|
| Status |
Public on Jul 01, 2012 |
| Title |
Expt 1 - RA and TNF - repeat 1 - mAdbID:68681 |
| Sample type |
RNA |
| |
|
| Source name |
THP-1 RA and TNF
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: bone marrow
cell line: THP-1 cells
cell type: human myeloid cells
|
| Treatment protocol |
Treatment type: compound
Agent: at-RA (All-trans-Retinoic acid); TNF-alpha (tumor necrosis factor)
Treatment dose: 20 nM; 5ng/ml
Treatment time: 40 hours
In-vitro treatment: THP-1 cells were treated with 20 nM of RA for 16 hours, followed by treatment with 20nM of RA and 5 ng/ml of TNF-alpha for 24 hours. All cells were harvested at the 40 hour time point.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using Trizol extraction.
|
| Label |
biotin
|
| Label protocol |
Affymetrix labeling protocol: cDNA was synthesized, labeled, and purified according to vendor's (Affymetrix Inc., Santa Clara, CA) instructions.
|
| |
|
| Hybridization protocol |
Affymetrix Hybridization Protocol: The arrays were hybridized overnight at 45°C and washed using the fluidics station, then stained with streptavidin-phycoerythrin using the standard antibody amplification protocol (GeneChip Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA).
|
| Scan protocol |
Affymetrix Scanning Protocol: The arrays were scanned at 488 nm at 11-micron resolution using an Affymetrix Gene Chip Scanner.
|
| Description |
mAdb experiment ID: 68681
|
| Data processing |
Data were acquired using Genechip Operating Software (GCOS, Affymetrix) and uploaded onto the NCI website mAdb (http://nciarray.nci.nih.gov/). Data were analyzed by setting the signal floor value to 1 and centering each array to the median signal intensity. The results were expressed as log 2-transformed signal intensities and the log 2 of the median intensity for each array was set to 0.
|
| |
|
| Submission date |
Apr 30, 2011 |
| Last update date |
Jul 01, 2012 |
| Contact name |
A. Catharine Ross |
| E-mail(s) |
acr6@psu.edu
|
| Phone |
814 865 4721
|
| Fax |
814 863 6103
|
| URL |
http://nutrition.hhdev.psu.edu/faculty/profiles.cfm?facultyid=23
|
| Organization name |
Penn State
|
| Department |
Nutritional Sciences
|
| Street address |
110 Chandlee Laboratory
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE28995 |
THP-1 cell study: RA and TNF Treatments; RA time course |
|
