|
| Status |
Public on Oct 15, 2014 |
| Title |
Fasted liver wild-type rep4 |
| Sample type |
RNA |
| |
|
| Source name |
Liver, 2-month old male, fasted, wild-type
|
| Organism |
Mus musculus |
| Characteristics |
gender: Male
strain: 129/S6 (taconic)
tissue: Liver
animal age: 2-months
nutritional status: Overnight fast (~16 hours)
genotype/variation: Wild-type
|
| Treatment protocol |
Mice were fasted overnight for ~ 16 hours and sacrificed between 9 and 10 AM.
|
| Growth protocol |
Mice were maintained on a 12 hr day/night cycle with the lights coming on a 8 AM. They were given water and low fat rodent chow Ad libitum. They were killed mid-morning.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total liver RNA was extracted with Trizol (life technologies) following standard protocol
|
| Label |
Biotin
|
| Label protocol |
Labeled cDNA was prepared from 250 ng of total RNA using the standard procedure of the Ambion WT Expression Kit (Life Technologies)
|
| |
|
| Hybridization protocol |
Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Mouse Gene 2.0 ST GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. A GeneChip 3000 7G scanner was used to collect fluorescence signal.
|
| Scan protocol |
A GeneChip 3000 7G scanner was used to collect fluorescence signal.
|
| Description |
Fasted_liver-4
|
| Data processing |
Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of the microarray sectors was set as background and subtracted from all features in that sector.
|
| |
|
| Submission date |
Apr 25, 2014 |
| Last update date |
Oct 15, 2014 |
| Contact name |
John Pehrson |
| E-mail(s) |
pehrson@vet.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Street address |
3800 Spruce Street
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL16570 |
| Series (2) |
| GSE57088 |
Expression data from fasted macroH2A1/2 double knockout adult mouse liver |
| GSE57089 |
Role of MacroH2A core histone variants in liver |
|
