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Sample GSM1633149 Query DataSets for GSM1633149
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
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
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

Data table header descriptions
ID_REF
VALUE Normalized transcript abundance

Data table
ID_REF VALUE
FSHB 0.5273781
SH3GL2 0.5068092
RBM34 1.0435671
NCAPH 0.9885571
EGF 0.6849797
TRIO 0.9696356
COL6A3 0.5273781
ABLIM1 0.9877064
ITGA9 0.6115326
NTS 0.7729484
SERPINB2 0.4447903
MMP7 0.5192268
PRKG2 0.4447903
EDG4 0.4887149
NOS2A 0.5871693
EPHA4 0.5086628
SP100 0.6297966
FMO1 0.7967414
GPX2 0.568454
ATP4B 0.5030149

Total number of rows: 262

Table truncated, full table size 4 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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