|
| Status |
Public on Aug 10, 2011 |
| Title |
EtOH, WT, set 3 |
| Sample type |
RNA |
| |
|
| Source name |
F9 WT treated 8hr with EtOH
|
| Organism |
Mus musculus |
| Characteristics |
treatment: EtOH + cycloheximide
genotype: WT
cell line: F9
|
| Treatment protocol |
All-trans retinoic acid (atRA) (Cat. #R2625, Sigma, MD) and cycloheximide (chx) (Cat. #C7698, Sigma, MD) were dissolved in 100% ethanol (EtOH). The cells were pretreated with 1 µg/ml chx for 30 min before 7.5hr treatment with RA (1 µM) or vehicle (EtOH, 0.1%).
|
| Growth protocol |
F9 Wt and RARaKO cells were propagated in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 5% calf serum and 5% fetal calf serum and maintained at 95% humidity in 37°C incubators equilibrated with 10% CO2. Prior to plating the tissue culture dishes were coated with 0.3% gelatin. For the microarray analysis 2 million cells were plated on 10 cm tissue culture dishes were plated 16 hr prior to drug treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix MG-430.2 expression array. The chips were washed and stained in the Affymetrix Fluidics stations FS450.
|
| Scan protocol |
GeneChips were scanned using the GeneChip scanner 3000-7G.
|
| Description |
Set3
Gene expression data from EtOH treated WT cells
|
| Data processing |
The data were analyzed with GenespringGX version 7.0 using Affymetrix default analysis settings. The data sets were summarized using the GC-RMA algorithm, followed by a three-step normalization process consisting of: A) data transformation, converting values less than 0.01 to 0.01, B) chip normalization to the 50th percentile of total intensity and C) per gene normalization to median intensity. Genes were filtered by expression level to exclude genes with a raw signal below 100.
|
| |
|
| Submission date |
Aug 09, 2011 |
| Last update date |
Aug 10, 2011 |
| Contact name |
Kristian Bruun Laursen |
| E-mail(s) |
krl2004@med.cornell.edu
|
| Organization name |
Weill Cornell Medical College
|
| Department |
Pharmacology
|
| Lab |
Lorraine Gudas
|
| Street address |
1300 York Avenue
|
| City |
New York |
| ZIP/Postal code |
NY 10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE31280 |
Transcript level in F9 teratocarcinoma WT and RARalpha knockout in presence and absence of all-trans retinoic acid |
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