|
| Status |
Public on Sep 23, 2021 |
| Title |
Huh75 HCV Tela rep1 |
| Sample type |
genomic |
| |
|
| Source name |
HCV Telaprevir
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: liver
cell line: Huh75
disease: HCC
|
| Treatment protocol |
Each cell line (referred to as the ‘parent’ cell line) was electroporated with full-length HCV JFH-1 RNA or JFH-1/GND (replication defective control) and selected with G418 for two weeks). Following establishment of clonal derivatives with stable HCV replication, cells were treated with either interferon-α (Sigma-Aldrich human recombinant interferon-α 407294-5MU; 1200IU/mL every 3 days for 2 weeks) or the direct-acting antiviral (DAA) Telaprevir (Incivek Telaprevir 375mg resuspended in DMSO; 30µM final concentration every 3 days for 2 weeks).
|
| Growth protocol |
All cultured cells were grown in DMEM with 10% FBS.
|
| 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 Methylation assay protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting
|
| Description |
Huh75_HCV_Tela_1
|
| Data processing |
Subset-quantile Within Array Normalization (SWAN) via R Bioconductor package "minfi".
matrix signal intensities value definition: Unmethylated and methylated signal intensities
matrix processed :Average Beta
|
| |
|
| Submission date |
Mar 03, 2021 |
| Last update date |
Sep 23, 2021 |
| 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 |
GPL21145 |
| Series (2) |
| GSE168185 |
Interferon drives hepatitis C virus scarring of the epigenome and creates targetable vulnerabilities following viral clearance [array] |
| GSE168186 |
Hepatitis C virus scarring of the epigenome and creates targetable vulnerabilities following viral clearance |
|
