gene expression measurements and differentially expressed gene (DEG) detection. The results showed a strong correlation between the two platforms, yet it also confirmed the existence of fixed and proportional biases on the gene expression measurements between microarray and RNA-Seq. The DEG analysis indicated the relative superiority of DESeq method in terms of its performance; high consistency was confirmed between DESeq, baySeq methods from RNA-Seq and SAM/eBayes from microarray data. Experiment on human colon cancer HT29 cell line treated with 3 concentrations of 5-aza-deoxy-cytidine						
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	Xu	Li	Williams	Antoniou	McCombie	Denoya	Xu
Person First Name	Xiao	Ellen	Jennie	Eric	W	Paula	Xiao
Person Mid Initials					R		
Person Email	slowsmile820@gmail.com						
Person Affiliation	Stony Brook University BME						
Person Address	Stony Brook University BME, Stony Brook University, Stony Brook, NY, USA						
Person Roles	submitter						
Protocol Name	P-GSE41586-4	P-GSE41586-1	P-GSE41586-3	P-GSE41586-2			
Protocol Description	Illumina Casava1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and low quality bases (first 3 bases), then mapped to hg19 whole genome using tophatv 2.0.1 with parameters -r 10 -p 4 mapped reads from tophat were further quantifiled through Cufflink program (version 1.3.0) Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated to represent gene expression intensities Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.	Triplicate cultures of HT-29 cells were treated in the following three experimental groups: 1.) Vehicle (DMSO) alone or 0 ﾵM 5-Aza-deoxycytidine (5-Aza); 2.) 5 ﾵM 5-Aza; 3.) 10 ﾵM 5-Aza	Each monolayer was washed with PBS, scraped and centrifuged into a pellet. RNA was extracted from each pellet using Tri-Reagent according to the manufacturer's protocol. Paired end 100 bp RNA-Seq libraries were prepared for sequencing using standard Illumina protocols	HT-29 colon cancer cells were cultured as monolayers in 150 mm dishes in DMEM with 10% fetal bovine serum, 1% kanamycin, streptomycin-penicillin at 37 CO2 5% .			
Protocol Type	normalization data transformation protocol	sample treatment protocol	nucleic acid library construction protocol	growth protocol			
Publication Title	Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets.						
Publication Author List	Xu X, Zhang Y, Williams J, Antoniou E, McCombie WR, Wu S, Zhu W, Davidson NO, Denoya P, Li E						
PubMed ID	23902433						
Publication DOI	10.1186/1471-2105-14-S9-S1						
Comment[SecondaryAccession]	GSE41586						
Comment[GEOReleaseDate]	2013-09-17						
Comment[ArrayExpressSubmissionDate]	2012-10-15						
Comment[GEOLastUpdateDate]	2013-09-30						
Comment[AEExperimentType]	RNA-seq of coding RNA						
Comment[SecondaryAccession]	SRP016118						
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR592573-SRR592581						
SDRF File	E-GEOD-41586.sdrf.txt						
Experimental Factor Name	compound	dose					
Experimental Factor Type	compound	dose