Search results for the GEO ID: GSE21267  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM531774 | GPL1261 |
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Dox-1
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Esophagus from Dox-stimulated CC10-IL-13 mouse
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tissue: esophagus
background: CC10-IL-13 transgenic in FVB/N background
age: 3-4 months
diet: with doxycycline
|
Affymetrix Mouse Genome 430 2.0 Array Chips were used. GeneChip CEL files were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly. GeneSpring 7.3.1 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering and filtering. Samples were normalized pair-wise to respective unstimulated controls.
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| Sample_geo_accession | GSM531774
| | Sample_status | Public on Jul 01 2010
| | Sample_submission_date | Apr 08 2010
| | Sample_last_update_date | Jun 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the Trizol kit (Invitrogen).
| | Sample_extract_protocol_ch1 | Quality control steps: RNA quality was assessed by using the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA) and only those samples with 28S/18S ratios between 1.3 and 2 were subsequently used.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Modified Epicentre protocol (Epicentre biotechnologies) with random primer.
| | Sample_hyb_protocol | Full Protocol Description: Create a hybridization cocktail for a single probe array that contains 0.067 ug/uL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 10% DMSO, and 1X Hybridization Buffer. Heat hybridization cocktail to 99C for 5 minutes, to 45C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 uL of 1X Hybridization Buffer. Incubate at 45C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 uL of the hybridization cocktail. Incubate at 45?C for 16 hrs in the Hybridization Oven rotating at 60 rpm.
| | Sample_hyb_protocol | Fluidics: Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0004. Arrays were stained with phycoerythrin-conjugated streptavidin (Molecular Probes, Eugene, OR) and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA), as described in the Affymetrix GeneChip® Expression Analysis Manual
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 (Affymetrix).
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings, then normalized to the median of controls (NO DOX) with GeneSpring version 7.3.1.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Li,,Zuo
| | Sample_contact_email | Li.Zuo@cchmc.org
| | Sample_contact_phone | 513-636-2745
| | Sample_contact_laboratory | Rothenberg
| | Sample_contact_department | Allergy and Immunology
| | Sample_contact_institute | Cincinanti Children's Hospital
| | Sample_contact_address | 3333 Burnet Ave
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531774/suppl/GSM531774.CEL.gz
| | Sample_series_id | GSE21267
| | Sample_data_row_count | 45101
| | |
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GSM531775 | GPL1261 |
|
Dox-2
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Esophagus from Dox-stimulated CC10-IL-13 mouse
|
tissue: esophagus
background: CC10-IL-13 transgenic in FVB/N background
age: 3-4 months
diet: with doxycycline
|
Affymetrix Mouse Genome 430 2.0 Array Chips were used. GeneChip CEL files were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly. GeneSpring 7.3.1 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering and filtering. Samples were normalized pair-wise to respective unstimulated controls.
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| Sample_geo_accession | GSM531775
| | Sample_status | Public on Jul 01 2010
| | Sample_submission_date | Apr 08 2010
| | Sample_last_update_date | Jun 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the Trizol kit (Invitrogen).
| | Sample_extract_protocol_ch1 | Quality control steps: RNA quality was assessed by using the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA) and only those samples with 28S/18S ratios between 1.3 and 2 were subsequently used.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Modified Epicentre protocol (Epicentre biotechnologies) with random primer.
| | Sample_hyb_protocol | Full Protocol Description: Create a hybridization cocktail for a single probe array that contains 0.067 ug/uL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 10% DMSO, and 1X Hybridization Buffer. Heat hybridization cocktail to 99C for 5 minutes, to 45C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 uL of 1X Hybridization Buffer. Incubate at 45C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 uL of the hybridization cocktail. Incubate at 45?C for 16 hrs in the Hybridization Oven rotating at 60 rpm.
| | Sample_hyb_protocol | Fluidics: Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0004. Arrays were stained with phycoerythrin-conjugated streptavidin (Molecular Probes, Eugene, OR) and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA), as described in the Affymetrix GeneChip® Expression Analysis Manual
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 (Affymetrix).
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings, then normalized to the median of controls (NO DOX) with GeneSpring version 7.3.1.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Li,,Zuo
| | Sample_contact_email | Li.Zuo@cchmc.org
| | Sample_contact_phone | 513-636-2745
| | Sample_contact_laboratory | Rothenberg
| | Sample_contact_department | Allergy and Immunology
| | Sample_contact_institute | Cincinanti Children's Hospital
| | Sample_contact_address | 3333 Burnet Ave
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531775/suppl/GSM531775.CEL.gz
| | Sample_series_id | GSE21267
| | Sample_data_row_count | 45101
| | |
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GSM531776 | GPL1261 |
|
Dox-3
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Esophagus from Dox-stimulated CC10-IL-13 mouse
|
tissue: esophagus
background: CC10-IL-13 transgenic in FVB/N background
age: 3-4 months
diet: with doxycycline
|
Affymetrix Mouse Genome 430 2.0 Array Chips were used. GeneChip CEL files were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly. GeneSpring 7.3.1 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering and filtering. Samples were normalized pair-wise to respective unstimulated controls.
|
| Sample_geo_accession | GSM531776
| | Sample_status | Public on Jul 01 2010
| | Sample_submission_date | Apr 08 2010
| | Sample_last_update_date | Jun 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the Trizol kit (Invitrogen).
| | Sample_extract_protocol_ch1 | Quality control steps: RNA quality was assessed by using the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA) and only those samples with 28S/18S ratios between 1.3 and 2 were subsequently used.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Modified Epicentre protocol (Epicentre biotechnologies) with random primer.
| | Sample_hyb_protocol | Full Protocol Description: Create a hybridization cocktail for a single probe array that contains 0.067 ug/uL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 10% DMSO, and 1X Hybridization Buffer. Heat hybridization cocktail to 99C for 5 minutes, to 45C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 uL of 1X Hybridization Buffer. Incubate at 45C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 uL of the hybridization cocktail. Incubate at 45?C for 16 hrs in the Hybridization Oven rotating at 60 rpm.
| | Sample_hyb_protocol | Fluidics: Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0004. Arrays were stained with phycoerythrin-conjugated streptavidin (Molecular Probes, Eugene, OR) and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA), as described in the Affymetrix GeneChip® Expression Analysis Manual
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 (Affymetrix).
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings, then normalized to the median of controls (NO DOX) with GeneSpring version 7.3.1.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Li,,Zuo
| | Sample_contact_email | Li.Zuo@cchmc.org
| | Sample_contact_phone | 513-636-2745
| | Sample_contact_laboratory | Rothenberg
| | Sample_contact_department | Allergy and Immunology
| | Sample_contact_institute | Cincinanti Children's Hospital
| | Sample_contact_address | 3333 Burnet Ave
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531776/suppl/GSM531776.CEL.gz
| | Sample_series_id | GSE21267
| | Sample_data_row_count | 45101
| | |
|
GSM531777 | GPL1261 |
|
NO Dox-1
|
Esophagus from No Dox CC10-IL-13 mouse
|
tissue: esophagus
background: CC10-IL-13 transgenic in FVB/N background
age: 3-4 months
diet: without doxycycline
|
Affymetrix Mouse Genome 430 2.0 Array Chips were used. GeneChip CEL files were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly. GeneSpring 7.3.1 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering and filtering. Samples were normalized pair-wise to respective unstimulated controls.
|
| Sample_geo_accession | GSM531777
| | Sample_status | Public on Jul 01 2010
| | Sample_submission_date | Apr 08 2010
| | Sample_last_update_date | Jun 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the Trizol kit (Invitrogen).
| | Sample_extract_protocol_ch1 | Quality control steps: RNA quality was assessed by using the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA) and only those samples with 28S/18S ratios between 1.3 and 2 were subsequently used.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Modified Epicentre protocol (Epicentre biotechnologies) with random primer.
| | Sample_hyb_protocol | Full Protocol Description: Create a hybridization cocktail for a single probe array that contains 0.067 ug/uL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 10% DMSO, and 1X Hybridization Buffer. Heat hybridization cocktail to 99C for 5 minutes, to 45C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 uL of 1X Hybridization Buffer. Incubate at 45C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 uL of the hybridization cocktail. Incubate at 45?C for 16 hrs in the Hybridization Oven rotating at 60 rpm.
| | Sample_hyb_protocol | Fluidics: Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0004. Arrays were stained with phycoerythrin-conjugated streptavidin (Molecular Probes, Eugene, OR) and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA), as described in the Affymetrix GeneChip® Expression Analysis Manual
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 (Affymetrix).
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings, then normalized to the median of controls (NO DOX) with GeneSpring version 7.3.1.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Li,,Zuo
| | Sample_contact_email | Li.Zuo@cchmc.org
| | Sample_contact_phone | 513-636-2745
| | Sample_contact_laboratory | Rothenberg
| | Sample_contact_department | Allergy and Immunology
| | Sample_contact_institute | Cincinanti Children's Hospital
| | Sample_contact_address | 3333 Burnet Ave
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531777/suppl/GSM531777.CEL.gz
| | Sample_series_id | GSE21267
| | Sample_data_row_count | 45101
| | |
|
GSM531778 | GPL1261 |
|
NO Dox-2
|
Esophagus from No Dox CC10-IL-13 mouse
|
tissue: esophagus
background: CC10-IL-13 transgenic in FVB/N background
age: 3-4 months
diet: without doxycycline
|
Affymetrix Mouse Genome 430 2.0 Array Chips were used. GeneChip CEL files were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly. GeneSpring 7.3.1 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering and filtering. Samples were normalized pair-wise to respective unstimulated controls.
|
| Sample_geo_accession | GSM531778
| | Sample_status | Public on Jul 01 2010
| | Sample_submission_date | Apr 08 2010
| | Sample_last_update_date | Jun 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the Trizol kit (Invitrogen).
| | Sample_extract_protocol_ch1 | Quality control steps: RNA quality was assessed by using the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA) and only those samples with 28S/18S ratios between 1.3 and 2 were subsequently used.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Modified Epicentre protocol (Epicentre biotechnologies) with random primer.
| | Sample_hyb_protocol | Full Protocol Description: Create a hybridization cocktail for a single probe array that contains 0.067 ug/uL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 10% DMSO, and 1X Hybridization Buffer. Heat hybridization cocktail to 99C for 5 minutes, to 45C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 uL of 1X Hybridization Buffer. Incubate at 45C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 uL of the hybridization cocktail. Incubate at 45?C for 16 hrs in the Hybridization Oven rotating at 60 rpm.
| | Sample_hyb_protocol | Fluidics: Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0004. Arrays were stained with phycoerythrin-conjugated streptavidin (Molecular Probes, Eugene, OR) and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA), as described in the Affymetrix GeneChip® Expression Analysis Manual
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 (Affymetrix).
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings, then normalized to the median of controls (NO DOX) with GeneSpring version 7.3.1.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Li,,Zuo
| | Sample_contact_email | Li.Zuo@cchmc.org
| | Sample_contact_phone | 513-636-2745
| | Sample_contact_laboratory | Rothenberg
| | Sample_contact_department | Allergy and Immunology
| | Sample_contact_institute | Cincinanti Children's Hospital
| | Sample_contact_address | 3333 Burnet Ave
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531778/suppl/GSM531778.CEL.gz
| | Sample_series_id | GSE21267
| | Sample_data_row_count | 45101
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