|
| Status |
Public on Jan 31, 2014 |
| Title |
hcc_029 [tumor from HCC patient] |
| Sample type |
RNA |
| |
|
| Source name |
hcc_029
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: hepatocellular carcinoma
tissue: AS-FFPE tumor
%p-call: 0.176130000211314
inter-sample correlation: 0.585900092468532
prediction in as-ffpe: S2 (HCC subclass: alpha-fetoprotein positivity as well as MYC and AKT activation)
prediction confidence p-value in as-ffpe: 0.642452516
prediction in as-ffpe (%p-call>20%): NA
prediction confidence p-value in as-ffpe (%p-call>20%): NA
prediction in fc-ffpe: S1 (HCC subclass: aberrant activation of the TGF-beta/WNT signaling pathways)
prediction confidence p-value in fc-ffpe: 0.000333222
geo accession of fc-ffpe profile: GSM256444
|
| Treatment protocol |
FFPE tissue sections (10 micron-thick) sliced from 5~16-year-old FFPE blocks and archived for 6~7 years on glass slide
|
| Growth protocol |
na
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with Triazol reagent (Invitrogen) according to manufacturer’s protocol.
|
| Label |
biotin
|
| Label protocol |
Refer to the Illumina beadarray Assay System Manual
|
| |
|
| Hybridization protocol |
Refer to the Illumina beadarray Assay System Manual
|
| Scan protocol |
Refer to the Illumina beadarray Assay System Manual
|
| Description |
Sample name: hcc_029
|
| Data processing |
For each probe, replicated mesurements (beads) were averaged after removing outliers by Genome Studio software v.3 (Illumina). Data were were then normalized using qubic spline algorithm implemented in GenePattern Illumina normalizer module (www.broadinstitute.org/genepattern) after setting a floor value of 1.
|
| |
|
| Submission date |
Apr 27, 2013 |
| Last update date |
Jan 31, 2014 |
| Contact name |
Yujin Hoshida |
| Organization name |
University of Texas Southwestern Medical Center
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL13369 |
| Series (2) |
| GSE46444 |
Gene-expression profiles of archived section of formalin-fixed paraffin-embedded (AS-FFPE) liver and tumor tissues from hepatocellular carcinoma patients |
| GSE47595 |
Gene-expression profiles of archived section of formalin-fixed paraffin-embedded (AS-FFPE) liver and tumor tissues from hepatocellular carcinoma patients (Illumina and Nanostring) |
|
| Relations |
| Affiliated with |
GSM256444 |
