|
| Status |
Public on Jan 06, 2015 |
| Title |
KO_22726_422 |
| Sample type |
RNA |
| |
|
| Source name |
Rev-erb{alpha} KO Liver
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Nr1d1-/-
strain: C57Bl/6
gender: male
time: ZT10
|
| Treatment protocol |
Mice were euthanized at 5pm (ZT10).
|
| Growth protocol |
Wild-type (WT) C57Bl/6 mice were purchased from the Jackson Laboratories. The Rev-erb{alpha} -/- mice were obtained from B. Vennström, and backcrossed at least 7 generations with C57Bl/6 mice. 10-12 weeks old WT and mutant male mice were fed normal chow and housed under standard 12h-light/12h-dark cycles, with lights on (ZT0) at 7AM and lights off (ZT12) at 7PM. All animal care and procedures followed the guidelines of the Institutional Animal Care and Use Committee of the University of Pennsylvania.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each mouse liver sample using Trizol extraction followed by QIAGEN Rneasy Kit according to the manufacture's instructions.
|
| Label |
biotin
|
| Label protocol |
RNA from each liver was individually processed with the Ambion WT expression kit and GeneChIP WT terminal labeling and control kit (Affymetrix) and hybridized to the Mouse Gene 1.0 ST arrays (Affymetrix)
|
| |
|
| Hybridization protocol |
About 2ug cDNA was hybridized at 45°C for 16h to the Mouse Gene 1.0ST array. Arrays were washed and stained using the GeneChIP Hybridization, Wash and Stain Kit (Affymetrix).
|
| Scan protocol |
Array images were captured on a GCS3000 laser scanner (Affymetrix)
|
| Description |
Hepatic gene expression from Rev-erb{alpha} -/- mice at ZT10
|
| Data processing |
Raw images were analyzed using Partek Genomics Suite to extract individual probe intensities. Subsequent data analysis was performed using BioConductor. Raw probe signal values were background and quantile normalized and summarized by probe sets using the RMA algorithm. Final differential expression calls were determined using the SAM algorithm with 10% false-discovery rate and an absolute fold-change threshold of 1.3.
|
| |
|
| Submission date |
Jul 16, 2014 |
| Last update date |
Jan 07, 2015 |
| Contact name |
Logan J Everett |
| Organization name |
U.S. Environmental Protection Agency
|
| Department |
Office of Research and Development
|
| Lab |
Center for Computational Toxicology and Exposure
|
| Street address |
109 T.W. Alexander Dr
|
| City |
RTP |
| State/province |
North Carolina |
| ZIP/Postal code |
27711 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE59460 |
Circadian Enhancers Coordinate Multiple Phases of Rhythmic Gene Transcription In Vivo |
|
