Result

Search results for the GEO ID: GSE23040

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Source name

Description

Characteristics

GSM568514

GPL1261

mouse jejunum_hnf1alphamutant_rep1

adult mouse jejunum, hnf1alpha mutant

strain: mixed background age: 4 months genotype: hnf1alpha KO tissue: jejunum sample type: mutant

Monitor the effect of Hnf1alpha loss in the mouse jejunum epithelium.

Sample_geo_accession	GSM568514
Sample_status	Public on Jan 01 2011
Sample_submission_date	Jul 20 2010
Sample_last_update_date	Jan 01 2011
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 a pathogen-free environnment.
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 ug 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).
Sample_data_processing	The scanned images were analyzed using the GeneChip Analysis Suite 3.3 (Affymetrix) to identify genes differentially expressed among the RNA samples. Data were normalized using the 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/GSM568nnn/GSM568514/suppl/GSM568514.CEL.gz
Sample_series_id	GSE23040
Sample_data_row_count	45037

GSM568515

GPL1261

mouse jejunum_hnf1alphamutant_rep2

adult mouse jejunum, hnf1alpha mutant

strain: mixed background age: 4 months genotype: hnf1alpha KO tissue: jejunum sample type: mutant

Monitor the effect of Hnf1alpha loss in the mouse jejunum epithelium.

Sample_geo_accession	GSM568515
Sample_status	Public on Jan 01 2011
Sample_submission_date	Jul 20 2010
Sample_last_update_date	Jan 01 2011
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 a pathogen-free environnment.
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 ug 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).
Sample_data_processing	The scanned images were analyzed using the GeneChip Analysis Suite 3.3 (Affymetrix) to identify genes differentially expressed among the RNA samples. Data were normalized using the 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/GSM568nnn/GSM568515/suppl/GSM568515.CEL.gz
Sample_series_id	GSE23040
Sample_data_row_count	45037

GSM568516

GPL1261

mouse jejunum_hnf1alphamutant_rep3

adult mouse jejunum, hnf1alpha mutant

strain: mixed background age: 4 months genotype: hnf1alpha KO tissue: jejunum sample type: mutant

Monitor the effect of Hnf1alpha loss in the mouse jejunum epithelium.

Sample_geo_accession	GSM568516
Sample_status	Public on Jan 01 2011
Sample_submission_date	Jul 20 2010
Sample_last_update_date	Jan 01 2011
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 a pathogen-free environnment.
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 ug 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).
Sample_data_processing	The scanned images were analyzed using the GeneChip Analysis Suite 3.3 (Affymetrix) to identify genes differentially expressed among the RNA samples. Data were normalized using the 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/GSM568nnn/GSM568516/suppl/GSM568516.CEL.gz
Sample_series_id	GSE23040
Sample_data_row_count	45037

GSM568585

GPL1261

mouse jejunum_hnf1alphacontrol_rep1

adult mouse jejunum, hnf1alpha control

strain: mixed background age: 4 months genotype: wildtype tissue: jejunum sample type: control littermate

Monitor the effect of Hnf1alpha loss in the mouse jejunum epithelium.

Sample_geo_accession	GSM568585
Sample_status	Public on Jan 01 2011
Sample_submission_date	Jul 20 2010
Sample_last_update_date	Jan 01 2011
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 a pathogen-free environnment.
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 ug 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).
Sample_data_processing	The scanned images were analyzed using the GeneChip Analysis Suite 3.3 (Affymetrix) to identify genes differentially expressed among the RNA samples. Data were normalized using the 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/GSM568nnn/GSM568585/suppl/GSM568585.CEL.gz
Sample_series_id	GSE23040
Sample_data_row_count	45037

GSM568586

GPL1261

mouse jejunum_hnf1alphacontrol_rep2

adult mouse jejunum, hnf1alpha control

strain: mixed background age: 4 months genotype: wildtype tissue: jejunum sample type: control littermate

Monitor the effect of Hnf1alpha loss in the mouse jejunum epithelium.

Sample_geo_accession	GSM568586
Sample_status	Public on Jan 01 2011
Sample_submission_date	Jul 20 2010
Sample_last_update_date	Jan 01 2011
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 a pathogen-free environnment.
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 ug 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).
Sample_data_processing	The scanned images were analyzed using the GeneChip Analysis Suite 3.3 (Affymetrix) to identify genes differentially expressed among the RNA samples. Data were normalized using the 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/GSM568nnn/GSM568586/suppl/GSM568586.CEL.gz
Sample_series_id	GSE23040
Sample_data_row_count	45037

GSM568620

GPL1261

mouse jejunum_hnf1alphacontrol_rep3

adult mouse jejunum, hnf1alpha control

strain: mixed background age: 4 months genotype: wildtype tissue: jejunum sample type: control littermate

Monitor the effect of Hnf1alpha loss in the mouse jejunum epithelium.

Sample_geo_accession	GSM568620
Sample_status	Public on Jan 01 2011
Sample_submission_date	Jul 20 2010
Sample_last_update_date	Jan 01 2011
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 a pathogen-free environnment.
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 ug 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).
Sample_data_processing	The scanned images were analyzed using the GeneChip Analysis Suite 3.3 (Affymetrix) to identify genes differentially expressed among the RNA samples. Data were normalized using the 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/GSM568nnn/GSM568620/suppl/GSM568620.CEL.gz
Sample_series_id	GSE23040
Sample_data_row_count	45037

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