|
| Status |
Public on Dec 22, 2021 |
| Title |
JHUc003 |
| Sample type |
RNA |
| |
|
| Source name |
liver biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: liver
diagnosis: chronic hepatitis C + HIV
future fibrosis progression (2 or more f stages within 5 years): Yes
|
| Treatment protocol |
FFPE tissue sections (10 micron-thick) sliced from FFPE blocks
|
| Growth protocol |
na
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using High Pure RNA Paraffin kit (Roche) according to manufacturer’s protocol.
|
| Label |
biotin
|
| Label protocol |
Refer to the NanoString nCounter Assay System Manual
|
| |
|
| Hybridization protocol |
Refer to the NanoString nCounter Assay System Manual
|
| Scan protocol |
Refer to the NanoString nCounter Assay System Manual
|
| 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 |
Aug 05, 2021 |
| Last update date |
Dec 22, 2021 |
| 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) |
| GSE85547 |
Prognostic Liver Signature profiles in biopsy tissues from chronic hepatitis C patients with HIV co-infection followed for fibrosis progression |
| GSE85550 |
Molecular signature predictive of long-term liver fibrosis progression to inform anti-fibrotic drug development |
|
