|
| Status |
Public on Aug 15, 2014 |
| Title |
unpaired liver biopsy with relapse rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
unpaired liver biopsy with relapse rep 1
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: unpaired liver biopsy with relapse
gender: M
age: 47
agent/dose: SOF-400mg/RBV-1200mg
|
| Treatment protocol |
Paired liver biopsies: Core liver biopsies obtained transcutaneously with an 18-guage needle were immediately placed in RNAlater (Ambion) and stored at -80°C PBMC: Blood samples were collected at or prior to initiation of treatment, within 6-11 days of treatment initiation, and at EOT. Blood cells were Ficoll separated from whole blood on the day of collection and re-suspended in RPMI containing 10% FCS and 7.5% DMSO for storage in liquid nitrogen. EOT liver biopsies: Liver biopsies collected in RNAlater then thawed and homogenized in TRizol (Thermofisher Scientific, Waltham, MA) using the FastPrep Green lysing matrix (MP Biomedicals, Solon, OH), combined with 200 µL of 1-bromo-3-chloropropane (Sigma-Aldrich), and centrifuged at 4 °C at 16,000 x g for 15 minutes.
|
| Growth protocol |
Sixty treatment-naïve, chronic HCV genotype-1 patients were treated with SOF (400 mg daily) and low (600 mg daily) or weight-based (400mg AQM with 600mg QPM if < 75kg or 600mg BID if >75kg) RBV for 24 weeks and from this group certain members were selected for the three different microarray experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy 96 kit according to manufacturer’s recommendations
|
| Label |
biotin
|
| Label protocol |
RNA was used to prepare biotinylated aRNA and hybridized to the HGu219 plate; DNA microarray probes were synthesized using the Ovation Pico WTA system (Nugen Inc., San Carlos, CA) and used for hybridization on the Affymetrix GeneChip Human Gene 2.0 ST array
|
| |
|
| Hybridization protocol |
Samples starting with 16P and 24U were hybridized onto Affymetrix HGU219 and samples 5142-5166 were hybridized to GeneChip human gene 2.0 ST arrays according to manufacturer's recommendations
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.
|
| Description |
Gene expression data from_unpaired liver biopsy with relapse rep 1
|
| Data processing |
The data were analyzed with EC 1.1 using Affymetrix default analysis with an RMA-sketch normalization method.
|
| |
|
| Submission date |
Oct 25, 2013 |
| Last update date |
Aug 15, 2014 |
| Contact name |
Dan Sturdevant |
| E-mail(s) |
dsturdevant@niaid.nih.gov
|
| Phone |
4063639248
|
| Organization name |
NIH
|
| Department |
NIAID
|
| Lab |
RTS
|
| Street address |
903 S 4th street
|
| City |
Hamilton |
| State/province |
MT |
| ZIP/Postal code |
59840 |
| Country |
USA |
| |
|
| Platform ID |
GPL16686 |
| Series (1) |
| GSE51699 |
Endogenous Intrahepatic Interferons and Association with IFN-free HCV Treatment Outcome |
|
