|
| Status |
Public on Oct 15, 2008 |
| Title |
Hepatitis/cirrhotic liver (bkg_005) |
| Sample type |
RNA |
| |
|
| Source name |
hepatitis/cirrhotic liver
|
| Organism |
Homo sapiens |
| Characteristics |
bkg_id: bkg_005
survival time (days): 1683
survival_status (0: alive_or_censored, 1:dead): 1
ethnicity: Japanese
egf level: Low
used for prognostic prediction: Yes
recurrence status (0: no recurrence of censored, 1: recurrence): 1
time to hcc recurrence (days): 682
early recurrence status (0: no recurrence of censored, 1: recurrence < 2 years): 1
late recurrence status (0: no recurrence of censored, 1: recurrence >= 2 years): 0
|
| Treatment protocol |
na
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Using 10µm sections taken from formalin-fixed paraffin-embeded tissue blocks, total RNA was extracted using High Pure Paraffin FFPE kit (Roche).
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Refer to the Illumina DASL Assay System Manual
|
| |
|
| Hybridization protocol |
Refer to the Illumina DASL Assay System Manual. Hybridization was performed for 4 DASL assay oligo pool (DAP)s, DAP1~4, including 1536 probes each on 4 separate microarrays.
|
| Scan protocol |
Refer to the Illumina DASL Assay System Manual
|
| Description |
none
|
| Data processing |
For each probe, Red and Green intensities are computed as average of single bead values. The final signal is the sum of the Red and Green intensities. Data were were then normalized using the cubic spline algorithm for each DAP.
|
| |
|
| Submission date |
Jan 10, 2008 |
| Last update date |
Jul 29, 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 |
GPL5474 |
| Series (3) |
| GSE10140 |
Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma (Training Set, Liver) |
| GSE10143 |
Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma |
| GSE20140 |
Combining Clinical, Pathology, and Gene Expression Data to Predict Recurrence of Hepatocellular Carcinoma |
|
| Relations |
| Affiliated with |
GSM1130194 |
