|
| Status |
Public on Aug 08, 2014 |
| Title |
Rat_Liver_Vehicle__5d_NU_OG_Test_Rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Liver
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
mode_of_action: Control
chemical: Vehicle
vehicle: CORN OIL 100 %
route: ORAL GAVAGE
duration: 5 d
tissue: LIVER
animal_id: S020429-022
Sex: M
rna_id: 98048
hyb_date: Tue Feb 14 00:00:00 EST 2006
target_prep_date: Mon Jan 30 00:00:00 EST 2006
rna_extraction_date: Wed Jan 25 00:00:00 EST 2006
toxicology_experiment_date: Mon Apr 29 00:00:00 EDT 2002
vehicle_route_designation: NU_OG
|
| Treatment protocol |
Animals were acclimated for one week to the testing laboratory prior to dosing. After dosing, all liver samples were harvested as 100 mg punches using six millimeter disposable biopsy punches. An appropriately staggered schedule was employed so that the harvest times were accurate to ±30 min of the designed dose-to-harvest interval.
|
| Growth protocol |
Upon delivery to testing laboratory male Sprague-Dawley (Crl:CD® (SD)|GS BR) were housed individually in hanging, stainless steel, wire-bottom cages in a ventilated room (temperature, 22±3 ◦C; humidity, 30–70%; 12-h light:12-h dark cycle per day, 6:00 a.m.–6:00 p.m.) and received Certified Rodent Diet #5002 (PMI Feeds Inc.. Richmond, IN); chlorinated tap water was available ad libidum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Automated RNA isolation was performed according to the manufacture’s protocol using the RNeasy Kit from Qiagen (Germantown, MD).
|
| Label |
Biotin
|
| Label protocol |
cRNA target preparation and fragmentation was carried out using the GeneChip® One-Cycle Target Labeling and Control Reagents Kit (P/N 900493) from Affymetrix (Affymetrix Inc., Santa Clara, CA) according to the Affymetrix GeneChip® Expression Analysis Technical Manual (subsections: Total RNA and mRNA isolation for one-cycle target labeling, one-cycle cDNA synthesis, cleanup of double-stranded cDNA for both the one-cycle and two-cycle target labeling assays, synthesis of biotin-labeled cRNA for both the one-cycle and two-cycle target labeling assays, cleanup and quantification of biotin-labeled cRNA, and fragmenting the cRNA for target preparation) using 20 mg of isolated RNA. cRNA fragmentation mix was as follows: 20 μg RNA, 8 μL 5X Fragmentation Buffer, RNase-free water to a final volume of 40μL.
|
| |
|
| Hybridization protocol |
The array hybridization cocktail was as follows: 15 μg cRNA, 5 μL control oligo B2 (3 nM), 15 μL 20X eukaryotic hybridization controls (bioB, bioC, bioD and cre), 150 μL 2X hybridization mix, 10 μL DMSO, and water to a final volume of 300 μL. Arrays were hybridized for 16 hours in the GeneChip® hybridization oven 640.
|
| Scan protocol |
The arrays were washed, stained and scanned in accordance with protocols outlined in Affymetrix GeneChip® Expression Analysis Technical Manual (subsection: Eukaryotic Arrays: Washing, Staining, and Scanning) using a GeneChip® Fluidics Station 450.
|
| Description |
Test set
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
|
| |
|
| Submission date |
Jun 12, 2013 |
| Last update date |
Aug 08, 2014 |
| Contact name |
Leming Shi |
| E-mail(s) |
lemingshi@fudan.edu.cn
|
| Phone |
+86-18616827008
|
| Organization name |
Fudan University
|
| Department |
School of Life Sciences
|
| Lab |
Center for Pharmacogenomics
|
| Street address |
2005 Songhu Road
|
| City |
Shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
| |
|
| Platform ID |
GPL1355 |
| Series (2) |
|
