|
| Status |
Public on Jan 31, 2014 |
| Title |
bkg_052 [liver from HCC patient] |
| Sample type |
RNA |
| |
|
| Source name |
bkg_052
|
| Organism |
Homo sapiens |
| Characteristics |
prediction in as-ffpe (ncounter): poor
prediction confidence p-value in as-ffpe (ncounter): 0.003498251
prediction in fc ffpe (dasl): good
prediction in fc ffpe (dasl): 0.002
prediction in fc ffpe (re-prediction within these 24 samples): poor
prediction confidence p-value in fc ffpe (re-prediction within these 24 samples): 0.12043978
geo accession of fc-ffpe profile: GSM256376
disease state: hepatocellular carcinoma
tissue: AS-FFPE liver (cirrhotic)
|
| 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
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with High Pure RNA paraffin kit (Roche) according to manufacturer’s protocol.
|
| Label |
biotin
|
| Label protocol |
standard NanoString nCounter Assay protocol
|
| |
|
| Hybridization protocol |
standard NanoString nCounter Assay protocol
|
| Scan protocol |
standard NanoString nCounter Assay protocol
|
| Data processing |
For each probe, transcript count data were log2 transformed and scaled by geometric mean of the normalization genes by NanoString normalizer module of GenePattern toolkit (www.broadinstitute.org/genepattern) after setting a floor value of 1.1.
|
| |
|
| Submission date |
Jun 03, 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 |
GPL17230 |
| Series (2) |
| GSE47594 |
Gene-expression profiles of archived section of formalin-fixed paraffin-embedded (AS-FFPE) liver 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) |
|
