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Series GSE36580 Query DataSets for GSE36580
Status Public on Mar 08, 2013
Title AcceSssIble: an array-based assay for the study of chromatin accessibility and DNA methylation using the CpG methyltransferase SssI
Organism Homo sapiens
Experiment type Methylation profiling by array
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.
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
Contributor(s) Liang G
Citation(s) 23408854
Submission date Mar 16, 2012
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
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (10)
GSM897809 HCT116_NoE_rep1
GSM897810 HCT116_SSS1_rep1
GSM897811 DKO1_NoE
This SubSeries is part of SuperSeries:
GSE38858 AcceSssIble Assay to Study the Chomatin Accessibility and DNA Methylation
BioProject PRJNA153743

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE36580_RAW.tar 183.1 Mb (http)(custom) TAR
GSE36580_raw_methylation_intensity.txt.gz 46.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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