|
| Status |
Public on Jan 08, 2009 |
| Title |
cirrhosis, biological rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
liver tissue with cirrhosis
|
| Organism |
Homo sapiens |
| Characteristics |
Tissue: cirrhosis
|
| Treatment protocol |
Five mm frozen section slides were made and stained with H&E for Pathologist evaluation to determine tumor content. After Pathologist evaluation, normal/necrotic tissue was macrodissected. Twenty 20 mm sections were performed in a 15 ml tube with 10 ml of Trizol.
|
| Growth protocol |
Fresh tissue specimens were collected from the consented patients in the operating room and processed immediately after extraction to minimize RNA degradation. Liver tissue samples were collected in liquid nitrogen or RNA later solution (Ambion, Inc, Austin, TX), and stored at -80°C until use.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.The precipitated product was further purified using RNeasy Mini Kit (Qiagen, CA).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using GeneChip® Scanner 3000 by Affymetrix.
|
| Description |
Gene expression using RMA method
|
| Data processing |
The CEL files from the two Affymetrix series were combined using the matchprobes package in the R programming environment. Thereafter, the RMA method in the R affy package was used to obtain probe set expression summaries.
|
| |
|
| Submission date |
Jan 07, 2009 |
| Last update date |
Jan 07, 2009 |
| Contact name |
Kellie J. Archer |
| E-mail(s) |
archer.43@osu.edu
|
| Phone |
(614) 247-6167
|
| Organization name |
Ohio State University
|
| Department |
Division of Biostatistics
|
| Street address |
1841 Neil Ave
|
| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43210 |
| Country |
USA |
| |
|
| Platform ID |
GPL571 |
| Series (1) |
| GSE14323 |
RMA expression data for liver samples from subjects with HCV, HCV-HCC, or normal liver |
|
