|
| Status |
Public on Oct 26, 2012 |
| Title |
OxPAPC BXD27/TyJ-9 |
| Sample type |
RNA |
| |
|
| Source name |
macrophage
|
| Organism |
Mus musculus |
| Characteristics |
gender: male
age: 16 weeks
strain: BXD27/TyJ
treatment condition: OxPAPC
cell type: macrophage
|
| Treatment protocol |
Cells were washed once with PBS the day after plating and incubated for 4 hours with 1%FBS DMEM media in control-treated cells, with control media plus 2ng/mL LPS (List Biological Inc., Campbell, CA, 201), or with control media plus 50μg/mL OxPAPC. OxPAPC was prepared from PAPC (Avanti Polar Lipids, Alabaster, AL) as previously described (Watson et al., 1997). After treatment, media was removed and cells were washed once with PBS.
|
| Growth protocol |
16 week male mice maintained on 12 hr light dark cycle fed a chow diet
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from macrophage samples using RNeasy columns (Qiagen, Valencia, CA), using on-column DNase digestion (Qiagen) and according to manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays.
|
| |
|
| Hybridization protocol |
The HT_MG-430A Array plate consists of 96 single MG-430A arrays arranged into standard SBS 96 well plate format. All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.
|
| Scan protocol |
Scanned images were subjected to visual inspection and a chip quality report was generated by the Affymetrix's GeneChip Operating System (GCOS) and Expression console (Affymetrix).
|
| Data processing |
The image data was processed using the Affymetrix GCOS algorithm utilizing the Robust Multiarray method (RMA) to determine the specific hybridizing signal for each gene. To avoid detecting variation signal intensity as an artifact of SNP variation in transcripts, prior to RMA normalization we excluded individual probes in probe-sets that aligned to sequences with SNPs, and excluded entire probe-sets where at least 8 of the probes in the set aligned to a sequence with SNPs.
|
| |
|
| Submission date |
Jun 13, 2012 |
| Last update date |
Oct 26, 2012 |
| Contact name |
Calvin Pan |
| Organization name |
UCLA
|
| Street address |
675 Charles Young Dr South
|
| City |
Los Angeles |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL8759 |
| Series (1) |
| GSE38705 |
Macrophage samples from the HMDP |
|
