|
| Status |
Public on Mar 08, 2007 |
| Title |
Macrophage_Ifnbeta knock out_DMXAA_3h |
| Sample type |
RNA |
| |
|
| Source name |
Macrophage_Ifnbeta knock out
|
| Organism |
Mus musculus |
| Characteristics |
Strain;N8 on a C57BL/6 background
|
| Treatment protocol |
Thioglycollate-elicited murine peritoneal macrophages from IFN-beta knock out grown in media alone.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from the cells using TriReagent following the manufacturer's protocol (Molecular Research Center, Inc., Cincinnati, OH). Integrity of the RNA was confirmed by analysis with the Agilent 2100 Bioanalyzer (Palo Alto, CA) using the RNA 6000 LabChip® kit.
|
| Label |
SAPE
|
| Label protocol |
cRNA targets for the Affymetrix arrays were synthesized, labeled, and purified according to vendor's (Affymetrix) instructions. Briefly, 10 μg of total RNA was used to make double-stranded cDNA using reagents and protocols obtained from Invitrogen (Carlsbad, CA). Linear amplification was carried out by a modification of the Eberwine T7 method [56], and biotin was incorporated into the cRNA using the Enzo High Yield RNA Transcript labeling Kit (EnzoDiagnostics, Farmingdale, NY).
|
| |
|
| Hybridization protocol |
The Affymetrix arrays were hybridized and washed using the manufacturer's protocol. The arrays were then stained with streptavidin-phycoerythrin using the standard antibody amplification protocol (GeneChip® Expression Manual, Affymetrix, Inc., Santa Clara, CA).
|
| Scan protocol |
Affymetrix arrays were scanned with the Affymetrix GeneArray scanner at 488 nm and 3-micron resolution.
|
| Description |
Macrophage_Ifnbeta knock out
|
| Data processing |
The images were analyzed using Microarray Suite 5.0 software (MAS5; Affymetrix Inc., Santa Clara, CA). Expression ratios were computed by comparative analysis of MAS5 values. The data were filtered using MAS5's signal detection and change calls generated at recommended default settings. The ratios included were those that had present calls for signal detection or an increase or decrease call associated with the ratio
|
| |
|
| Submission date |
Mar 05, 2007 |
| Last update date |
Mar 18, 2009 |
| Contact name |
Stefaine Vogel |
| E-mail(s) |
svogel@som.umaryland.edu
|
| Phone |
(410) 706-4838
|
| Fax |
(410) 706-8607
|
| Organization name |
Univ. of Maryland
|
| Department |
Dept. of Microbiology and Immunology
|
| Street address |
660 W. Redwood Street
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21201 |
| Country |
USA |
| |
|
| Platform ID |
GPL8321 |
| Series (1) |
| GSE7194 |
The Chemotherapeutic Agent, 5,6-Dimethylxanthenone-4-Acetic Acid, |
|
