|
| Status |
Public on Mar 08, 2010 |
| Title |
Human hepatitis C virus liver biopsy sample 25 Replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
human hepatitis C virus liver biopsy sample
|
| Organism |
Homo sapiens |
| Characteristics |
sample: HCV positive
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen liver tissues were disrupted in Trizol Reagent (Invitrogen, Carlsbad, CA) using a Polytron homogenizer (PowerGene 700, Fisher Scientific), and total RNA was isolated according to the Trizol protocol. The quality of amplified RNA was evaluated by capillary electrophoresis using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA)
|
| Label |
Cy5
|
| Label protocol |
Probe labeling was performed using Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies, Santa Clara, CA). Total input RNA was 200-400ng per reaction.
|
| |
|
| Channel 2 |
| Source name |
common reference sample
|
| Organism |
Homo sapiens |
| Characteristics |
sample: Reference
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen liver tissues were disrupted in Trizol Reagent (Invitrogen, Carlsbad, CA) using a Polytron homogenizer (PowerGene 700, Fisher Scientific), and total RNA was isolated according to the Trizol protocol. The quality of amplified RNA was evaluated by capillary electrophoresis using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA)
|
| Label |
Cy3
|
| Label protocol |
Probe labeling was performed using Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies, Santa Clara, CA). Total input RNA was 200-400ng per reaction.
|
| |
|
| |
| Hybridization protocol |
A single experiment comparing two mRNA samples was done with four replicate Human 1A (V2)22K oligonucleotide expression arrays (Agilent Technologies) using the dye label reverse technique (Agilent Microarray protocol, version 2). The common reference sample was pooled RNA obtained from normal donor livers.
|
| Scan protocol |
Scanned on an Agilent G2505B Scanner
|
| Description |
Hepatitis C virus positive (HCV+) and negative (HCV-) tissue samples from percutaneous core needle biopsy specimens from liver transplantation patients were obtained according to clinical protocols at the University of Washington Medical Center.
|
| Data processing |
Agilent Feature Extraction v9.5.3, default mRNA parameters. For a complete description of the columns in the supplemental array data files, see Agilent's Reference Guide for Feature Extraction Software v9.5, http://www.chem.agilent.com/en-US/Search/Library/_layouts/Agilent/PublicationSummary.aspx?whid=50416&liid=1568
|
| |
|
| Submission date |
Mar 20, 2009 |
| Last update date |
Mar 08, 2010 |
| Contact name |
Xinxia Peng |
| E-mail(s) |
xinxiap@u.washington.edu
|
| Organization name |
University of Washington
|
| Department |
Microbiology
|
| Lab |
Katze
|
| Street address |
Rosen Building, 960 Republican St.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL887 |
| Series (2) |
| GSE15331 |
mRNA expression in human hepatitis c virus (HCV) liver biopsy samples |
| GSE15387 |
microRNA and mRNA expression in human hepatitis C Virus |
|
