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Data released on February 05, 2015

Validation Data For Capture-based whole genome promoter bisulfite-seq for 8 pairs of HCC tumor and non-tumor liver (NTL) samples

Fei, G; Lu, H (2015): Validation Data For Capture-based whole genome promoter bisulfite-seq for 8 pairs of HCC tumor and non-tumor liver (NTL) samples GigaScience. http://dx.doi.org/10.5524/100120 RIS BibTeX Text

Epigenetic alterations such as aberrant DNA methylation of promoter and enhancer regions that lead to atypical gene expression have been associated with carcinogenesis. In HCC, genome-wide analysis of methylation is only recently used. Improving the analytic outcomes with even higher resolution is required to identify previously unknown regions and genes differentially methylated in HCC for better understanding of altered methylation in hepatocarcinogenesis. In this study, we used the optimized liquid hybridization capture-based bisulfite sequencing (LHC-BS) approach to quantitatively analyze 1,374,799 CpG sites of individual samples from 8 pairs of HCCs and their adjacent tissues (see GEO dataset linked below).
Here we present the gene specific methylation data of 12 genes of interested that were identified with altered promoter methylation in the genome-wide study. We utilized the Illumina MiSeq platform to assess DNA methylation levels in an additional 78 HCC tumour/normal matched pairs of samples. In correlation with the gene expression profiles, we were able to confirm 7 of the 12 genes, including SMAD6, IFITM1, LRRC4, CHST4, and TBX15 with promoter hypermethylation; and CCL20 and NQO1 with promoter hypomethylation in HCCs.

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Accessions (data not in GigaDB):

GEO: GSE55759

Epigenomic

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Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
100-HCC9606HumanhumanHomo sapiens Age:35
Body site:liver
Cancer stage:II-III
...
+
100-NTL9606HumanhumanHomo sapiens Age:35
Body site:liver
Cancer stage:NA
...
+
101-HCC9606HumanhumanHomo sapiens Age:54
Body site:liver
Cancer stage:II-III
...
+
101-NTL9606HumanhumanHomo sapiens Age:54
Body site:liver
Cancer stage:NA
...
+
102-HCC9606HumanhumanHomo sapiens Age:54
Body site:liver
Cancer stage:II-III
...
+
102-NTL9606HumanhumanHomo sapiens Age:54
Body site:liver
Cancer stage:NA
...
+
104-HCC9606HumanhumanHomo sapiens Age:35
Body site:liver
Cancer stage:II-III
...
+
104-NTL9606HumanhumanHomo sapiens Age:35
Body site:liver
Cancer stage:NA
...
+
105-HCC9606HumanhumanHomo sapiens Age:44
Body site:liver
Cancer stage:II-III
...
+
105-NTL9606HumanhumanHomo sapiens Age:44
Body site:liver
Cancer stage:NA
...
+
Displaying 1-10 of 156 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
100-NTLMethylome dataFASTQ1.79 MB2015-02-05
100-NTLMethylome dataFASTQ2.13 MB2015-02-05
100-NTLTabular dataTSV24.3 KB2015-02-05
100-HCCMethylome dataFASTQ1.7 MB2015-02-05
100-HCCMethylome dataFASTQ1.96 MB2015-02-05
100-HCCTabular dataTSV24.33 KB2015-02-05
101-NTLMethylome dataFASTQ2.22 MB2015-02-05
101-NTLMethylome dataFASTQ2.56 MB2015-02-05
101-NTLTabular dataTSV24.78 KB2015-02-05
101-HCCMethylome dataFASTQ1.88 MB2015-02-05
Displaying 1-10 of 468 File(s).

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