|
| Status |
Public on Jul 01, 2013 |
| Title |
U2OS DMSO treated, Replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
U2OS DMSO treated
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U2OS
cell type: osteosarcoma
agent: DMSO (control for Nutlin-treated cells)
|
| Treatment protocol |
for No Treatment: none; Doxorubicin: 0.6 ug/ml Doxorubicin for 24 hrs; DMSO; 0.1% DMSO for 24 hrs; Nutlin: 10 uM Nutlin-3 for 24 hrs
|
| Growth protocol |
U2OS expressing endogenous wild-type p53 was maintained in McCoy's 5A medium supplemented with 10% fetal calf serum and 1% Penicillin/Streptomycin at 37ºCin 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from U2OS cells was extracted using the RNeasy Midi kit with DNAse treatment according to the manufacturer's protocol (Qiagen). Quantity and quality was determined by Nanodrop ND1000 and Agilent 2100 Bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol.
|
| |
|
| Hybridization protocol |
12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.
|
| Scan protocol |
Arrays were scanned in an Affymetrix Scanner 3000.
|
| Description |
U2OS cells treated with 0.1% DMSO for 24 hr, control for Nutlin-treated cells
|
| Data processing |
data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files..
|
| |
|
| Submission date |
Apr 30, 2013 |
| Last update date |
Jul 01, 2013 |
| Contact name |
NIEHS Microarray Core |
| E-mail(s) |
microarray@niehs.nih.gov, liuliw@niehs.nih.gov
|
| Organization name |
NIEHS
|
| Department |
DIR
|
| Lab |
Microarray Core
|
| Street address |
111 T.W. Alexander Drive
|
| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE46493 |
Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells (Affymetrix) |
| GSE46642 |
Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells |
|
