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Sample GSM297808 Query DataSets for GSM297808
Status Public on Dec 01, 2008
Title mouse colon_hnf4mutant_rep1
Sample type RNA
 
Source name adult female mouse colon, Hnf4a mutant
Organism Mus musculus
Characteristics strain:C57BL/6; VillinCRE-HNF4loxp; female; tissue colon; mutant
Biomaterial provider Francois Boudreau
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 Extraction with the ambion Totally RNA kit
Label biotin
Label protocol Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization.
 
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 Monitor the effect of HNF4alpha lost in mouse colonic epithelium
Data processing RMA algorithm
 
Submission date Jun 11, 2008
Last update date Aug 28, 2018
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)
GSE11759 Role of HNF4alpha in the adult colon
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE RMA-calculated signal intensity

Data table
ID_REF VALUE
1455768_at 5.889133
1438583_at 4.834053
1433389_at 4.194301
1417798_at 8.046596
1434131_at 7.613324
1430239_at 3.813908
1442360_at 3.944463
1444204_at 5.823947
1440608_at 4.798691
1419612_at 5.560872
1458260_at 4.692406
1427256_at 5.140518
1455975_x_at 8.59164
1426171_x_at 2.727654
1424329_a_at 7.776469
1443253_at 4.583552
1430979_a_at 8.181025
1442185_at 4.524601
1441659_at 7.298856
1420690_at 4.988849

Total number of rows: 45101

Table truncated, full table size 894 Kbytes.




Supplementary file Size Download File type/resource
GSM297808.CEL.gz 5.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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