Array-based functional genomics data
KSE100635
Title
Methylome Dataset of Korean Colorectal Cancer
Study
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Title
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Methylome Dataset of Korean Colorectal Cancer |
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Summary
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Bisulphite converted DNAs from a large CRC patient cohort were hybridised to the Illumina InfiniumEPIC Human Methylation Beadchip
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Experimental design
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case control design
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Experimental type
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methylation profiling by array
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Organism
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Homo sapiens |
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Source name
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Colon, nontumor, patient #PM-AS-0003-N-A1 |
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Contributor(s)
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- |
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Submission type
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Complete |
Protocols
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Accession
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Type
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Description
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|---|---|---|
| KSP10005352 | Nucleic acid labeling protocol |
Standard Illumina Protocol
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| KSP10005353 | Nucleic acid hybridization to array protocol |
Bisulfite-converted genomic DNAs were hybridized to BeadChip using the standard recommended Illumina protocol
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| KSP10005354 | Array scanning and feature extraction protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
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| KSP10005350 | Sample collection protocol |
missing
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| KSP10005351 | 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
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| KSP10005355 | 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.
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Detailed Experiment information
Toggle table
Accession
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BioSamples
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BioProject
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KAP240420 |
| File Name | Sample IDS | Size | Format | File type | Release date | Download | |
|---|---|---|---|---|---|---|---|
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202285550025_R05C01_Grn.idat
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13,676,221 13,676,221 | idat |
Raw data file
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2023-10-01 | |||
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202285550025_R05C01_Red.idat
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13,676,221 13,676,221 | idat |
Raw data file
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2023-10-01 | |||
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Detected_P.txt
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1,006,403,823 1,006,403,823 | txt |
Epigenomic analysis file
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2023-10-01 | |||
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processed_beta.txt
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3,639,040,797 3,639,040,797 | txt |
Epigenomic analysis file
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2023-10-01 | |||
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raw_beta.txt
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5,302,644,242 5,302,644,242 | txt |
Epigenomic analysis file
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2023-10-01 |