|
| Status |
Public on Dec 22, 2010 |
| Title |
HepG2_HNF4a&HNF4g_knockdown_control_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
HNF4a&HNF4g_knockdown_control
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
cell type: hepatocellular carcinoma
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).
|
| Label |
biotin
|
| Label protocol |
In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
|
| |
|
| Hybridization protocol |
10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.
|
| Scan protocol |
Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.
|
| Description |
HepG2_HNF4a&HNF4gknockdouwncontrol_try1
|
| Data processing |
Affymetrix Microarray Suite v5.0 with target intensity=100
|
| |
|
| Submission date |
Aug 28, 2009 |
| Last update date |
Dec 22, 2010 |
| Contact name |
Kenji Daigo |
| E-mail(s) |
daigo@lsbm.org
|
| Phone |
+81-3-5452-5236
|
| Fax |
+81-3-5452-5236
|
| Organization name |
University of Tokyo
|
| Department |
Research Center for Advanced Science and Technology
|
| Lab |
Departments of Molecular Biology and Medicine
|
| Street address |
#35 4-6-1 Komaba
|
| City |
Meguro |
| State/province |
Tokyo |
| ZIP/Postal code |
153-8904 |
| Country |
Japan |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE18973 |
Global expression analysis of HNF4alpha and HNFgamma-mediated transcriptional control |
| GSE18990 |
Proteomic analysis of native hepatocyte nuclear factor-4{alpha} (HNF4{alpha}) isoforms, phosphorylation status, and interactive cofactors. |
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