Comment[GEAAccession]	E-GEAD-396
MAGE-TAB Version	1.1
Investigation Title	Methylation array of breast, colorectal and gastric cancer
Experiment Description	Accurate and early diagnosis and classification of cancer type based on histological and pathological subtype is critical for selecting the appropriate treatment and for predicting survival. In some cases, the complex anatomy of primary tumors makes it impossible to accurately identify the tissue of origin or tumor type due to the lack of tissue specificity information in histological and pathological diagnosis. DNA methylation is an epigenetic regulator of gene expression that usually results in gene silencing. Aberrations in methylation markers are a central feature of carcinogenesis, causing changes in the gene expression profile. Some methylation changes are found in almost all cases of a specific type of cancer. The methylation status of cytosine in specific regions has been shown to be organ-, tissue- or tumor-specific and may be useful in the diagnosis and classification of cancer types. We investigated DNA methylation status of 16 cancerous tissue of each of breast, colorectal and gastric cancer by methylation array. This data was applied to validate methylation panel we made to diagnose and classify cancers.
Experimental Design	disease state design
Experimental Factor Name	disease
Experimental Factor Type	disease
Person Last Name	shimizu
Person First Name	dai
Person Affiliation	nagoya university graduate school of medicine
Person Roles	submitter
Public Release Date	2021-12-08
Protocol Name	P-GEAD-642	P-GEAD-643	P-GEAD-644	P-GEAD-645	P-GEAD-646	P-GEAD-647
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol	array scanning and feature extraction protocol	normalization data transformation protocol
Protocol Description	Samples were obtaind from surgically resected primary breast cancer, COADREAD and gastric cancer tissues	Genomic DNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit of Qiagen according to the protocol.	Samples were processed according to the manufacturer's instructions for illumina Infinium MethylationEPIC Kit	Samples were processed according to the manufacturer's instructions for illumina Infinium MethylationEPIC Kit	The arrays were scanned on the Illumina iScan and image analysis was perfomed using Illumina's default image analysis algorithm.	The data were processed according to the manufacturer's instructions for GenomeStudio Methylation Module
SDRF File	E-GEAD-396.sdrf.txt
Comment[Number of channel]	dual-channel
Comment[Array Design REF]	A-GEOD-21145
Comment[AEExperimentType]	methylation profiling by array
Comment[BioProject]	PRJDB10600
Comment[Last Update Date]	2021-12-08