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Status |
Public on May 03, 2012 |
Title |
14d_retinoic acid_treated NT2 cells |
Sample type |
genomic |
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Source name |
14d_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.
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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.
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Label |
Cy5 and Cy3
|
Label protocol |
Standard Illumina Protocol
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Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol
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Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
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Data processing |
GenomeStudio V2010.3 [(Unmethylated and methylated) signal_intensities.txt is provided as a Series supplementary file]
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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 |
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