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Sample GSM248748 Query DataSets for GSM248748
Status Public on Jun 22, 2008
Title NY224
Sample type RNA
 
Source name hepatocellular carcinoma
Organism Homo sapiens
Characteristics vascular invasion: Yes
bclc_staging: C
age: 42
Sex: M
code: resection
class: Proliferation
afp: 13787
tp53 mutation: 195G>GT | E271E/X
ctnnb1 mutation: 0
immunohistochemistry: pRPS6 : 1
immunohistochemistry: pIGFR1 : 0
immunohistochemistry: pAkt : 1
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
Relations
Reanalyzed by GSE51798
Reanalyzed by GSE119087

Data table header descriptions
ID_REF
VALUE log2 RMA probeset summary

Data table
ID_REF VALUE
1007_s_at 8.161466002
1053_at 8.106418278
117_at 6.417055806
121_at 8.454387266
1255_g_at 3.194187421
1294_at 7.804008119
1316_at 5.336301916
1320_at 5.26958389
1405_i_at 5.634380009
1431_at 8.585613499
1438_at 5.683722715
1487_at 8.045902099
1494_f_at 9.130254498
1552256_a_at 10.73495156
1552257_a_at 7.66768785
1552258_at 4.930317388
1552261_at 4.95070221
1552263_at 4.5685147
1552264_a_at 7.087152477
1552266_at 3.442918714

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM248748.CEL.gz 8.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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