|
| Status |
Public on Feb 17, 2017 |
| Title |
N7 [methylation] |
| Sample type |
genomic |
| |
|
| Source name |
Adjacent normal from patient #7
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: hepatocellular carcinoma (HCC) patient
patient id: patient #7
gender: Male
age: 42
tumor size (cm): 38
hbv infection: Yes
cirrhosis: Yes
tissue: Adjacent normal
|
| Treatment protocol |
None
|
| Growth protocol |
Fresh-frozen clinical tissue samples
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sample DNA was extracted using DNeasy Blood &Tissue Kit (Cat#69506, QIAGEN, GmBH, Germany), following the manufacturer’s instructions. We used Nano Drop (Cat#ND-1000, Thermo Fisher, Waltham, MA, US) and ran a 1% agarose gel electrophoresis to check the quantity and quality of purified DNA.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Data processing |
GenomeStudio Methylation Module v1.8, Methylated signal intensity/( Mehtylated signal intensity + Unmethylated signal intensity + 100 )
normalized data matrix (*.txt) contains Average Beta values
|
| |
|
| Submission date |
Jan 27, 2016 |
| Last update date |
Feb 17, 2017 |
| Contact name |
Jin Gu |
| E-mail(s) |
[email protected]
|
| Organization name |
Tsinghua University
|
| Department |
Automation
|
| Street address |
FIT Building 1-112C
|
| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE77269 |
DNA methylation analysis of hepatocellular carcinoma with portal vein tumor thrombosis |
| GSE77276 |
The molecular landscape of hepatocellular carcinoma with portal vein tumor thrombosis |
|
