|
| Status |
Public on Jul 11, 2017 |
| Title |
DMSO control biological rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
DMSO control, C10
|
| Organism |
Mus musculus |
| Characteristics |
cell line: non-tumorigenic alveolar type II cell line C10
tissue of origin: lung
agent: DMSO
dose: control
time: 4hr
replicate: 1
|
| Treatment protocol |
C10 cells were treated with a 1:1 ratio PAH mixture (1-methlyanthracene:fluoranthene; 20uM each) for 4 or 8 hr time points.
|
| Growth protocol |
C10 cells were cultured in CMRL 1066 containing 10% FBS and 1% glutamate in a humidified atmosphere at 37 C, 5% CO2 , and 95% air. Following confluence, C10s underwent complete serum deprivation for 24 h in normal growth medium. Cells were then treated with PAH or vehicle (DMSO) directly to the plate from a stock solution.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from C10 cells using Macherey-Nagel NucleoSpin RNA II kit . Total RNA was quality tested using an Agilent Tapestation Bioanalyzer (Agilent) and only those samples passing with a RIN of 7 or higher were used.
|
| Label |
biotin
|
| Label protocol |
150 ng total RNA was processed according to the UserGuide GeneChip® WT PLUS Reagent Kit Rev3 protocol. Biotinylated cRNA was prepared using the Affymetrix TdT and biotinylated labeling reagents.
|
| |
|
| Hybridization protocol |
3.5ug of fragmented and biotinylated ss-cDNA was hybridizised to the Affymetrix Mouse Gene 2.0 ST arrays in the GeneChip Hybridization Oven 640 with rotation at 60 rpm for 16 hours at 45°C.
|
| Scan protocol |
GeneChips were scanned in an Affymetrix GCS3000 scanner with autoloader.
|
| Data processing |
Partek Genomics Suite 6.6 software was used to normalize the data. The CEL file data was RMA normalized and log 2 transformed.
|
| |
|
| Submission date |
Jul 20, 2016 |
| Last update date |
Jul 12, 2017 |
| Contact name |
Alison Kendall Bauer |
| E-mail(s) |
alison.bauer@ucdenver.edu
|
| Organization name |
University of Colorado Denver
|
| Department |
Environmental and Occupational Health
|
| Street address |
12850 E. Montview Blvd.; Rm 3125
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL16570 |
| Series (1) |
| GSE84649 |
Binary polycyclic aromatic hydrocarbon exposure alters the transcriptome inducing inflammation and inhibiting cell communication through p38 MAPK in lung cells |
|
