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Sample GSM186709 Query DataSets for GSM186709
Status Public on Jun 11, 2007
Title C57BL/6J female number 1, DNFB-treated allergic ear (#4_Wt-Tr-3)
Sample type RNA
 
Source name whole ear tissue, DNFB-treated allergic ear 48h after 2nd challenge
Organism Mus musculus
Characteristics C57BL/6J female number 1, 2 months old, whole ear tissue, DNFB-treated allergic ear
Treatment protocol DNFB (1-fluoro-2,4 dinitrobenzene, Merck) was diluted in acetone/olive oil (4:1) immediately before use. Mice without any skin lesions and ear tags were sensitized by painting 50 µl of 0.2% DNFB on the shaved abdomen on two consecutive days. Controls were treated with 50 µl acetone-olive oil. For elicitation of CHS, ears of mice were painted with 10 µl of 0.3% DNFB on day 5. Ear thickness was measured 24 h, 48 h and 72 h after challenge using an engineers micrometer (Oditest, Fa. Kroeplin, Schlüchtern, Germany) and ear swelling was calculated in each mouse as the difference in ear thickness between the unchallenged control (left) and the challenged (right) ear. Experimental mice of either wildtype C57BL/6J line or CB1/CB2 double knockout mice (Cnr1-/-/Cnr2-/-) were used in the age of 8-10 weeks. Right ears of the mice were treated with DNFB, whereas left ears were untreated and used as control. All experimental animals were females. DNFB treated and control ears from three Cnr1-/-/Cnr2-/- and three Cnr1+/+/Cnr2+/+ mice were used for the gene expression analysis. Whole ear tissue was harvested 48h after the 2nd DNFB-challenge and immediately snap frozen in liquid nitrogen. Tissue was stored on –80°C until RNA isolation.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Trizol (Invitrogen) and purified using RNeasy columns (Qiagen). RNA intergrity was assessed using Agilent 2100 Bioanalyzer (www.agilent.com). Five μg of total RNA was converted into double-stranded cDNA using T7-oligodT coupled primers. Ten μg of fragmented cRNA samples were hybridized to MG_430 2.0 Affymetrix GeneChips following the manufacturer´s instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on MG_430 2.0 Affymetrix GeneChips . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol We used an Affymetrix GeneChip® Scanner 3000.
Description wt mouse number 1
Data processing Microarry expression values were generated using GC-RMA using software ArrayAssist® 3.0 (Stratagene). The GC-RMA-obtained log2-transformed expression values were imported into searchable database using this software.. For the treatment effects, which were independent of the genotype, all control (n=6) and DNFB-treated ears (n=6) were statistically analyzed using t-test with p ≤ 0.05 after Bonferroni correction and a differential expression higher than fourfold (given as an average log 2 ratio; ALR). The genotype effects were obtained by comparison of DNFB-treated ears of Cnr1+/+/Cnr2+/+ (n=3) versus Cnr1-/-/Cnr2-/- (n=3) with p ≤ 0.001 and ALR ≥ 1. Results for treatment and genotype effects were compared using Venn diagram.
Hierarchical clustering was performed on log2 transformed values using “ArrayAssist 3.0” (Stratagene) in two dimensions (e.g. both genes and samples).
 
Submission date May 02, 2007
Last update date Aug 28, 2018
Contact name Meliha Karsak
Organization name University of Bonn
Department Molecular Psychiatry
Street address Sigmund-Freud-Str. 25
City Bonn
ZIP/Postal code 53127
Country Germany
 
Platform ID GPL1261
Series (1)
GSE7694 Cannabinoid receptor double knockout mice (Cnr1 -/- /Cnr2 -/-) in CHS model
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE GCOS
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 100.976 P 0.000581214
AFFX-BioB-M_at 161.773 P 4.42873e-05
AFFX-BioB-3_at 120.514 P 4.42873e-05
AFFX-BioC-5_at 328.832 P 5.16732e-05
AFFX-BioC-3_at 472.363 P 4.42873e-05
AFFX-BioDn-5_at 815.928 P 4.42873e-05
AFFX-BioDn-3_at 1506.29 P 5.16732e-05
AFFX-CreX-5_at 4019.36 P 5.16732e-05
AFFX-CreX-3_at 5034.66 P 4.42873e-05
AFFX-DapX-5_at 219.297 P 4.42873e-05
AFFX-DapX-M_at 378.789 P 9.4506e-05
AFFX-DapX-3_at 470.314 P 4.42873e-05
AFFX-LysX-5_at 26.1728 P 7.00668e-05
AFFX-LysX-M_at 47.3913 P 0.000509415
AFFX-LysX-3_at 100.132 P 7.00668e-05
AFFX-PheX-5_at 41.7788 P 0.000970379
AFFX-PheX-M_at 53.9872 P 7.00668e-05
AFFX-PheX-3_at 56.1381 P 6.01289e-05
AFFX-ThrX-5_at 60.498 P 0.000195116
AFFX-ThrX-M_at 86.0564 P 4.42873e-05

Total number of rows: 45101

Table truncated, full table size 1395 Kbytes.




Supplementary file Size Download File type/resource
GSM186709.CEL.gz 5.7 Mb (ftp)(http) CEL
GSM186709.CHP.gz 10.5 Mb (ftp)(http) CHP
GSM186709.EXP.gz 502 b (ftp)(http) EXP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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