|
| Status |
Public on Sep 16, 2014 |
| Title |
HCV HCC-2 |
| Sample type |
genomic |
| |
|
| Source name |
liver
|
| Organism |
Homo sapiens |
| Characteristics |
disease status: HCCHCV
tissue: liver
|
| Growth protocol |
Normal hepatocytes were prepared as previously described (Zhu et al)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted by proteinase K treatment, phenol:chloroform extraction, and ethanol precipitation.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Infinium HD Methylation assay 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 Illumina iScan using standard recommended Illumina scanner setting
|
| Description |
259T
|
| Data processing |
Subset-quantile Within Array Normalization (SWAN) via R Bioconductor package minfi. The file Unmethylated_and_methylated_signal_intensities.txt contains the raw unmethylated and methylated signal intensities and is available on the series record.
|
| |
|
| Submission date |
Aug 26, 2014 |
| Last update date |
Sep 16, 2014 |
| Contact name |
Keith D Robertson |
| E-mail(s) |
robertson.keith@mayo.edu
|
| Phone |
507-266-4886
|
| Organization name |
Mayo Clinic
|
| Department |
Molecular Pharmacology & Experimental Therapeutics
|
| Lab |
Epigenetic Etiology of Human Disease Laboratory
|
| Street address |
200 First Street SW, Stabile 12-70
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55905 |
| Country |
USA |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE60753 |
Epigenetic signatures of alcohol abuse and hepatitis infection during hepatocarcinogenesis |
|
