E-GEOD-13471 - Transcription profiling by array of human normal pre-frontal cortex, liver, and colon tissues and colon tumors

Status
Released on 23 January 2009, last updated on 10 October 2012
Organism
Homo sapiens
Samples (18)
Arrays (2)
Protocols (5)
Description
DNA methylation, at CpG islands and promoters, is often inversely correlated with gene expression. We used expression microarrays to determine the relationship between DNA methylation and gene expression in 5 normal prefrontal cortex samples and 5 normal liver samples from the same individuals as well as between 4 colon tumor and matched normal colon mucosa (from the same individuals). Experiment Overall Design: We isolated RNA from pre-frontal cortex and liver tissue from 5 individuals for which we have genome-wide DNA methylation data and hybridized to Affymetrix gene expression microarrays. Similarly, we isolated RNA from 4 tumor and matched normal colon samples that we have genome-wide DNA methylation data..

This experiment was reloaded in November 2010 after additional curation.
Experiment types
transcription profiling by array, co-expression
Contact
Citation
The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, Ji H, Potash JB, Sabunciyan S, Feinberg AP.
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-13471.idf.txt
Sample and data relationshipE-GEOD-13471.sdrf.txt
Raw data (1)E-GEOD-13471.raw.1.zip
Processed data (1)E-GEOD-13471.processed.1.zip
Array designsA-AFFY-33.adf.txt, A-AFFY-44.adf.txt
R ExpressionSetE-GEOD-13471.eSet.r
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