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Series GSE54503 Query DataSets for GSE54503
Status Public on Jan 30, 2014
Title Exploring genome-wide DNA methylation profiles altered in hepatocellular carcinoma using Infinium HumanMethylation 450 BeadChips
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary We examine genome-wide DNA methylation profiles in 66 pairs of HCC tumor and adjacent non-tumor tissues. After Bonferroni adjustment, a total of 130,512 CpG sites significantly differed in methylation level in tumor compared to non-tumor tissues, with 28,017 CpG sites hypermethylated and 102,495 hypomethylated in tumor tissues. Most (60.1%) significantly hypermethylated CpG sites are located in CpG islands. These results demonstrate the significance of aberrant DNA methylation in HCC tumorigenesis.
Overall design Bisulfite modification of 1µg DNA was conducted using an EZ DNA Methylation Kit (Zymo Research, Irvine, CA) according to the manufacturer’s procedure. The Infinium Methylation 450K assay was performed according to Illumina’s standard protocol. Six HCC tumor/adjacent non-tumor tissue pairs were processed on the same chip to avoid chip-to-chip variation.
Contributor(s) Shen J, Santella R
Citation(s) 23208076, 25861255
Submission date Jan 29, 2014
Last update date Jul 31, 2019
Contact name Jing Shen
Organization name Columbia University
Street address 650 W. 168th St. Black Building Rm.1608
City New York
ZIP/Postal code 10032
Country USA
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (132)
GSM1317042 6089 adjacent non-tumor tissue
GSM1317043 6090 HCC tumor
GSM1317044 6093 adjacent non-tumor tissue
BioProject PRJNA236737

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE54503_450K.intensities.csv.gz 539.1 Mb (ftp)(http) CSV
GSE54503_RAW.tar 183.1 Mb (http)(custom) TAR
Processed data included within Sample table

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