|
| Status |
Public on Nov 01, 2013 |
| Title |
HAK-1A HCC clone overexpressing TCF-4J under normoxia |
| Sample type |
RNA |
| |
|
| Source name |
HAK-1A HCC clone overexpressing TCF-4J under normoxia
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HAK-1A hepatocellular carcinoma (HCC) cell
|
| Treatment protocol |
To generate the stable clones overexpressing TCF-4J or TCF-4K, HAK-1A cells were transfected with each plasmid construct by using TransIT-LT1 Reagent (Mirus Bio Co., Madison, WI) according to the manufacturers’ instructions, and selected by G418 (Invitrogen, Carlsbad, CA). Empty vector (EV) clone and HCV Core protein-expressing clones were also prepared by the same method. The expression of exogenous TCF-4 isoform in the established stable clones was confirmed by Western blot analysis. These clones were maintained under either hypoxic (0% Oxgen) or normoxic (20% Oxygen) conditions, and used for the microarray analysis.
|
| Growth protocol |
HAK-1A cells were maintained in DMEM supplemented with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from RNA using Agilent Low-Input Quick Amp Labeling Kit (One-color) (Agilent Technologies, Santa Clara, CA) according to the manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
Cy3-labelled cRNA was fragmented and tohybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) using the Gene Expression Hybridization Kit as recommended by Agilent Technologies.
|
| Scan protocol |
The slides were scanned using a DNA Microarray Scanner (Agilent Technologies) immediately after washing.
|
| Data processing |
The scanned images were analyzed with Agilent Feature Extraction Software (Agilent Technologies). The data were subjected to quantile normalization. The normalization was performed using R software (R Development Core Team).
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| |
|
| Submission date |
Nov 26, 2012 |
| Last update date |
Nov 01, 2013 |
| Contact name |
Miran Kim |
| E-mail(s) |
miran_kim@brown.edu
|
| Organization name |
Liver Research Center, Rhode Island Hospital and Warren Alpert Medical School of Brown University
|
| Street address |
55 Claverick St
|
| City |
Providence |
| State/province |
RI |
| ZIP/Postal code |
02903 |
| Country |
USA |
| |
|
| Platform ID |
GPL13497 |
| Series (1) |
| GSE42512 |
Human HAK-1A hepatocellular carcinoma (HCC) cells: TCF-4J-overexpressing clone (under normoxia) vs. TCF-4K-overexpressing clone (under normoxia) |
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