|
| Status |
Public on Jun 28, 2021 |
| Title |
Patient3_DMSO |
| Sample type |
RNA |
| |
|
| Source name |
Patient3_DMSO
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Tissue
exposure with etiological agent: Cryptogenic
duration with etiological agent: n.a.
intervention: DMSO
duration of intervention: n.a.
cell line: liver
|
| Treatment protocol |
DMSO-differentiated Huh7.5.1 cells, HepG2-NTCP cells, Huh7.5.1-NTCP cells or clinical liver tissue slices were exposed to mock, HCV, HBV, or EtOH, and treated with interferon, direct-acting anti-HCVs, erlotinib, pioglitazone, or metformin or co-culture with hepatic stellate cell line, LX2. Cells/tissues were harvested for RNA isolation and gene expression profiling by NanoString assay.
|
| Growth protocol |
Huh7.5.1 cells, HepG2 cells, and clinical liver tissue slices were cultured in DMEM with 1% DMSO for 2 to 10 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using RNeasy kit (Qiagen) 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 |
Mar 12, 2015 |
| Last update date |
Jun 28, 2021 |
| Contact name |
Yujin Hoshida |
| E-mail(s) |
Yujin.Hoshida@UTSouthwestern.edu
|
| 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 |
GPL19886 |
| Series (2) |
| GSE66841 |
Gene expression profiles of Huh7.5.1 and HepG2 cells infected with HCV, HBV, HDV, and alcohol, and clinical liver tissues treated with various compounds of co-culture with LX2 cells |
| GSE66843 |
A cell-based model unravels drivers for hepatocarcinogenesis and targets for clinical chemoprevention |
|
