|
Status |
Public on Sep 16, 2014 |
Title |
HBV Cirrhosis-6 |
Sample type |
genomic |
|
|
Source name |
liver
|
Organism |
Homo sapiens |
Characteristics |
disease status: CirrHBV 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 |
542N
|
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 |
|