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Sample GSM127079 Query DataSets for GSM127079
Status Public on Aug 12, 2006
Title Rat liver, untreated (control), extrated 48 hours after treatment (no treatment in this case), biological rep1
Sample type RNA
 
Source name Rat liver, left lateral lobe
Organism Rattus norvegicus
Characteristics Male Sprague-Dawley (Crl:CD(SD)IGS Br
Age: between 5 and 6 weeks old
Biomaterial provider Scantox, Lille Skensved, Denmark
Treatment protocol The animals were sacrificed 48 hours after treatment and organs were frozen for later analysis. Tissue samples of the left lateral lobe of the liver were snap frozen in liquid nitrogen, transferred to dry ice and stored at approximately -80?C
Extracted molecule total RNA
Extraction protocol Frozen liver samples were homogenized in 2 ml TRIzol® reagent (Invitrogen ; Life Technologies, Scotland) using an Ultra Turrax T25 basic homogenizer (IKA Labortechnik; IKA-Werke, Staufen, Germany). Chloroform (400 ?l) was added and homogenized samples were shaken vigorously by hand for 15 seconds. Phase separation was achieved by centrifugation for 15 min at 10,000 × g at 4°C. Total RNA from the aqueous phase was purified using the RNeasy 96 Qiagen vacuum system following the “Clean-up” procedure.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230 version 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned on GeneChip® Scanner 3000 7G 4C
Description Gene expression data from rat liver 48 hours after treatment with compound.
Data processing The data were analyzed with RMA. R was used with the affy package. Expresso with the following settings (bgcorrect.method=rma, normalize.method = quantiles.robust, pmcorrect.method=pmonly, summary.method=liwong) was used to normalize
 
Submission date Aug 11, 2006
Last update date Aug 09, 2011
Contact name Jeppe Skytte Spicker
E-mail(s) skytte@cbs.dtu.dk
Organization name Danish University of Technology
Department CBS
Street address Building 208
City Lundtofte
ZIP/Postal code XXXX
Country Denmark
 
Platform ID GPL1355
Series (1)
GSE5509 Expression data from Rat liver 48 hours after treated with different toxic compounds.
Relations
Reanalyzed by GSE31289

Data table header descriptions
ID_REF
VALUE RMA-calculated Signal intensity

Data table
ID_REF VALUE
1367452_at 1372.8
1367453_at 1524.6
1367454_at 921.1
1367455_at 1946.4
1367456_at 2475.3
1367457_at 1163.9
1367458_at 1201.1
1367459_at 4338.8
1367460_at 2741.1
1367461_at 678
1367462_at 3218.2
1367463_at 1777.4
1367464_at 1216.8
1367465_at 2441.3
1367466_at 1614.4
1367467_at 3078.6
1367468_at 2007.4
1367469_at 3299
1367470_at 1458.2
1367471_at 927.3

Total number of rows: 31099

Table truncated, full table size 500 Kbytes.




Supplementary file Size Download File type/resource
GSM127079.CEL.gz 4.0 Mb (ftp)(http) CEL

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