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Array-based functional genomics data
KSE102925
Title
DNA methylation signature for detection of early-stage hepatocellular carcinoma
Study
Study Fields - Title, Summary, Experimental design, Experimental type, Organism, Source name, Contributor(s) Citation, Submission type
Title
 DNA methylation signature for detection of early-stage hepatocellular carcinoma
Summary
Total of 305 samples from HCC resected patients were analyzed for DNA methylation microarray with llumina HumanMethylation850 Beadchip.
Experimental design
case control design
Experimental type
methylation profiling by array
Organism
 Homo sapiens
Source name
 HCC , Normal liver
Contributor(s)
 -
Submission type
 Complete
Protocols
Protocols - Accession, Type, Description
Accession
Type
Description
KSP10028360 Nucleic acid labeling protocol
Illumina Protocol
KSP10028361 Nucleic acid hybridization to array protocol
Bisulphite converted DNA was hybridized to Illumina EPIC BeadChip according to manufacturer's protocol
KSP10028362 Array scanning and feature extraction protocol
Standard Illumina iScan scanning protocol
KSP10028358 Sample collection protocol
missing
KSP10028359 Nucleic acid extraction protocol
genomic DNA was extracted using MagListo™ 5M Genomic DNA Extraction Kit (Bioneer) according to manufacturer's protocol
KSP10028363 Normalization data transformation protocol
Normalized Average Beta using Functioanl Normalization Method in Bioconduct minfi R package
Detailed Experiment information
Toggle table
Showing 1-25 of 305
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
KAX10003522 KAS24106924 Normal liver 1 Homo sapiens 9606 Complete genomic DNA-Normal liver 1 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT) GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 201105900135_R04C01_Grn.idat; 201105900135_R04C01_Red.idat 850K_HCC.txt
KAX10003523 KAS24106925 Normal liver 2 Homo sapiens 9606 Complete genomic DNA-Normal liver 2 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 200861170061_R01C01_Grn.idat; 200861170061_R01C01_Red.idat 850K_HCC.txt
KAX10003524 KAS24106926 Normal liver 3 Homo sapiens 9606 Complete genomic DNA-Normal liver 3 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 200861170061_R02C01_Grn.idat; 200861170061_R02C01_Red.idat 850K_HCC.txt
KAX10003525 KAS24106927 Normal liver 4 Homo sapiens 9606 Complete genomic DNA-Normal liver 4 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 200861170061_R03C01_Grn.idat; 200861170061_R03C01_Red.idat 850K_HCC.txt
KAX10003526 KAS24106928 Normal liver 5 Homo sapiens 9606 Complete genomic DNA-Normal liver 5 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 200861170045_R04C01_Grn.idat; 200861170045_R04C01_Red.idat 850K_HCC.txt
KAX10003527 KAS24106929 Normal liver 6 Homo sapiens 9606 Complete genomic DNA-Normal liver 6 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 200861170045_R05C01_Grn.idat; 200861170045_R05C01_Red.idat 850K_HCC.txt
KAX10003528 KAS24106930 Normal liver 8 Homo sapiens 9606 Complete genomic DNA-Normal liver 8 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 200861170045_R06C01_Grn.idat; 200861170045_R06C01_Red.idat 850K_HCC.txt
KAX10003529 KAS24106931 Normal liver 9 Homo sapiens 9606 Complete genomic DNA-Normal liver 9 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 200861170045_R07C01_Grn.idat; 200861170045_R07C01_Red.idat 850K_HCC.txt
KAX10003530 KAS24106932 Normal liver 10 Homo sapiens 9606 Complete genomic DNA-Normal liver 10 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 200861170045_R08C01_Grn.idat; 200861170045_R08C01_Red.idat 850K_HCC.txt
KAX10003531 KAS24106933 Normal liver 11 Homo sapiens 9606 Complete genomic DNA-Normal liver 11 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 200861170055_R01C01_Grn.idat; 200861170055_R01C01_Red.idat 850K_HCC.txt
KAX10003532 KAS24106934 Normal liver 12 Homo sapiens 9606 Complete genomic DNA-Normal liver 12 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 200861170055_R02C01_Grn.idat; 200861170055_R02C01_Red.idat 850K_HCC.txt
KAX10003533 KAS24106935 Normal liver 13 Homo sapiens 9606 Complete genomic DNA-Normal liver 13 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 200861170055_R03C01_Grn.idat; 200861170055_R03C01_Red.idat 850K_HCC.txt
KAX10003534 KAS24106936 Normal liver 14 Homo sapiens 9606 Complete genomic DNA-Normal liver 14 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 200861170055_R04C01_Grn.idat; 200861170055_R04C01_Red.idat 850K_HCC.txt
KAX10003535 KAS24106937 Normal liver 15 Homo sapiens 9606 Complete genomic DNA-Normal liver 15 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 200861170055_R05C01_Grn.idat; 200861170055_R05C01_Red.idat 850K_HCC.txt
KAX10003536 KAS24106938 Normal liver 16 Homo sapiens 9606 Complete genomic DNA-Normal liver 16 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 200861170061_R04C01_Grn.idat; 200861170061_R04C01_Red.idat 850K_HCC.txt
KAX10003537 KAS24106939 Normal liver 17 Homo sapiens 9606 Complete genomic DNA-Normal liver 17 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 200861170061_R05C01_Grn.idat; 200861170061_R05C01_Red.idat 850K_HCC.txt
KAX10003538 KAS24106940 Normal liver 18 Homo sapiens 9606 Complete genomic DNA-Normal liver 18 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 200861170061_R06C01_Grn.idat; 200861170061_R06C01_Red.idat 850K_HCC.txt
KAX10003539 KAS24106941 Normal liver 21 Homo sapiens 9606 Complete genomic DNA-Normal liver 21 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 200861170061_R08C01_Grn.idat; 200861170061_R08C01_Red.idat 850K_HCC.txt
KAX10003540 KAS24106942 Normal liver 23 Homo sapiens 9606 Complete genomic DNA-Normal liver 23 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 200861170083_R02C01_Grn.idat; 200861170083_R02C01_Red.idat 850K_HCC.txt
KAX10003541 KAS24106943 Normal liver 24 Homo sapiens 9606 Complete genomic DNA-Normal liver 24 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 200861170083_R03C01_Grn.idat; 200861170083_R03C01_Red.idat 850K_HCC.txt
KAX10003542 KAS24106944 Normal liver 25 Homo sapiens 9606 Complete genomic DNA-Normal liver 25 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 200861170083_R04C01_Grn.idat; 200861170083_R04C01_Red.idat 850K_HCC.txt
KAX10003543 KAS24106945 Normal liver 26 Homo sapiens 9606 Complete genomic DNA-Normal liver 26 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 200861170083_R05C01_Grn.idat; 200861170083_R05C01_Red.idat 850K_HCC.txt
KAX10003544 KAS24106946 Normal liver 27 Homo sapiens 9606 Complete genomic DNA-Normal liver 27 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 200861170083_R06C01_Grn.idat; 200861170083_R06C01_Red.idat 850K_HCC.txt
KAX10003545 KAS24106947 Normal liver 28 Homo sapiens 9606 Complete genomic DNA-Normal liver 28 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 200861170083_R07C01_Grn.idat; 200861170083_R07C01_Red.idat 850K_HCC.txt
KAX10003546 KAS24106948 Normal liver 29 Homo sapiens 9606 Complete genomic DNA-Normal liver 29 Normal liver genomic DNA Cy3 and Cy5 normal tissue adjacent to the tumor (NAT)-Paired GPL23976 KSP10028359, KSP10028360, KSP10028361, KSP10028362, KSP10028363 201105900135_R05C01_Grn.idat; 201105900135_R05C01_Red.idat 850K_HCC.txt
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Accession
Accession - RUNs, BIOSAMPLEs
BioSamples
KAS24106924 , KAS24106925 , KAS24106926 , KAS24106927 , KAS24106928 , KAS24106929 , KAS24106930 , KAS24106931 , KAS24106932 , KAS24106933 , KAS24106934 , KAS24106935 , KAS24106936 , KAS24106937 , KAS24106938 , KAS24106939 , KAS24106940 , KAS24106941
287 more
less
BioProject
 KAP241042
Files
KEA file 목록
File Name Sample IDS Size Format File type Release date Download
201105900135_R04C01_Grn.idat
KAS24106924
13,686,964 13,686,964 idat
Raw data file
 2024-12-05
201105900135_R04C01_Red.idat
KAS24106924
13,686,964 13,686,964 idat
Raw data file
 2024-12-05
850K_HCC.txt
KAS24106924 KAS24106925
303 more
less
4,793,943,141 4,793,943,141 txt
Epigenomic analysis file
 2024-12-05
200861170061_R01C01_Grn.idat
KAS24106925
13,686,964 13,686,964 idat
Raw data file
 2024-12-05
200861170061_R01C01_Red.idat
KAS24106925
13,686,964 13,686,964 idat
Raw data file
 2024-12-05
200861170061_R02C01_Grn.idat
KAS24106926
13,686,964 13,686,964 idat
Raw data file
 2024-12-05
200861170061_R02C01_Red.idat
KAS24106926
13,686,964 13,686,964 idat
Raw data file
 2024-12-05
200861170061_R03C01_Grn.idat
KAS24106927
13,686,964 13,686,964 idat
Raw data file
 2024-12-05
200861170061_R03C01_Red.idat
KAS24106927
13,686,964 13,686,964 idat
Raw data file
 2024-12-05
200861170045_R04C01_Grn.idat
KAS24106928
13,686,979 13,686,979 idat
Raw data file
 2024-12-05
200861170045_R04C01_Red.idat
KAS24106928
13,686,979 13,686,979 idat
Raw data file
 2024-12-05
200861170045_R05C01_Grn.idat
KAS24106929
13,686,982 13,686,982 idat
Raw data file
 2024-12-05
200861170045_R05C01_Red.idat
KAS24106929
13,686,982 13,686,982 idat
Raw data file
 2024-12-05
200861170045_R06C01_Grn.idat
KAS24106930
13,686,979 13,686,979 idat
Raw data file
 2024-12-05
200861170045_R06C01_Red.idat
KAS24106930
13,686,979 13,686,979 idat
Raw data file
 2024-12-05
200861170045_R07C01_Grn.idat
KAS24106931
13,686,979 13,686,979 idat
Raw data file
 2024-12-05
200861170045_R07C01_Red.idat
KAS24106931
13,686,979 13,686,979 idat
Raw data file
 2024-12-05
200861170045_R08C01_Grn.idat
KAS24106932
13,686,979 13,686,979 idat
Raw data file
 2024-12-05
200861170045_R08C01_Red.idat
KAS24106932
13,686,979 13,686,979 idat
Raw data file
 2024-12-05
200861170055_R01C01_Grn.idat
KAS24106933
13,686,974 13,686,974 idat
Raw data file
 2024-12-05
200861170055_R01C01_Red.idat
KAS24106933
13,686,974 13,686,974 idat
Raw data file
 2024-12-05
200861170055_R02C01_Grn.idat
KAS24106934
13,686,974 13,686,974 idat
Raw data file
 2024-12-05
200861170055_R02C01_Red.idat
KAS24106934
13,686,974 13,686,974 idat
Raw data file
 2024-12-05
200861170055_R03C01_Grn.idat
KAS24106935
13,686,974 13,686,974 idat
Raw data file
 2024-12-05
200861170055_R03C01_Red.idat
KAS24106935
13,686,974 13,686,974 idat
Raw data file
 2024-12-05
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