NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM230987 Query DataSets for GSM230987
Status Public on Mar 01, 2008
Title rat_liver_day10_control_replicate2
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 10-day APFR (days 0-9): ad libitum – 16 – 14 – 11 – 8 – 6 – 4 – 4 – 2 – 1 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 powdered 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 ten 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 ten-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

Data table header descriptions
ID_REF
VALUE GCRMA signal

Data table
ID_REF VALUE
1367452_at 10.50396584
1367453_at 9.971396512
1367454_at 10.018384
1367455_at 12.23490131
1367456_at 12.2524015
1367457_at 9.032832704
1367458_at 8.189166311
1367459_at 12.98478892
1367460_at 11.73821919
1367461_at 9.886625716
1367462_at 10.88731937
1367463_at 11.37027925
1367464_at 10.07496104
1367465_at 10.26063429
1367466_at 9.969203404
1367467_at 12.11015649
1367468_at 9.25590279
1367469_at 12.75769078
1367470_at 10.83593627
1367471_at 9.556848453

Total number of rows: 31099

Table truncated, full table size 698 Kbytes.




Supplementary file Size Download File type/resource
GSM230987.CEL.gz 2.7 Mb (ftp)(http) CEL
GSM230987.DAT.gz 50.4 Mb (ftp)(http) DAT
GSM230987.EXP.gz 485 b (ftp)(http) EXP
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap