Comment[ArrayExpressAccession]	E-GEOD-51903
MAGE-TAB Version	1.1						
Public Release Date	2014-06-14
Investigation Title	Control of 5mC and 5hmC by TET dioxygenases in human embryonic carcinoma cells						
Comment[Submitted Name]	Control of 5mC and 5hmC by TET dioxygenases in human embryonic carcinoma cells
Experiment Description	This SuperSeries is composed of the SubSeries listed below. Refer to individual Series						
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	Robertson						
Person First Name	Keith						
Person Mid Initials	D						
Person Email	robertson.keith@mayo.edu						
Person Affiliation	Mayo Clinic						
Person Phone	507-266-4886						
Person Address	Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Stabile 12-70, Rochester, MN, USA						
Person Roles	submitter						
Protocol Name	P-GSE51903-1	P-GSE51903-4	P-GSE51903-5	P-GSE51903-7	P-GSE51903-3	P-GSE51903-2	P-GSE51903-6
Protocol Description	Intensities of arrays have been quantile-normalized using Partek Genomic Suite (v6.6).  Differential expressions were calculated using ANOVA of Partek package. ID_REF =  VALUE = log2 GC-RMA	Biotinylated cDNAs were prepared according to the standard Ambion and Affymetrix protocol from 250 ng total RNA (The Ambion WT Expression Kit and GeneChip Terminal Labeling Kit, Affymetrix).	Following labeling, cDNAs were hybridized for 16 hr at 45C on Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.	Genomic DNA was isolated by proteinase digestion and phenol:chloroform extraction. Affinity purification was performed according to manufacturers' protocols. DNA sequencing libraries were constructed according to Illumina's protocol for TruSeq DNA sample preparation kit	Trizol extraction of total RNA was performed according to the manufacturer's instructions.	NCCIT cells were cultured in McCoy’s 5A medium (Invitrogen) supplemented with 2 mm L-glutamine (Mediatech) and 10% heat-inactivated fetal bovine serum (Hyclone).	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid library construction protocol	nucleic acid library construction protocol	growth protocol	array scanning protocol
Experimental Factor Name	TRANSFECTANT	AFFINITY PURIFICATION METHOD					
Experimental Factor Type	transfectant	affinity purification method					
Comment[SecondaryAccession]	GSE51903						
Comment[GEOReleaseDate]	2014-06-14						
Comment[ArrayExpressSubmissionDate]	2013-10-30						
Comment[GEOLastUpdateDate]	2014-06-16						
Comment[AEExperimentType]	transcription profiling by array						
Comment[AEExperimentType]	methylation profiling by high throughput sequencing						
SDRF File	E-GEOD-51903.hyb.sdrf.txt	E-GEOD-51903.seq.sdrf.txt