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Sample GSM127052 Query DataSets for GSM127052
Status Public on Aug 12, 2006
Title Rat liver, treated with ANIT, 125 mg/kg in corn oil per orally, extrated 48 hours after treatment, biological rep4
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 1890.9
1367453_at 1789.2
1367454_at 1295.5
1367455_at 3203.4
1367456_at 3134.7
1367457_at 1103
1367458_at 1111.2
1367459_at 4677.1
1367460_at 3037.6
1367461_at 665.4
1367462_at 3666.6
1367463_at 2176.1
1367464_at 1381.4
1367465_at 2635.6
1367466_at 1536.9
1367467_at 3204
1367468_at 2108.1
1367469_at 3569.9
1367470_at 1737.6
1367471_at 1161.5

Total number of rows: 31099

Table truncated, full table size 499 Kbytes.




Supplementary file Size Download File type/resource
GSM127052.CEL.gz 4.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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