Comment[ArrayExpressAccession]	E-GEOD-29661
Public Release Date	2012-05-21							
Investigation Title	Cellular aging can be monitored by DNA-methylation changes at specific CpG sites							
Comment[Submitted Name]	Cellular aging can be monitored by DNA-methylation changes at specific CpG sites
Experiment Description	Long-term culture associated changes need to be considered for quality control of cell preparations – especially in cellular therapy. Here we describe a simple method to track cellular aging based on continuous DNA-methylation changes at six specific CpG sites. This epigenetic signature can be used as a biomarker for various cell types to predict the state of cellular aging with regard to the number of passages or days of in vitro culture. 8 samples of human dermal fibroblasts.  4 samples of mesenchymal stem cells (MSC) from human adipose tissue.							
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Term Source Name	EFO
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Term Source File	http://www.ebi.ac.uk/efo/efo.owl							
Person Last Name	Wagner	Koch	Joussen	Schellenberg	Lin	Zenke	Wagner	
Person First Name	Wolfgang	Carmen	Sylvia	Anne	Qiong	Martin	Wolfgang	
Person Mid Initials		M						
Person Email	wwagner@ukaachen.de							
Person Affiliation	RWTH Aachen University							
Person Phone	+49 241 8088611							
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Person Address	Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany							
Person Roles	submitter							
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Protocol Name	P-GSE29661-1	P-GSE29661-6	P-GSE29661-5	P-GSE29661-2	P-GSE29661-3	P-GSE29661-8	P-GSE29661-4	P-GSE29661-7
Protocol Description	ID_REF = <br>VALUE = Average Beta value<br>Detection Pval = 	The HumanMethylation27 BeadChip (Illumina, San Diego, USA) was scanned using the BeadArray Reader.	The HumanMethylation27 BeadChip (Illumina, San Diego, USA) was hybridized with 200ng DNA.	Cells were harvested by trypsination after early or late passages.	Genomic DNA of approximately 10(6) dermal fibroblasts was isolated using the QIAGEN DNA Blood Midi-Kit. DNA quality was assessed with a NanoDrop ND-1000 spectrometer (NanoDrop Technologies, Wilmigton, Del) and average fragment length was assessed by gel electrophoresis.	Genomic DNA of approximately 10(6) human mesenchymal stem cells (MSC) from adipose tissue was isolated using the QIAGEN DNA Blood Midi-Kit. DNA quality was assessed with a NanoDrop ND-1000 spectrometer (NanoDrop Technologies, Wilmigton, Del) and average fragment length was assessed by gel electrophoresis.	Genomic DNA (600 ng) from each sample was bisulfite converted using the EpiTect Bisulfite Kit (Qiagen, Hilden, Germany). This step leads to the deamination of non-methylated cytosines to uracils, while methylated cytosines are refractory to the effects of bisulfite and remain cytosine. After bisulfate conversion each sample was whole genome amplified and enzymatically fragmented.	Initial data analysis was performed with the BeadStudio Methylation software from Illumina (ie, BeadStudio Methylation Analysis Module 3.2.0). Raw data were background normalized.
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Protocol Type	bioassay_data_transformation	image_aquisition	hybridization	specified_biomaterial_action	nucleic_acid_extraction	nucleic_acid_extraction	labeling	feature_extraction
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Publication Title	Monitoring of cellular senescence by DNA-methylation at specific CpG sites.							
Publication Author List	Koch CM, Joussen S, Schellenberg A, Lin Q, Zenke M, Wagner W							
PubMed ID	22221451							
Publication DOI	10.1111/j.1474-9726.2011.00784.x							
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Comment[SecondaryAccession]	GSE29661							
Comment[AdditionalFile:Data1]	GSE29661_raw_data.txt							
Comment[GEOLastUpdateDate]	2012-05-21
Comment[AEExperimentType]	methylation profiling by array							
Comment[GEOReleaseDate]	2012-05-20
Comment[ArrayExpressSubmissionDate]	2011-05-31
SDRF File	E-GEOD-29661.sdrf.txt