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| Status |
Public on Mar 08, 2013 |
| Title |
Functional DNA methylation is accompanied by chromatin accessibility [methylation] |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by array
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| Summary |
Analysis of nucleosome positioning and chromatin state by using CpG methyltransferase M.SssI to methylate nuclei. Unmethylated regions that gain methylation (low to high beta value) are known to be accessible and nucleosome depleted. Method used to study changes after epigenetic drug treatments identified that majority of demethylation events are not accompanied by chromatin accessibility changes.
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| Overall design |
Intact nuclei are harvested from cells and treated with M.SssI. DNA is then extracted, bisulfite converted and run on an Infinium methylation array, along with a no-enzyme control. Background subtracted beta values (listed below) are used to determine regions that have gained methylation on enzyme treatment compared to the control - and these are used to infer chromatin state
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| Contributor(s) |
Liang G |
| Citation(s) |
23408854 |
| Submission date |
Jan 29, 2013 |
| Last update date |
Mar 22, 2019 |
| Contact name |
Kurinji Pandiyan |
| Organization name |
University of Southern California
|
| Department |
Department of Urology - Norris Comprehensive Cancer Center
|
| Street address |
1441 Eastlake Avenue NOR 7344
|
| City |
Los Angeles |
| ZIP/Postal code |
90033 |
| Country |
USA |
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| Platforms (1) |
| GPL13534 |
Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482) |
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| Samples (20)
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| This SubSeries is part of SuperSeries: |
| GSE38858 |
AcceSssIble Assay to Study the Chomatin Accessibility and DNA Methylation |
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| Relations |
| BioProject |
PRJNA187585 |
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