|
| Status |
Public on Jun 22, 2008 |
| Title |
NY204 |
| Sample type |
RNA |
| |
|
| Source name |
hepatocellular carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
vascular invasion: No
bclc_staging: A
age: 70
Sex: M
code: resection
class: CTNNB1
afp: 8.3
tp53 mutation: 0
ctnnb1 mutation: 260C>CT | T41T/I
immunohistochemistry: pRPS6 : 0
immunohistochemistry: pIGFR1 : 0
immunohistochemistry: pAkt : 0
immunohistochemistry: CTNNB1 : 1
used for prognostic prediction: yes
used for microrna profiling: Yes
uhrf1 study: Used in UHRF1 study (Mudbhary, et al., 2013)
|
| Growth protocol |
Tumors obtained at time of surgical resection or transplantation, according to institutional review board approved protocols
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized according to the standardized protocol from Affymetrix
|
| Scan protocol |
Affymetrix standard procedure
|
| Description |
91 hepatocellular carcinomas were obtained at the time of surgical resection or orthotopic transplantation.
|
| Data processing |
RMA. Supplementary data file also contains RMA based on AceView probeset remappings (PMID: 15850491, 16925834)
|
| |
|
| Submission date |
Dec 11, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Derek Chiang |
| E-mail(s) |
chiang@med.unc.edu
|
| Organization name |
University of North Carolina
|
| Department |
Department of Genetics
|
| Street address |
UNC Lineberger Cancer Center, 450 West Drive, CB #7295
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7295 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (4)
|
| GSE9829 |
Focal gains of VEGFA and molecular classification of hepatocellular carcinoma |
| GSE9843 |
Gene expression profiling of 91 hepatocellular carcinomas with hepatitis C virus etiology |
| GSE20238 |
Gene Signature to Identify Vascular Invasion in Human Hepatocellular Carcinoma |
| GSE20596 |
MicroRNA-Based Classification of Hepatocellular Carcinoma and Oncogenic Role of miR-517a |
|
| Relations |
| Reanalyzed by |
GSE51798 |
| Reanalyzed by |
GSE119087 |
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