Comment[ArrayExpressAccession]	E-GEOD-47076
MAGE-TAB Version	1.1											
Public Release Date	2013-12-31
Investigation Title	Analysis of expression and epigenetic changes in human colorectal cancer and matching mucosa tissues											
Comment[Submitted Name]	Analysis of expression and epigenetic changes in human colorectal cancer and matching mucosa tissues
Experiment Description	This SuperSeries is composed of the SubSeries listed below. Refer to individual Series											
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	Wu											
Person First Name	Xiwei											
Person Email	xwu@coh.org											
Person Affiliation	City of Hope National Medical Center											
Person Address	Molecular and Cellular Biology, City of Hope National Medical Center, 1500 E. Duarte Rd., Duarte, CA, USA											
Person Roles	submitter											
Protocol Name	P-GSE47076-1	P-GSE47076-2	P-GSE47076-5	P-GSE47076-9	P-GSE47076-10	P-GSE47076-6	P-GSE47076-3	P-GSE47076-8	P-GSE47076-4	P-GSE47076-12	P-GSE47076-7	P-GSE47076-11
Protocol Description	Data were background corrected with GC bin, quantile normalized and summarized by interPLIER algorithm with Affymetrix Expression Console. ID_REF =  VALUE = log2 Expression Console processed intensity	For each array, Loess normalization was applied excluding top 5% probes with the largest original Cy5/Cy3 log2 ratio. Quantile normalization was then applied across all the arrays. ID_REF =  VALUE = Loess and quantile normalized Cy5/Cy3 log2 ratio	One µg of each sample was processed using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay (https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf).	According to standard NimbleGen Protocol.	According to NimbleGen Kit.	The hybridization cocktails containing 2.5 ug of the fragmented, end-labeled cDNA were applied to the GeneChip® Human Gene 2.0 ST arrays. Hybridization was performed for 16 hours, and the arrays were washed and stained with the GeneChip Fluidics Station 450 using FS450_0007 script.	Human tissue samples.	For chromatin immunoprecipitation, frozen tissues were homogenized in cold phosphate-buffered saline (PBS) and fixed for 10 min at room temperature in 1% formaldehyde. After adding of glycine to 0.125M final concentration, chromatin was sonicated and incubated with the following antibodies overnight: anti-H3K4me3 (39159, Active Motif), and anti-H3K27me3 (07-449, Millipore). For obtaining the H3K4me3 profile, the H3K4me3 antibodies were pre-blocked with an H3K9me3 peptide (Abcam) to remove minor cross-reactivity of this antibody. After genome amplification, immunoprecipitated DNA was hybridized versus input DNA on human CpG island/promoter microarrays (NimbleGen).	Total RNA from patient samples was purified by using the mirVana kit (Ambion, Life Technologies).	For analysis of genomic 5mC patterns, the methylated CpG island recovery assay (MIRA) was used. For this procedure, sonicated genomic DNA was incubated with MBD2b-GST and MBD3L1-HIS protein complex overnight at +4C with further capturing of methylated DNA fraction by GST-magnetic beads (Promega). After genome amplification, DNA was hybridized versus input on human CpG island/promoter microarrays (NimbleGen).	Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.4 to produce CEL intensity files.	Follow NimbleScan's default using Agilent Scanner.
Protocol Type	normalization data transformation protocol	normalization data transformation protocol	labelling protocol	labelling protocol	hybridization protocol	hybridization protocol	growth protocol	nucleic acid extraction protocol	nucleic acid extraction protocol	nucleic acid extraction protocol	array scanning protocol	array scanning protocol
Experimental Factor Name	PATIENT IDENTIFIER	ENRICHMENT PROCEDURE	CHIP ANTIBODY	ORGANISM PART								
Experimental Factor Type	patient identifier	enrichment procedure	chip antibody	organism part								
Comment[SecondaryAccession]	GSE47076											
Comment[GEOReleaseDate]	2013-12-31											
Comment[ArrayExpressSubmissionDate]	2013-05-17											
Comment[GEOLastUpdateDate]	2014-01-01											
Comment[AEExperimentType]	transcription profiling by array											
Comment[AEExperimentType]	methylation profiling by array											
Comment[AEExperimentType]	ChIP-chip by tiling array											
SDRF File	E-GEOD-47076.sdrf.txt