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Sample GSM149360 Query DataSets for GSM149360
Status Public on Dec 06, 2007
Title 6 month old adult male mutant mouse Hq/Y, biol rep1
Sample type RNA
 
Source name microdissected olfactory epithelium
Organism Mus musculus
Characteristics Genotype: Hq/Y; strain B6CBACAw-J/A-Pdcd8-Hq/J; male, 6 months old, olfactory epithelium
Treatment protocol Following euthanasia with carbon dioxide, the olfactory epithelium was quickly microdissected, weighed, and snap-frozen in liquid nitrogen.
Growth protocol The mice were purchased from Jackson Laboratories (Bar Harbor, ME) at 13 weeks of age and were maintained in an animal facility at the University of Kentucky Department of Laboratory Animal Research (DLAR) until they reached six months of age. At the DLAR, they were kept on a 12 hr light:dark cycle in Bioclean units with sterile-filtered air and provided food and water ad libitum.
Extracted molecule total RNA
Extraction protocol Snap-frozen microdissected olfactory epithelium was pulverized in TRI Reagent (Sigma-Aldrich, St. Louis, MO) and processed through a QIAshredder column (Qiagen, Valencia, CA). The total RNA was further purified using the Qiagen RNeasy Mini-Kit according to the manufacturer’s protocol. Total RNA yield and purity was assessed with a spectrophotometer and with the model 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA); all samples had A260/A280 ratios of 1.9–2.2 and showed two sharp peaks corresponding to 18S and 28S RNA on the Bioanalyzer electropherograms.
Label biotin
Label protocol Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
 
Hybridization protocol Following fragmentation, 13.33 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GCS 3000 7G scanner
Description Gene expression data from olfactory epithelium of Harlequin mutant mice (Hq/Y)
Data processing The data were analyzed with Affymetrix MicroArray Suite 5.0 using Affymetrix default analysis settings. A threshold value of 1,500 was used to normalize the data across all the microarrays.
 
Submission date Dec 08, 2006
Last update date Aug 28, 2018
Contact name Marilyn L. Getchell
E-mail(s) mgetch@uky.edu
Organization name University of Kentucky
Department Anatomy and Neurobiology
Lab Sanders-Brown Center on Aging
Street address 800 South Limestone St.
City Lexington
State/province KY
ZIP/Postal code 40536-0230
Country USA
 
Platform ID GPL1261
Series (1)
GSE6485 Expression data from olfactory epithelium of Harlequin mutant mice compared to littermate controls
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF Affymetrix probe set name
VALUE MAS5-calculated signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 258.5 P 0.000509
AFFX-BioB-M_at 405.4 P 0.000044
AFFX-BioB-3_at 264.7 P 0.000052
AFFX-BioC-5_at 810 P 0.000052
AFFX-BioC-3_at 884.1 P 0.000052
AFFX-BioDn-5_at 1583.8 P 0.000044
AFFX-BioDn-3_at 3535.8 P 0.000052
AFFX-CreX-5_at 9356.7 P 0.000052
AFFX-CreX-3_at 12853 P 0.000044
AFFX-DapX-5_at 18 A 0.250796
AFFX-DapX-M_at 15.8 A 0.327079
AFFX-DapX-3_at 10.7 A 0.783476
AFFX-LysX-5_at 1.2 A 0.922034
AFFX-LysX-M_at 4.3 A 0.760937
AFFX-LysX-3_at 16.1 P 0.021893
AFFX-PheX-5_at 2.2 A 0.941572
AFFX-PheX-M_at 2.3 A 0.916408
AFFX-PheX-3_at 6.4 A 0.631562
AFFX-ThrX-5_at 25 A 0.239063
AFFX-ThrX-M_at 1.6 A 0.941556

Total number of rows: 45101

Table truncated, full table size 1215 Kbytes.




Supplementary file Size Download File type/resource
GSM149360.cel.gz 3.9 Mb (ftp)(http) CEL

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