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Status |
Public on Jun 28, 2021 |
Title |
HCV10^4/ml_3 |
Sample type |
RNA |
|
|
Source name |
HCV10^4/ml_3
|
Organism |
Homo sapiens |
Characteristics |
sample type: Cell (Huh7.5.1dif) exposure with etiological agent: HCV Jc1 infection (TCID50/mL=10^4/mL) duration with etiological agent: 10 days intervention: None duration of intervention: n.a. cell line: Huh7.5.1
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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
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|
|
Hybridization protocol |
Refer to the NanoString nCounter Assay System Manual
|
Scan protocol |
Refer to the NanoString nCounter Assay System Manual
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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.
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|
|
Submission date |
Mar 12, 2015 |
Last update date |
Jun 28, 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) |
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 |
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