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Sample GSM187138 Query DataSets for GSM187138
Status Public on Jun 11, 2007
Title Cnr1-/-/Cnr2-/- female number 3, DNFB-treated allergic ear (#12_Ko-Tr-7)
Sample type RNA
 
Source name whole ear tissue, DNFB-treated allergic ear 48h after 2nd challenge
Organism Mus musculus
Characteristics Cnr1-/-/Cnr2-/- female number 3, 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 ko mouse number 3
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 03, 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 92.1085 P 0.000662269
AFFX-BioB-M_at 171.735 P 4.42873e-05
AFFX-BioB-3_at 102.135 P 4.42246e-05
AFFX-BioC-5_at 334.439 P 4.42873e-05
AFFX-BioC-3_at 443.832 P 4.42873e-05
AFFX-BioDn-5_at 727.966 P 4.42873e-05
AFFX-BioDn-3_at 1440.14 P 4.42873e-05
AFFX-CreX-5_at 3671.82 P 5.16732e-05
AFFX-CreX-3_at 4733.32 P 4.42873e-05
AFFX-DapX-5_at 164.322 P 6.02111e-05
AFFX-DapX-M_at 304.433 P 0.00010954
AFFX-DapX-3_at 483.751 P 4.42873e-05
AFFX-LysX-5_at 19.3357 P 0.000146581
AFFX-LysX-M_at 34.7535 P 0.000445901
AFFX-LysX-3_at 83.4582 P 6.02111e-05
AFFX-PheX-5_at 31.7922 P 0.00110197
AFFX-PheX-M_at 41.9397 P 6.02111e-05
AFFX-PheX-3_at 50.5351 P 4.42873e-05
AFFX-ThrX-5_at 45.0088 P 0.000126798
AFFX-ThrX-M_at 62.8385 P 4.42873e-05

Total number of rows: 45101

Table truncated, full table size 1395 Kbytes.




Supplementary file Size Download File type/resource
GSM187138.CEL.gz 5.6 Mb (ftp)(http) CEL
GSM187138.CHP.gz 10.5 Mb (ftp)(http) CHP
GSM187138.EXP.gz 501 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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