Comment[ArrayExpressAccession] E-GEOD-43851 MAGE-TAB Version 1.1 Public Release Date 2013-03-08 Investigation Title Functional DNA methylation is accompanied by chromatin accessibility [methylation] Comment[Submitted Name] Functional DNA methylation is accompanied by chromatin accessibility [methylation] Experiment Description 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. 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 Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Pandiyan Liang Person First Name Kurinji Gangning Person Email geo@ncbi.nlm.nih.gov Person Affiliation University of Southern California Person Address Department of Urology - Norris Comprehensive Cancer Center, University of Southern California, 1441 Eastlake Avenue NOR 7344, Los Angeles, USA Person Roles submitter Protocol Name P-GSE43851-1 P-GSE43851-6 P-GSE43851-3 P-GSE43851-8 P-GSE43851-7 P-GSE43851-2 P-GSE43851-4 P-GSE43851-5 Protocol Description ID_REF = VALUE = Beta value was calculated as M/(M+U). Detection P values were obtained using the Z-score formula as previously described (Noushmehr et al., 2010, Cancer Cell). Bisulfite converted DNA was amplified, fragmented and hybridized to the Illumina 450k methylation array using standard Illumina protocols Cells were grown under standard conditions Mean non-background corrected signal intensities of the methylated (M) and unmethylated (U) for each CpG locus were extracted using the Illumina BeadStudio software v3.2.Data points were marked “NA” if 1) Probes contained single-nucleotide polymorphisms (SNPs), 2) those that overlap with a repetitive element that covers the targeted CpG dinucleotide, 3) those that overlap with regions of insertions and deletions in the human genome. Beta values with detection P value greater than 0.05 were also replaced as NA. Furthermore, probes containing at least one “NA” across the tumor sample set were masked as “NA”. Beta values were background subtracted. Beadchips were imaged using Illumina BeadArray Reader using standard recommended Illumina scanner setting. 2x10^5 nuclei were treated with 1x M.SssI buffer and 50U of M.SssI for 15 minutes. A no-enzyme control was included. SAHA treatment was performed for 24hours with 1uM SAHA Genomic DNA was extracted using standard phenol chloform procedures with ethanol precipitation. Zymo EZ DNA kit was used for bisulfite conversion Standard Illumina labeling protocol Protocol Type bioassay_data_transformation hybridization grow feature_extraction image_aquisition specified_biomaterial_action nucleic_acid_extraction labeling Experimental Factor Name CELL LINE TREATMENT SEX Experimental Factor Type cell line treatment Sex Publication Title Functional DNA demethylation is accompanied by chromatin accessibility. Publication Author List Pandiyan K, You JS, Yang X, Dai C, Zhou XJ, Baylin SB, Jones PA, Liang G PubMed ID 23408854 Publication DOI 10.1093/nar/gkt077 Comment[SecondaryAccession] GSE43851 Comment[GEOReleaseDate] 2013-03-08 Comment[ArrayExpressSubmissionDate] 2013-01-29 Comment[GEOLastUpdateDate] 2013-03-08 Comment[AEExperimentType] methylation profiling by array Comment[AdditionalFile:Data1] GSE43851_raw-intensities.txt SDRF File E-GEOD-43851.sdrf.txt