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Sample GSM801347 Query DataSets for GSM801347
Status Public on May 03, 2012
Title 7d_retinoic acid_treated NT2 cells
Sample type genomic
Source name 7d_retinoic acid_treated NT2 cells
Organism Homo sapiens
Characteristics gender: Male
cell line: NT2
cell type: embryocarcinoma
Treatment protocol NT2 cells were induced to differentiate with 10 µM all-trans retinoic acid (Sigma). Medium containing RA was changed every 2 days.
Growth protocol NT2 cells were maintained in Dulbecco's Modified Eagle Medium (D-MEM, with l-glutamine, 4500 mg/l d-glucose, without sodium pyruvat; Gibco) supplemented with 10% fetal bovine serum and 200 U/ml penicillin and 200 µg/ml streptomycin (all from Gibco) in a humidified atmosphere of 5% CO2 in air.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA from RA-induced and untreated NT2 tissue culture cells was prepared using the DNeasy Blood & Tissue Kit (Invitrogen) according the manufacturer's specifications. Genomic DNA (500 ng) from each sample was bisulfite converted using the EZ-96 DNA Methylation Kit (Zymo Research Corporation, Irvine, CA, USA) according to the manufacturer's recommendations.
Label Cy5 and Cy3
Label protocol Standard Illumina Protocol
Hybridization protocol Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol
Scan protocol Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
Data processing GenomeStudio V2010.3 [(Unmethylated and methylated) signal_intensities.txt is provided as a Series supplementary file]
Submission date Sep 24, 2011
Last update date May 03, 2012
Contact name michael thomas bocker
Organization name DKFZ Heidelberg
Street address Im Neuenheimer Feld
City heidelberg
ZIP/Postal code 69120
Country Germany
Platform ID GPL13534
Series (2)
GSE32362 Hydroxylation of 5-methylcytosine by TET2 maintains the active state of the mammalian HOXA cluster (Infinium HumanMethylation450 Beadchip)
GSE33130 Hydroxylation of 5-methylcytosine by TET2 maintains the active state of the mammalian HOXA cluster

Data table header descriptions
VALUE Average Beta
Detection Pval

Data table
ID_REF VALUE Detection Pval
cg00000029 0.7950634 0
cg00000108 0.9036237 0
cg00000109 0.8551264 0
cg00000165 0.6859795 0
cg00000236 0.8422866 0
cg00000289 0.628087 0
cg00000292 0.8831181 0
cg00000321 0.7057698 0
cg00000363 0.2249273 0
cg00000622 0.03020777 0
cg00000658 0.7758871 0
cg00000714 0.2050635 0
cg00000721 0.8670267 0
cg00000734 0.1009339 0
cg00000769 0.07123186 0
cg00000807 0.8711774 0
cg00000884 0.8154423 0
cg00000905 0.1297882 0
cg00000924 0.5563735 0
cg00000948 0.8804417 0

Total number of rows: 485577

Table truncated, full table size 10962 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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