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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 25, 2014 |
| Title |
H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells [MSCs] |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by array
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| Summary |
In differentiated cells, aging is associated with hypermethylation of DNA regions enriched in repressive histone posttranslational modifications. However, the chromatin marks associated with changes in DNA methylation in adult stem cells during lifetime are still largely unknown. Here, DNA methylation profiling of mesenchymal stem cells obtained from individuals aged 2 to 92 identified 18735 hypermethylated and 45407 hypomethylated CpG sites associated with aging. As in differentiated cells, hypermethylated sequences were enriched in chromatin repressive marks. Most importantly, hypomethylated CpG sites were strongly enriched in the active chromatin mark H3K4me1 in stem and differentiated cells, suggesting this is a cell type-independent chromatin signature of DNA hypomethylation during aging. Analysis of scedasticity showed that interindividual variability of DNA methylation increased during aging in MSCs and differentiated cells, providing a new avenue for the identification of DNA methylation changes over time. DNA methylation profiling of genetically identical individuals showed that both the tendency of DNA methylation changes and scedasticity depended on non-genetic as well as genetic factors. Our results indicate that the dynamics of DNA methylation during aging depend on a complex mixture of factors that include the DNA sequence, cell type and chromatin context involved, and that, depending on the locus, the changes can be modulated by genetic and/or external factors.
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| Overall design |
Total DNA isolated by standard procedures from human adult mesenchymal stem cells (MSCs) obtained from 34 individuals aged 2 to 92
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| Contributor(s) |
Fernandez AF, Bayón GF, Urdinguio RG, Toraño EG, Garcia MG, Carella A, Petrus-Reurer S, Ferrero C, Martinez-Camblor P, Cubillo I, García-Castro J, Delgado-Calle J, Perez-Campo FM, Riancho JA, Bueno C, Menendez P, Mentink A, Mareschi K, Claire F, Fagnani C, Medda E, Toccaceli V, Brescianini S, Moran S, Esteller M, Stolzing A, de Boer J, Nisticò L, Stazi MA, Fraga MF |
| Citation(s) |
25271306 |
| Submission date |
Nov 05, 2013 |
| Last update date |
Apr 04, 2019 |
| Contact name |
Agustin F Fernandez |
| E-mail(s) |
affernandez@hca.es, agusff@gmail.com
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| Phone |
985652411
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| Organization name |
Oviedo University-HUCA
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| Department |
IUOPA
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| Lab |
Epigenetics
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| Street address |
Avenida de Roma s/n
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| City |
Oviedo |
| State/province |
Asturias |
| ZIP/Postal code |
33011 |
| Country |
Spain |
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| Platforms (1) |
| GPL13534 |
Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482) |
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| Samples (34)
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| GSM1259851 |
MSC cultured in human MSC media, MSC-4 |
| GSM1259852 |
MSC cultured in human MSC media, MSC-5 |
| GSM1259853 |
MSC cultured in human MSC media, MSC-6 |
| GSM1259854 |
MSC cultured in human MSC media, MSC-7 |
| GSM1259855 |
MSC cultured in human MSC media, MSC-8 |
| GSM1259856 |
MSC cultured in human MSC media, MSC-9 |
| GSM1259857 |
MSC cultured in human MSC media, MSC-10 |
| GSM1259858 |
MSC cultured in human MSC media, MSC-11 |
| GSM1259859 |
MSC cultured in human MSC media, MSC-12 |
| GSM1259860 |
MSC cultured in human MSC media, MSC-13 |
| GSM1259861 |
MSC cultured in human MSC media, MSC-14 |
| GSM1259862 |
MSC cultured in human MSC media, MSC-15 |
| GSM1259863 |
MSC cultured in human MSC media, MSC-16 |
| GSM1259864 |
MSC cultured in human MSC media, MSC-17 |
| GSM1259865 |
MSC cultured in human MSC media, MSC-18 |
| GSM1259866 |
MSC cultured in human MSC media, MSC-19 |
| GSM1259867 |
MSC cultured in human MSC media, MSC-20 |
| GSM1512025 |
MSC cultured in human MSC media, MSC-21 |
| GSM1512026 |
MSC cultured in human MSC media, MSC-22 |
| GSM1512027 |
MSC cultured in human MSC media, MSC-23 |
| GSM1512028 |
MSC cultured in human MSC media, MSC-24 |
| GSM1512029 |
MSC cultured in human MSC media, MSC-25 |
| GSM1512030 |
MSC cultured in human MSC media, MSC-26 |
| GSM1512031 |
MSC cultured in human MSC media, MSC-27 |
| GSM1512032 |
MSC cultured in human MSC media, MSC-28 |
| GSM1512033 |
MSC cultured in human MSC media, MSC-29 |
| GSM1512034 |
MSC cultured in human MSC media, MSC-30 |
| GSM1512035 |
MSC cultured in human MSC media, MSC-31 |
| GSM1512036 |
MSC cultured in human MSC media, MSC-32 |
| GSM1512037 |
MSC cultured in human MSC media, MSC-33 |
| GSM1512038 |
MSC cultured in human MSC media, MSC-34 |
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| This SubSeries is part of SuperSeries: |
| GSE52114 |
H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells |
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| Relations |
| BioProject |
PRJNA226711 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE52112_RAW.tar |
183.1 Mb |
(http)(custom) |
TAR |
| GSE52112_methylated_unmethylated_signals.txt.gz |
115.5 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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