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E-GEOD-41049 - Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues (Gene Expression data)

Status
Released on 24 September 2012, last updated on 5 March 2015
Organism
Homo sapiens
Samples (14)
Array (1)
Protocols (7)
Description
DNA methylation has been comprehensively profiled in normal and cancer cells, but the dynamics that form, maintain and reprogram differentially methylated regions remain enigmatic. We show that methylation patterns within populations of cells from individual somatic tissues are heterogeneous and polymorphic. Using in vitro evolution of immortalized fibroblasts for over 300 generations, we track the dynamics of polymorphic methylation at regions developing significant differential methylation on average. The data indicate that changes in population-averaged methylation occur through a stochastic process that generates a stream of local and uncorrelated methylation aberrations. Despite the stochastic nature of the process, nearly deterministic epigenetic remodeling emerges on average at loci that lose or gain resistance to methylation accumulation. Changes in the susceptibility to methylation accumulation are correlated with changes in histone modifications and CTCF occupancy. Characterizing epigenomic polymorphism within cell populations is therefore critical for understanding methylation dynamics in normal and cancer cells. Gene expression profiled in duplicate throughout the microevolutionary timecourse using Affymetrix Gene 1.0 ST arrays.
Experiment type
transcription profiling by array 
Contacts
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-41049.idf.txt
Sample and data relationshipE-GEOD-41049.sdrf.txt
Raw data (1)E-GEOD-41049.raw.1.zip
Processed data (1)E-GEOD-41049.processed.1.zip
Array designA-AFFY-141.adf.txt
R ExpressionSetE-GEOD-41049.eSet.r
Links