|
| Status |
Public on Nov 21, 2011 |
| Title |
OHT treated 3 h replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
OHT treated
|
| Organism |
Rattus norvegicus |
| Characteristics |
age: 3h
tissue: fibroblasts
genotype: c-Myc active
|
| Treatment protocol |
Cells were plated at a density of 20% confluence 24 h prior to the addition of OHT (248 nM; for treated cells) or an equal volume of ethanol (for mock-treated cells).
|
| Growth protocol |
HOMycER12 cells were cultured, under exponential growth conditions, in Dulbecco’s modified Eagle’s medium (Invitrogen) supplemented with 10% calf serum (Hyclone) at 37°C and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested using the TRIZOL® reagent (Invitrogen) according to the manufacturer’s protocol.
|
| Label |
biotin
|
| Label protocol |
RNA was converted into biotinylated single stranded cDNA as described in the Affymetrix user manual, GENE CHIP WHOLE TRANSCRIPT (WT) SENSE TARGET LABELING ASSAY which can be found at the following URL: https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf
|
| |
|
| Hybridization protocol |
As described in the Affymetrix user manual, GENE CHIP WHOLE TRANSCRIPT (WT) SENSE TARGET LABELING ASSAY which can be found at the following URL: https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf
|
| Scan protocol |
Scanning was carried on a GCS3000 scanner
|
| Description |
OHT treated 3 h replicate 1
probe_group_file: ENTREZG.pgf
meta-probeset_file: RnEx10stv1_Rn_ENTREZG_map.txt
|
| Data processing |
The Probe Logarithmic Intensity Error (PLIER) algorithm, from the Affymetrix Power Tools (APT) software package, was used to generate gene and exon expression scores. Probes were filtered and remapped to rat genes with Entrez ID according to the tables provided by the Microarray Laboratory of the Molecular and Behavioral Neuroscience Institute, University of Michigan.
|
| |
|
| Submission date |
Feb 26, 2010 |
| Last update date |
Nov 21, 2011 |
| Contact name |
Chui Sun Yap |
| E-mail(s) |
chuisunyap@gmail.com
|
| Organization name |
Duke-NUS
|
| Street address |
8, College Road
|
| City |
Singapore |
| ZIP/Postal code |
169857 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL10112 |
| Series (1) |
| GSE20550 |
A high resolution analyis of c-Myc-regulated gene expression dynamics. |
|
