|
| Status |
Public on Mar 01, 2008 |
| Title |
rat_liver_day4_control_replicate1 |
| Sample type |
RNA |
| |
|
| Source name |
rat control liver
|
| Organism |
Rattus norvegicus |
| Characteristics |
Strain: Long-Evans (Turku/AB), Gender: Male, Age: 11-15 weeks, Tissue: liver, FeedRestriction: none, CornOil: 4 mL/kg
|
| Treatment protocol |
All rats were given corn oil (4 mL/kg) at the start of the experiment on day 0. Thereafter, the rats subjected to a 4-day APFR were provided the following amounts of feed daily (days 0-3): 18 – 12 – 9 – 6 g. The entire amount of feed was given at once every day during the light hours.
|
| Growth protocol |
Inbred male Long-Evans (Turku/AB) rats were employed in these studies. Our laboratory has a 20-year history of characterizing a wide range of physiological and toxicological responses of this strain (Pohjanvirta and Tuomisto, 1994). The rats were 11-15 weeks old at the start of the experiments and were free of specific pathogens as evidenced by regular health monitoring. The ambient conditions in the artificially-illuminated, air-conditioned animal room were: lighting 12/12 h (lights on at 7 a.m.), temperature 21.5 ± 1ºC, humidity 55 ± 10%. The rats were individually housed in stainless steel wire-mesh cages with free access to pelleted R36 feed (Ewos, Sweden) and water.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rats were euthanized by decapitation with a guillotine, and liver as well as a piece of inguinal WAT were rapidly excised. The adipose sample and small slices of liver (100-200 mg) were snap-frozen in liquid nitrogen and then stored at -80 ºC until analysis. Total RNA was extracted using RNeasy Mini Kits (Qiagen) according to the manufacturer’s instructions. DNase (Qiagen) was used to eliminate genomic DNA as recommended by the manufacturer. RNA yield was quantified by UV spectrophotometry and RNA integrity was verified with an Agilent 2100 Bioanalyser.
|
| Label |
biotin
|
| Label protocol |
The microarray facility at The Centre for Applied Genomics, Hospital for Sick Children (Toronto, ON) processed the gene chips as per the manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
The microarray facility at The Centre for Applied Genomics, Hospital for Sick Children (Toronto, ON) processed the gene chips as per the manufacturer’s instructions.
|
| Scan protocol |
The microarray facility at The Centre for Applied Genomics, Hospital for Sick Children (Toronto, ON) processed the gene chips as per the manufacturer’s instructions.
|
| Description |
The mRNA expression profile of the liver from a rat four days after corn oil vehicle was given.
|
| Data processing |
Array data were loaded into the R statistical environment (v2.4.1) using the affy package (v1.12.2) (Gautier et al., 2004) of the BioConductor open-source project (Gentleman et al., 2004). Data were investigated for spatial and distributional homogeneity. These data were pre-processed with a sequence-specific version of the RMA algorithm (Irizarry et al., 2003) termed GCRMA, as implemented in the gcrma package (v2.6.0) of BioConductor. Pre-processing was done with all four-day liver samples together as one group.
|
| |
|
| Submission date |
Sep 21, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Paul C Boutros |
| E-mail(s) |
Paul.Boutros@utoronto.ca
|
| Organization name |
Ontario Institute for Cancer Research
|
| Street address |
101 College Street, Suite 800
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 0A3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL1355 |
| Series (1) |
| GSE9121 |
Genome-wide effects of acute progressive feed restriction in liver and white adipose tissue |
|
