|
| Status |
Public on Jul 08, 2020 |
| Title |
CON_9h_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Control_rep2
|
| Organism |
Mus musculus |
| Characteristics |
cell line: TAMH
|
| Treatment protocol |
Cell treatments consisted of exposure to either media alone or toxicologically relevant concentrations of diquat (18uM) or paraquat (126uM) for 9 h.
|
| Growth protocol |
TAMH cells were grown in Dulbecco's Modified Eagle Medium/Ham's F-12 (1:1) media supplemented with 100nm dexamethasone, 10nM nicotinamide, 0.1% (v/v) gentamicin, and an ITS premix containing insulin (5mg/mL), transferrin (5mg/mL) and selenium (5ng/mL). Cell passages between 30 and 40 were grown in a humidified incubator with 5% CO2 and 95% air at 37C. During passages, cells were incubated for approximately one minute with trypsin. Cell detachment was monitored using a microscope. Once detachment was complete, 5mL of 0.5mg/mL soybean trypsin inhibitor in Hank’s balanced salt solution was added before plating.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from TAMH cells dosed with 18uM DQ, 126uM PQ or control culture media at the 9-hour timepoints. For each treatment, cells were grown to confluence in three 150cm2 tissue culture dishes and dosed. At the end of each treatment, cells were harvested using a rubber scraper. Cell pellets were collected by centrifugation, and washed using ice-cold DPBS. Trizol reagent was added to the DPBS-washed pellet, vortexed and passed through a 22G needle multiple times to ensure complete cell lysis. Chloroform was then added, and the mixture was spun in a microcentrifuge at 8200g. The aqueous phase was isolated and dissolved in 70% ethanol. The resulting mixture was loaded onto a Qiagen RNeasy column. Purified total RNAs were eluted in sterile water according to the manufacturer’s protocol.
|
| Label |
biotin
|
| Label protocol |
RNA was processed for hybridization to Affymetrix Mouse Gene 2.1 ST array strips according to the manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
The standard hybridization protocol was used as recommended by Affymterix.
|
| Scan protocol |
Gene array strips were scanned using the Affymetrix GeneAtlas System at the Pacific University School of Phrmacy Research Laboratory.
|
| Description |
TAMH cells treated with media alone (control) for 9 h (replicate 2)
|
| Data processing |
Affymetrix Expression Console v1.1 RMA normalization log2
|
| |
|
| Submission date |
Jul 07, 2020 |
| Last update date |
Jul 08, 2020 |
| Contact name |
Brendan D Stamper |
| E-mail(s) |
stamperb@pacificu.edu
|
| Phone |
5033527287
|
| Organization name |
Pacific University
|
| Department |
Pharmacy
|
| Street address |
222 SE 8th Ave #451
|
| City |
Hillsboro |
| State/province |
OR |
| ZIP/Postal code |
97123 |
| Country |
USA |
| |
|
| Platform ID |
GPL17400 |
| Series (1) |
| GSE153959 |
Expression profiling of viologen hebicides in a mouse hepatocyte model |
|
