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Sample GSM524185 Query DataSets for GSM524185
Status Public on Jan 01, 2011
Title HNF4fxVilCRE_CTRL3
Sample type RNA
 
Source name HNF4fxVilCRE_CTRL
Organism Mus musculus
Characteristics strain: B6.129X1(FVB)-Hnf4atm1.1Gonz/J
age: adult
tissue: jejunum
Biomaterial provider Jackson Laboratory, Cat#004665
Treatment protocol Injection of Ketamine/xylazine (300mg/kg; 40mg/kg) before sacrifice
Growth protocol Mice were maintained in pathogen free environnement.
Extracted molecule total RNA
Extraction protocol Total RNA with Ambion Totally RNA
Label Biotin
Label protocol Total RNA has been isolated by Ambion ToTALLY RNA kit from total jejunum biopsies
 
Hybridization protocol The hybridization mixture was prepared by mixing 15 mg biotinylated probe with control oligonucleotide B2 (final concentration 50 pM; Affymetrix), herring sperm DNA (final concentration 0.1 mg/ml; Research Genetics), acetylated bovine serum albumin (final concentration 0.5 mg/ml; Gibco BRL Life Technologies) in a final volume of 300 ml of 13 MES hybridization buffer (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween-20; all reagents from Sigma). The hybridization mixture was denatured for 10 minutes at 99 C, incubated for 5 minutes at 45 C, and spun for 5 minutes in a benchtop microcentrifuge. The microarray was warmed to room temperature and prehybridized in hybridization buffer for 10–20 minutes at 45 C. The prehybridization solution was removed and 150 ml of the hybridization mix was added to the array. The array and probe fragments were incubated at 45 C overnight (16–20 hours). After hybridization, nonspecifically bound probe was removed by washing with the GeneChip Fluidics station 400 (Affymetrix). In total, 10 low-stringency washes (63 SSPE, 0.01% Tween-20, 0.005% Antifoam) and 4 high-stringency washes (100 mM MES, 0.1 M NaCl, 0.01% Tween-20, 50 C) were performed (all reagents from Sigma).
Scan protocol Specifically bound probe was detected by incubating the arrays with SAPE (Molecular Probes) and scanning the chips with a Hewlett-Packard GeneArray scanner (Affymetrix). A second scan was performed after signal enhancement with biotinylated anti-streptavidin antibody Vector Laboratories). The scanned images were analyzed using the GeneChip Analysis Suite 3.3 (Affymetrix) to identify genes differentially expressed among the RNA samples.
Description YF060516MOT19.CEL
Data processing FlexArray 1.3 was used for data analysis (www.genomequebec.mcgill.ca)
 
Submission date Mar 19, 2010
Last update date Jan 01, 2011
Contact name Francois Boudreau
E-mail(s) francois.boudreau@usherbrooke.ca
Phone 819-820-6876
Fax 819-564-5320
Organization name University of Sherbrooke
Department Anatomy and Cell Biology
Lab Boudreau
Street address 3001 12e ave Nord
City Sherbrooke
State/province Quebec
ZIP/Postal code J1H 5N4
Country Canada
 
Platform ID GPL1261
Series (1)
GSE20968 Hepatocyte-nuclear-factor-4a promotes gut neoplasia in mice and protects against the production of reactive oxygen species

Data table header descriptions
ID_REF
VALUE RMA-calculated signal intensity (log2 scale)

Data table
ID_REF VALUE
1442360_at 2.784882
1440608_at 3.25269
1419612_at 4.701543
1458260_at 3.708242
1458562_at 3.877756
1443253_at 2.672873
1442185_at 3.417088
1446544_at 3.978054
1439946_at 4.296636
1420217_x_at 3.21854
1449650_at 2.267903
1457862_at 1.962569
1443799_at 3.129634
1443097_at 2.527762
1442949_at 3.49984
1459115_at 2.594255
1447561_at 2.663691
1444841_at 2.795656
1438903_at 2.737049
1440651_at 2.578254

Total number of rows: 45101

Table truncated, full table size 894 Kbytes.




Supplementary file Size Download File type/resource
GSM524185_YF060516MOT19.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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