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Sample GSM127087 Query DataSets for GSM127087
Status Public on Aug 12, 2006
Title Rat liver, untreated (control), extrated 48 hours after treatment (no treatment in this case), biological rep9
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 1715.8
1367453_at 1643.8
1367454_at 956.5
1367455_at 2109.1
1367456_at 2690.5
1367457_at 1061.3
1367458_at 817.5
1367459_at 4162.4
1367460_at 2020.8
1367461_at 703.2
1367462_at 2503
1367463_at 2324.1
1367464_at 1208.9
1367465_at 2327.2
1367466_at 1546.9
1367467_at 4529.9
1367468_at 1860.5
1367469_at 2798.3
1367470_at 1386
1367471_at 1164.7

Total number of rows: 31099

Table truncated, full table size 500 Kbytes.




Supplementary file Size Download File type/resource
GSM127087.CEL.gz 4.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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