|
| Status |
Public on Feb 10, 2012 |
| Title |
457:36:00_UNP-April 2008_human_liver_EAM7429 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
457:36, human liver, Cy3
|
| Organism |
Homo sapiens |
| Characteristics |
disease_state: HCV-infected
tissue: liver
patient/unp identifier: 457
|
| Treatment protocol |
PCT study Utah Normal Pool (UNP): Liver biopsies used to compare transcriptional profiles of responders (with sustained virologic response:SVR) vs. non-responders to IFN treatment during HCV infection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Biopsy specimens were disrupted in TRIzol reagent (Life Technologies, Carlsbad, CA) using a Polytron homogenizer (PowerGene 700; Fisher Scientific, Pittsburgh, PA). Total RNA was isolated according to the manufacturer’s protocol. All total RNA samples were amplified using the RiboAmp RNA Amplification Kit (Arcturus/MDS, Mountain View, CA). The quality of amplified RNA was determined by capillary electrophoresis using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
|
| Label |
Cy3
|
| Label protocol |
The Agilent Two-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA and Cy5-cDNA probe preparation.
|
| |
|
| Channel 2 |
| Source name |
UNP-April 2008, human liver, Cy5
|
| Organism |
Homo sapiens |
| Characteristics |
disease_state: normal
tissue: liver
patient/unp identifier: UNP-April 2008
|
| Treatment protocol |
PCT study Utah Normal Pool (UNP): Liver biopsies used to compare transcriptional profiles of responders (with sustained virologic response:SVR) vs. non-responders to IFN treatment during HCV infection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Biopsy specimens were disrupted in TRIzol reagent (Life Technologies, Carlsbad, CA) using a Polytron homogenizer (PowerGene 700; Fisher Scientific, Pittsburgh, PA). Total RNA was isolated according to the manufacturer’s protocol. All total RNA samples were amplified using the RiboAmp RNA Amplification Kit (Arcturus/MDS, Mountain View, CA). The quality of amplified RNA was determined by capillary electrophoresis using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
|
| Label |
Cy5
|
| Label protocol |
The Agilent Two-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA and Cy5-cDNA probe preparation.
|
| |
|
| |
| Hybridization protocol |
The Agilent Two-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred ng of each RNA sample was hybridized to one Agilent 22K Human oligo array.
|
| Scan protocol |
Scanned on an Agilent Scanner G2505B US23502338.
Images were quantified using Agilent Feature Extraction Software (version A.8.1.1.1).
|
| Description |
Agilent Oligo Hyb
|
| Data processing |
The limma package was used. Background correction was performed (method=normexp, offset=1). Data was normalized within arrays with the loess method, then normalized between arrays with the quantile normalization method, and then log2 transformed.
|
| |
|
| Submission date |
Feb 08, 2012 |
| Last update date |
Apr 03, 2012 |
| Contact name |
Michael Katze |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Washington
|
| Department |
Microbiology
|
| Lab |
Michael G. Katze, Ph.D
|
| Street address |
Rosen Building 960 Republican St.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-4325 |
| Country |
USA |
| |
|
| Platform ID |
GPL7264 |
| Series (1) |
| GSE34798 |
Early transcriptional programming links progression to hepatitis C virus-induced severe liver disease in transplant patients |
|
