|
| Status |
Public on Feb 20, 2013 |
| Title |
HCV-associated cirrhosis without HCC - patient 3 - specimen 2 |
| Sample type |
RNA |
| |
|
| Source name |
specimen obtained from explanted liver, CIR
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: HCV-associated cirrhosis without HCC
tissue: liver
gender: male
age: 47 years
patient identifier: CIR-3
|
| Treatment protocol |
Not applicable.
|
| Growth protocol |
Not applicable.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA, including microRNA, was extracted from frozen liver specimens using the miRNeasy Mini Kit (Qiagen).
|
| Label |
Biotin
|
| Label protocol |
500ng of total RNA, including microRNA, was poly(A) tailed and then directly ligated to a fluorescent dendrimer (a branched single- and double-stranded DNA molecule conjugated to biotin) using the FlashTag Biotin HSR RNA Labeling Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Hybridization was performed on Affymetrix GeneChip miRNA 2.0 arrays using standard protocols available at www.affymetrix.com. Standard Affymetrix protocols were also used for staining and washing of the arrays.
|
| Scan protocol |
Standard Affymetrix protocols was used for scanning of the arrays (available at www.affymetrix.com).
|
| Description |
CIR-3-2
microRNA
|
| Data processing |
Affymetrix probeset summaries were computed using the RMA algorithm. Data were then imported to BRB-ArrayTools (Version 4.2.1 - Stable Release (January 2012)) and subsequent data filtering, median normalization and statistical analyses were performed using this software.
Filtering: A first quantile normalization is included in the RMA method. After RMA, miRNAs with a percent of missing data exceeding 50% were excluded. The Sample data table contains only human miRNAs, which were included in the analysis.
|
| |
|
| Submission date |
Sep 10, 2012 |
| Last update date |
Feb 20, 2013 |
| Contact name |
Patrizia Farci |
| E-mail(s) |
pfarci@niaid.nih.gov
|
| Phone |
301-5942325
|
| Organization name |
National Institutes of Health
|
| Department |
National Institute of Allergy and Infectious Diseases
|
| Lab |
Hepatic Pathogenesis Section-Laboratory of Infectious Diseases
|
| Street address |
50 South Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892-8009 |
| Country |
USA |
| |
|
| Platform ID |
GPL14613 |
| Series (1) |
| GSE40744 |
Identification of microRNAs specifically expressed in HCV-associated hepatocellular carcinoma |
|
