Result

Search results for the GEO ID: GSE11759

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Title

Source name

Description

Characteristics

GSM297808

GPL1261

mouse colon_hnf4mutant_rep1

adult female mouse colon, Hnf4a mutant

strain:C57BL/6; VillinCRE-HNF4loxp; female; tissue colon; mutant

Monitor the effect of HNF4alpha lost in mouse colonic epithelium

Sample_geo_accession	GSM297808
Sample_status	Public on Dec 01 2008
Sample_submission_date	Jun 11 2008
Sample_last_update_date	Jun 12 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_biomaterial_provider_ch1	Francois Boudreau
Sample_treatment_protocol_ch1	Injection of Ketamine/xylazine (300mg/kg; 40mg/kg) before sacrifice
Sample_growth_protocol_ch1	Mice were maintained in pathogen free environnement.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Extraction with the ambion Totally RNA kit
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization.
Sample_hyb_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).
Sample_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.
Sample_data_processing	RMA algorithm
Sample_platform_id	GPL1261
Sample_contact_name	Francois,,Boudreau
Sample_contact_email	francois.boudreau@usherbrooke.ca
Sample_contact_phone	819-820-6876
Sample_contact_fax	819-564-5320
Sample_contact_laboratory	Boudreau
Sample_contact_department	Anatomy and Cell Biology
Sample_contact_institute	University of Sherbrooke
Sample_contact_address	3001 12e ave Nord
Sample_contact_city	Sherbrooke
Sample_contact_state	Quebec
Sample_contact_zip/postal_code	J1H 5N4
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297808/suppl/GSM297808.CEL.gz
Sample_series_id	GSE11759
Sample_data_row_count	45101

GSM297817

GPL1261

mouse colon_hnf4control_rep1

adult female mouse colon, wildtype

strain:C57BL/6; VillinCRE-HNF4loxp; female; tissue colon; control

Monitor the effect of HNF4alpha lost in mouse colonic epithelium

Sample_geo_accession	GSM297817
Sample_status	Public on Dec 01 2008
Sample_submission_date	Jun 11 2008
Sample_last_update_date	Jun 12 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_biomaterial_provider_ch1	Francois Boudreau
Sample_treatment_protocol_ch1	Injection of Ketamine/xylazine (300mg/kg; 40mg/kg) before sacrifice
Sample_growth_protocol_ch1	Mice were maintained in pathogen free environnement.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Extraction with the ambion Totally RNA kit
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization.
Sample_hyb_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).
Sample_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.
Sample_data_processing	RMA algorithm
Sample_platform_id	GPL1261
Sample_contact_name	Francois,,Boudreau
Sample_contact_email	francois.boudreau@usherbrooke.ca
Sample_contact_phone	819-820-6876
Sample_contact_fax	819-564-5320
Sample_contact_laboratory	Boudreau
Sample_contact_department	Anatomy and Cell Biology
Sample_contact_institute	University of Sherbrooke
Sample_contact_address	3001 12e ave Nord
Sample_contact_city	Sherbrooke
Sample_contact_state	Quebec
Sample_contact_zip/postal_code	J1H 5N4
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297817/suppl/GSM297817.CEL.gz
Sample_series_id	GSE11759
Sample_data_row_count	45101

GSM297818

GPL1261

mouse colon_hnf4control_rep2

adult female mouse colon, wildtype

strain:C57BL/6; VillinCRE-HNF4loxp; female; tissue colon; control

Monitor the effect of HNF4alpha lost in mouse colonic epithelium

Sample_geo_accession	GSM297818
Sample_status	Public on Dec 01 2008
Sample_submission_date	Jun 11 2008
Sample_last_update_date	Jun 12 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_biomaterial_provider_ch1	Francois Boudreau
Sample_treatment_protocol_ch1	Injection of Ketamine/xylazine (300mg/kg; 40mg/kg) before sacrifice
Sample_growth_protocol_ch1	Mice were maintained in pathogen free environnement.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Extraction with the ambion Totally RNA kit
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization.
Sample_hyb_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).
Sample_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.
Sample_data_processing	RMA algorithm
Sample_platform_id	GPL1261
Sample_contact_name	Francois,,Boudreau
Sample_contact_email	francois.boudreau@usherbrooke.ca
Sample_contact_phone	819-820-6876
Sample_contact_fax	819-564-5320
Sample_contact_laboratory	Boudreau
Sample_contact_department	Anatomy and Cell Biology
Sample_contact_institute	University of Sherbrooke
Sample_contact_address	3001 12e ave Nord
Sample_contact_city	Sherbrooke
Sample_contact_state	Quebec
Sample_contact_zip/postal_code	J1H 5N4
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297818/suppl/GSM297818.CEL.gz
Sample_series_id	GSE11759
Sample_data_row_count	45101

GSM297819

GPL1261

mouse colon_hnf4control_rep3

adult female mouse colon, wildtype

strain:C57BL/6; VillinCRE-HNF4loxp; female; tissue colon; control

Monitor the effect of HNF4alpha lost in mouse colonic epithelium

Sample_geo_accession	GSM297819
Sample_status	Public on Dec 01 2008
Sample_submission_date	Jun 11 2008
Sample_last_update_date	Jun 12 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_biomaterial_provider_ch1	Francois Boudreau
Sample_treatment_protocol_ch1	Injection of Ketamine/xylazine (300mg/kg; 40mg/kg) before sacrifice
Sample_growth_protocol_ch1	Mice were maintained in pathogen free environnement.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Extraction with the ambion Totally RNA kit
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization.
Sample_hyb_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).
Sample_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.
Sample_data_processing	RMA algorithm
Sample_platform_id	GPL1261
Sample_contact_name	Francois,,Boudreau
Sample_contact_email	francois.boudreau@usherbrooke.ca
Sample_contact_phone	819-820-6876
Sample_contact_fax	819-564-5320
Sample_contact_laboratory	Boudreau
Sample_contact_department	Anatomy and Cell Biology
Sample_contact_institute	University of Sherbrooke
Sample_contact_address	3001 12e ave Nord
Sample_contact_city	Sherbrooke
Sample_contact_state	Quebec
Sample_contact_zip/postal_code	J1H 5N4
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297819/suppl/GSM297819.CEL.gz
Sample_series_id	GSE11759
Sample_data_row_count	45101

GSM297820

GPL1261

mouse colon_hnf4mutant_rep2

adult male mouse colon, Hnf4a mutant

strain:C57BL/6; VillinCRE-HNF4loxp; male; tissue colon; mutant

Monitor the effect of HNF4alpha lost in mouse colonic epithelium

Sample_geo_accession	GSM297820
Sample_status	Public on Dec 01 2008
Sample_submission_date	Jun 11 2008
Sample_last_update_date	Jun 12 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_biomaterial_provider_ch1	Francois Boudreau
Sample_treatment_protocol_ch1	Injection of Ketamine/xylazine (300mg/kg; 40mg/kg) before sacrifice
Sample_growth_protocol_ch1	Mice were maintained in pathogen free environnement.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Extraction with the ambion Totally RNA kit
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization.
Sample_hyb_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).
Sample_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.
Sample_data_processing	RMA algorithm
Sample_platform_id	GPL1261
Sample_contact_name	Francois,,Boudreau
Sample_contact_email	francois.boudreau@usherbrooke.ca
Sample_contact_phone	819-820-6876
Sample_contact_fax	819-564-5320
Sample_contact_laboratory	Boudreau
Sample_contact_department	Anatomy and Cell Biology
Sample_contact_institute	University of Sherbrooke
Sample_contact_address	3001 12e ave Nord
Sample_contact_city	Sherbrooke
Sample_contact_state	Quebec
Sample_contact_zip/postal_code	J1H 5N4
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297820/suppl/GSM297820.CEL.gz
Sample_series_id	GSE11759
Sample_data_row_count	45101

GSM297821

GPL1261

mouse colon_hnf4mutant_rep3

adult male mouse colon, Hnf4a mutant

strain:C57BL/6; VillinCRE-HNF4loxp; male; tissue colon; mutant

Monitor the effect of HNF4alpha lost in mouse colonic epithelium

Sample_geo_accession	GSM297821
Sample_status	Public on Dec 01 2008
Sample_submission_date	Jun 11 2008
Sample_last_update_date	Jun 12 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_biomaterial_provider_ch1	Francois Boudreau
Sample_treatment_protocol_ch1	Injection of Ketamine/xylazine (300mg/kg; 40mg/kg) before sacrifice
Sample_growth_protocol_ch1	Mice were maintained in pathogen free environnement.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Extraction with the ambion Totally RNA kit
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization.
Sample_hyb_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).
Sample_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.
Sample_data_processing	RMA algorithm
Sample_platform_id	GPL1261
Sample_contact_name	Francois,,Boudreau
Sample_contact_email	francois.boudreau@usherbrooke.ca
Sample_contact_phone	819-820-6876
Sample_contact_fax	819-564-5320
Sample_contact_laboratory	Boudreau
Sample_contact_department	Anatomy and Cell Biology
Sample_contact_institute	University of Sherbrooke
Sample_contact_address	3001 12e ave Nord
Sample_contact_city	Sherbrooke
Sample_contact_state	Quebec
Sample_contact_zip/postal_code	J1H 5N4
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297821/suppl/GSM297821.CEL.gz
Sample_series_id	GSE11759
Sample_data_row_count	45101

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