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KEA Functional genomics database

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Array-based functional genomics data

KSE100557

Title

Methylome Dataset of Korean Colorectal Cancer

Study

Study Fields - Title, Summary, Experimental design, Experimental type, Organism, Source name, Contributor(s) Citation, Submission type
Title	Methylome Dataset of Korean Colorectal Cancer
Summary	Bisulphite converted DNAs from a large CRC patient cohort were hybridised to the Illumina InfiniumEPIC Human Methylation Beadchip
Experimental design	case control design
Experimental type	methylation profiling by array
Organism	Homo sapiens
Source name	Colon, tumor, patient #PM-PU-1168-T-A1
Contributor(s)	-
Submission type	Complete

Protocols

Protocols - Accession, Type, Description
Accession	Type	Description
KSP10004572	Nucleic acid labeling protocol	Standard Illumina Protocol
KSP10004573	Nucleic acid hybridization to array protocol	Bisulfite-converted genomic DNAs were hybridized to BeadChip using the standard recommended Illumina protocol
KSP10004574	Array scanning and feature extraction protocol	Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
KSP10004570	Sample collection protocol	missing
KSP10004571	Nucleic acid extraction protocol	genomic DNA was extracted and purified from normal or tumor tissue samples using Purelink DNA mini Kit according to standard instructions
KSP10004575	Normalization data transformation protocol	For DNA methylome data analysis, CpG methylation values were calculated as average-b values using the minfi package (version 1.36.0) of R software, and we used the subset-quantile within array normalization (SWAN) to reduce technical variations within and between arrays.

Detailed Experiment information

Showing 1-1 of 1

Validations details list
Accession ID	BioSample accession ID	Sample name	Organism	NCBI taxonomy ID	sampleGroup	Complete	Reference data ID type	Reference data ID	Detailed sample title	Source name	Molecule	Label	Description	Platform ID	Protocols	Factor value	Raw data file	Abundance matrix file	Epigenomic analysis file	Variant analysis file	Others	Primary analysis file
KAX10001496	KAS24077472	PM-PU-1168-T-A1	Homo sapiens	9606		Complete			PM-PU-1168-T-A1	Colon, tumor, patient #PM-PU-1168-T-A1	genomic DNA	Cy3 and Cy5	tumor	GPL21145	KSP10004571, KSP10004572, KSP10004573, KSP10004574, KSP10004575		204668820020_R06C01_Grn.idat; 204668820020_R06C01_Red.idat		Detected_P.txt; processed_beta.txt; raw_beta.txt

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Accession

Accession - RUNs, BIOSAMPLEs
BioSamples	KAS24077472
BioProject	KAP240419

KEA file 목록
file 선택	File Name	Sample IDS	Size	Format	File type	Release date	Download
file 선택	204668820020_R06C01_Grn.idat	KAS24077472	13,677,905 13,677,905	idat	Raw data file	2023-10-01
file 선택	204668820020_R06C01_Red.idat	KAS24077472	13,677,905 13,677,905	idat	Raw data file	2023-10-01
file 선택	Detected_P.txt	KAS24077472	1,327,990,952 1,327,990,952	txt	Epigenomic analysis file	2023-10-01
file 선택	processed_beta.txt	KAS24077472	4,849,869,650 4,849,869,650	txt	Epigenomic analysis file	2023-10-01
file 선택	raw_beta.txt	KAS24077472	6,930,093,142 6,930,093,142	txt	Epigenomic analysis file	2023-10-01

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