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Sample GSM151594 Query DataSets for GSM151594
Status Public on Dec 14, 2007
Title Lip-O-treated 48 hr OBX C57 mouse, biol rep3
Sample type RNA
 
Source name microdissected olfactory epithelium
Organism Mus musculus
Characteristics Genotype: w/t; strain C57BL/6J; male, 6 weeks old, olfactory epithelium
Treatment protocol For controls, mice were anesthetized with isoflurane and injected intranasally (i.n.) with 50 µl of empty liposomes (Lip-O) once per day at 4 PM for three consecutive days and injected intravenously (i.v.) with 200 µl Lip-O in the lateral tail vein on the first and third days of i.n. injections at the same time of day. Mice underwent bilateral olfactory bulbectomy on the second day of i.n. injections. Mice were euthanized at 48 h following OBX. 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 5 weeks of age and were maintained in an animal facility at the University of Kentucky Department of Laboratory Animal Research (DLAR) until they reached 6 weeks 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 Lip-O-treated 48 hr OBX C57 mice
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 15, 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)
GSE6540 Expression data from olfactory epithelium of Lip-C-treated mice compared to Lip-O-treated control mice
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 356 P 0.000662
AFFX-BioB-M_at 390.8 P 0.000044
AFFX-BioB-3_at 346 P 0.00006
AFFX-BioC-5_at 1141.5 P 0.000052
AFFX-BioC-3_at 1220.3 P 0.000044
AFFX-BioDn-5_at 2163.4 P 0.000044
AFFX-BioDn-3_at 4620.4 P 0.00006
AFFX-CreX-5_at 12305.7 P 0.000052
AFFX-CreX-3_at 15330.7 P 0.000044
AFFX-DapX-5_at 20.1 A 0.313723
AFFX-DapX-M_at 22.7 A 0.250796
AFFX-DapX-3_at 12.1 A 0.52976
AFFX-LysX-5_at 2.1 A 0.631562
AFFX-LysX-M_at 3.6 A 0.712274
AFFX-LysX-3_at 17.4 A 0.072682
AFFX-PheX-5_at 2.3 A 0.897835
AFFX-PheX-M_at 2.5 A 0.904333
AFFX-PheX-3_at 32.9 A 0.327079
AFFX-ThrX-5_at 8.5 A 0.544591
AFFX-ThrX-M_at 2.3 A 0.852061

Total number of rows: 45101

Table truncated, full table size 1217 Kbytes.




Supplementary file Size Download File type/resource
GSM151594.CEL.gz 3.9 Mb (ftp)(http) CEL

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