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Sample GSM1633159 Query DataSets for GSM1633159
Status Public on Jun 28, 2021
Title Control_to_HCVflag_3
Sample type RNA
 
Source name Control_to_HCVflag_3
Organism Homo sapiens
Characteristics sample type: Cell (Huh7.5.1dif)
exposure with etiological agent: Mock infection
duration with etiological agent: 7 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 0.4630524
SH3GL2 0.4896543
RBM34 1.0560634
NCAPH 0.9673768
EGF 0.628258
TRIO 0.9275973
COL6A3 0.470903
ABLIM1 1.0113187
ITGA9 0.5330412
NTS 0.724168
SERPINB2 0.4896543
MMP7 0.4096066
PRKG2 0.3865868
EDG4 0.4575222
NOS2A 0.5000574
EPHA4 0.468342
SP100 0.5984793
FMO1 0.9250186
GPX2 0.5432447
ATP4B 0.4782775

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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