Search results for the GEO ID: GSE20299  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM508871 | GPL8759 |
|
ST_WT1 Mice
|
Stomach
|
tissue: Stomach
strain: C57BL/6
|
Stomach sample from wild Type of Mice
|
| Sample_geo_accession | GSM508871
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | Feb 12 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | None
| | Sample_growth_protocol_ch1 | 16 week old mice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Flash frozen samples (–80°C) were homogenized. RNA was isolated using TRIzol Reagent (Invitrogen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For transcriptional profiling, total RNA was converted into cRNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA) and hybridized to Affymetrix HT Mouse Genome 430 microarrays.
| | Sample_hyb_protocol | All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays. The HT_MG-430A Array plate consists of 24 single MG-430A arrays arranged into standard SBS 24 well plate format. All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.
| | Sample_scan_protocol | HT Plate Scanner
| | Sample_data_processing | The data were extracted with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL8759
| | Sample_contact_name | BIDMC ,,Genomics
| | Sample_contact_email | mbhasin@bidmc.harvard.edu
| | Sample_contact_phone | 617 735 2509
| | Sample_contact_fax | 6177352510
| | Sample_contact_institute | Beth Israel Deaconess Medical Center
| | Sample_contact_address | 330 Brookline Avenue RN 380F
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508871/suppl/GSM508871_ST_WT1.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508871/suppl/GSM508871_ST_WT1.CHP.gz
| | Sample_series_id | GSE20299
| | Sample_data_row_count | 22716
| | |
|
GSM508872 | GPL8759 |
|
ST_WT2 Mice
|
Stomach
|
tissue: Stomach
strain: C57BL/6
|
Stomach sample from wild Type of Mice
|
| Sample_geo_accession | GSM508872
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | Feb 12 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | None
| | Sample_growth_protocol_ch1 | 16 week old mice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Flash frozen samples (–80°C) were homogenized. RNA was isolated using TRIzol Reagent (Invitrogen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For transcriptional profiling, total RNA was converted into cRNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA) and hybridized to Affymetrix HT Mouse Genome 430 microarrays.
| | Sample_hyb_protocol | All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays. The HT_MG-430A Array plate consists of 24 single MG-430A arrays arranged into standard SBS 24 well plate format. All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.
| | Sample_scan_protocol | HT Plate Scanner
| | Sample_data_processing | The data were extracted with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL8759
| | Sample_contact_name | BIDMC ,,Genomics
| | Sample_contact_email | mbhasin@bidmc.harvard.edu
| | Sample_contact_phone | 617 735 2509
| | Sample_contact_fax | 6177352510
| | Sample_contact_institute | Beth Israel Deaconess Medical Center
| | Sample_contact_address | 330 Brookline Avenue RN 380F
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508872/suppl/GSM508872_ST_WT2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508872/suppl/GSM508872_ST_WT2.CHP.gz
| | Sample_series_id | GSE20299
| | Sample_data_row_count | 22716
| | |
|
GSM508873 | GPL8759 |
|
ST_Spdef_HET1 Mice
|
Stomach
|
tissue: Stomach
strain: C57BL/6
|
Stomach sample from Spdef heterzygous mice
|
| Sample_geo_accession | GSM508873
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | Feb 12 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | None
| | Sample_growth_protocol_ch1 | 16 week old mice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Flash frozen samples (–80°C) were homogenized. RNA was isolated using TRIzol Reagent (Invitrogen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For transcriptional profiling, total RNA was converted into cRNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA) and hybridized to Affymetrix HT Mouse Genome 430 microarrays.
| | Sample_hyb_protocol | All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays. The HT_MG-430A Array plate consists of 24 single MG-430A arrays arranged into standard SBS 24 well plate format. All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.
| | Sample_scan_protocol | HT Plate Scanner
| | Sample_data_processing | The data were extracted with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL8759
| | Sample_contact_name | BIDMC ,,Genomics
| | Sample_contact_email | mbhasin@bidmc.harvard.edu
| | Sample_contact_phone | 617 735 2509
| | Sample_contact_fax | 6177352510
| | Sample_contact_institute | Beth Israel Deaconess Medical Center
| | Sample_contact_address | 330 Brookline Avenue RN 380F
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508873/suppl/GSM508873_ST_HET1.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508873/suppl/GSM508873_ST_HET1.CHP.gz
| | Sample_series_id | GSE20299
| | Sample_data_row_count | 22716
| | |
|
GSM508874 | GPL8759 |
|
ST_Spdef_HET2 Mice
|
Stomach
|
tissue: Stomach
strain: C57BL/6
|
Stomach sample from Spdef heterzygous mice
|
| Sample_geo_accession | GSM508874
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | Feb 12 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | None
| | Sample_growth_protocol_ch1 | 16 week old mice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Flash frozen samples (–80°C) were homogenized. RNA was isolated using TRIzol Reagent (Invitrogen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For transcriptional profiling, total RNA was converted into cRNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA) and hybridized to Affymetrix HT Mouse Genome 430 microarrays.
| | Sample_hyb_protocol | All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays. The HT_MG-430A Array plate consists of 24 single MG-430A arrays arranged into standard SBS 24 well plate format. All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.
| | Sample_scan_protocol | HT Plate Scanner
| | Sample_data_processing | The data were extracted with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL8759
| | Sample_contact_name | BIDMC ,,Genomics
| | Sample_contact_email | mbhasin@bidmc.harvard.edu
| | Sample_contact_phone | 617 735 2509
| | Sample_contact_fax | 6177352510
| | Sample_contact_institute | Beth Israel Deaconess Medical Center
| | Sample_contact_address | 330 Brookline Avenue RN 380F
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508874/suppl/GSM508874_ST_HET2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508874/suppl/GSM508874_ST_HET2.CHP.gz
| | Sample_series_id | GSE20299
| | Sample_data_row_count | 22716
| | |
|
GSM508875 | GPL8759 |
|
ST_Spdef_KN1 Mice
|
Stomach
|
tissue: Stomach
strain: C57BL/6
|
Stomach sample from Spdef knockout mice
|
| Sample_geo_accession | GSM508875
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | Feb 12 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | None
| | Sample_growth_protocol_ch1 | 16 week old mice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Flash frozen samples (–80°C) were homogenized. RNA was isolated using TRIzol Reagent (Invitrogen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For transcriptional profiling, total RNA was converted into cRNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA) and hybridized to Affymetrix HT Mouse Genome 430 microarrays.
| | Sample_hyb_protocol | All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays. The HT_MG-430A Array plate consists of 24 single MG-430A arrays arranged into standard SBS 24 well plate format. All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.
| | Sample_scan_protocol | HT Plate Scanner
| | Sample_data_processing | The image data was processed using the the Robust Multiarray method (RMA) to determine the specific hybridizing signal for eachprobe.
| | Sample_platform_id | GPL8759
| | Sample_contact_name | BIDMC ,,Genomics
| | Sample_contact_email | mbhasin@bidmc.harvard.edu
| | Sample_contact_phone | 617 735 2509
| | Sample_contact_fax | 6177352510
| | Sample_contact_institute | Beth Israel Deaconess Medical Center
| | Sample_contact_address | 330 Brookline Avenue RN 380F
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508875/suppl/GSM508875_ST_Spdef_KN1.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508875/suppl/GSM508875_ST_Spdef_KN1.CHP.gz
| | Sample_series_id | GSE20299
| | Sample_data_row_count | 22716
| | |
|
GSM508876 | GPL8759 |
|
ST_Spdef_KN2 Mice
|
Stomach
|
tissue: Stomach
strain: C57BL/6
|
Stomach sample from Spdef knockout mice
|
| Sample_geo_accession | GSM508876
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | Feb 12 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | None
| | Sample_growth_protocol_ch1 | 16 week old mice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Flash frozen samples (–80°C) were homogenized. RNA was isolated using TRIzol Reagent (Invitrogen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For transcriptional profiling, total RNA was converted into cRNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA) and hybridized to Affymetrix HT Mouse Genome 430 microarrays.
| | Sample_hyb_protocol | All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays. The HT_MG-430A Array plate consists of 24 single MG-430A arrays arranged into standard SBS 24 well plate format. All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.
| | Sample_scan_protocol | HT Plate Scanner
| | Sample_data_processing | The image data was processed using the the Robust Multiarray method (RMA) to determine the specific hybridizing signal for eachprobe.
| | Sample_platform_id | GPL8759
| | Sample_contact_name | BIDMC ,,Genomics
| | Sample_contact_email | mbhasin@bidmc.harvard.edu
| | Sample_contact_phone | 617 735 2509
| | Sample_contact_fax | 6177352510
| | Sample_contact_institute | Beth Israel Deaconess Medical Center
| | Sample_contact_address | 330 Brookline Avenue RN 380F
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508876/suppl/GSM508876_ST_Spdef_KN2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508876/suppl/GSM508876_ST_Spdef_KN2.CHP.gz
| | Sample_series_id | GSE20299
| | Sample_data_row_count | 22716
| | |
|
GSM508877 | GPL8759 |
|
CL_WT1 Mice
|
Colon
|
tissue: Colon
strain: C57BL/6
|
Colon sample from wild Type of Mice
|
| Sample_geo_accession | GSM508877
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | Feb 12 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | None
| | Sample_growth_protocol_ch1 | 16 week old mice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Flash frozen samples (–80°C) were homogenized. RNA was isolated using TRIzol Reagent (Invitrogen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For transcriptional profiling, total RNA was converted into cRNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA) and hybridized to Affymetrix HT Mouse Genome 430 microarrays.
| | Sample_hyb_protocol | All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays. The HT_MG-430A Array plate consists of 24 single MG-430A arrays arranged into standard SBS 24 well plate format. All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.
| | Sample_scan_protocol | HT Plate Scanner
| | Sample_data_processing | The image data was processed using the the Robust Multiarray method (RMA) to determine the specific hybridizing signal for eachprobe.
| | Sample_platform_id | GPL8759
| | Sample_contact_name | BIDMC ,,Genomics
| | Sample_contact_email | mbhasin@bidmc.harvard.edu
| | Sample_contact_phone | 617 735 2509
| | Sample_contact_fax | 6177352510
| | Sample_contact_institute | Beth Israel Deaconess Medical Center
| | Sample_contact_address | 330 Brookline Avenue RN 380F
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508877/suppl/GSM508877_CL_WT1.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508877/suppl/GSM508877_CL_WT1.CHP.gz
| | Sample_series_id | GSE20299
| | Sample_data_row_count | 22716
| | |
|
GSM508878 | GPL8759 |
|
CL_WT2 Mice
|
Colon
|
tissue: Colon
strain: C57BL/6
|
Colon sample from wild Type of Mice
|
| Sample_geo_accession | GSM508878
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | Feb 12 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | None
| | Sample_growth_protocol_ch1 | 16 week old mice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Flash frozen samples (–80°C) were homogenized. RNA was isolated using TRIzol Reagent (Invitrogen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For transcriptional profiling, total RNA was converted into cRNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA) and hybridized to Affymetrix HT Mouse Genome 430 microarrays.
| | Sample_hyb_protocol | All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays. The HT_MG-430A Array plate consists of 24 single MG-430A arrays arranged into standard SBS 24 well plate format. All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.
| | Sample_scan_protocol | HT Plate Scanner
| | Sample_data_processing | The data were extracted with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL8759
| | Sample_contact_name | BIDMC ,,Genomics
| | Sample_contact_email | mbhasin@bidmc.harvard.edu
| | Sample_contact_phone | 617 735 2509
| | Sample_contact_fax | 6177352510
| | Sample_contact_institute | Beth Israel Deaconess Medical Center
| | Sample_contact_address | 330 Brookline Avenue RN 380F
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508878/suppl/GSM508878_CL_WT2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508878/suppl/GSM508878_CL_WT2.CHP.gz
| | Sample_series_id | GSE20299
| | Sample_data_row_count | 22716
| | |
|
GSM508879 | GPL8759 |
|
CL_Spdef_HET1 Mice
|
Colon
|
tissue: Colon
strain: C57BL/6
|
Colon sample from Spdef heterzygous mice
|
| Sample_geo_accession | GSM508879
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | Feb 12 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | None
| | Sample_growth_protocol_ch1 | 16 week old mice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Flash frozen samples (–80°C) were homogenized. RNA was isolated using TRIzol Reagent (Invitrogen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For transcriptional profiling, total RNA was converted into cRNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA) and hybridized to Affymetrix HT Mouse Genome 430 microarrays.
| | Sample_hyb_protocol | All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays. The HT_MG-430A Array plate consists of 24 single MG-430A arrays arranged into standard SBS 24 well plate format. All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.
| | Sample_scan_protocol | HT Plate Scanner
| | Sample_data_processing | The data were extracted with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL8759
| | Sample_contact_name | BIDMC ,,Genomics
| | Sample_contact_email | mbhasin@bidmc.harvard.edu
| | Sample_contact_phone | 617 735 2509
| | Sample_contact_fax | 6177352510
| | Sample_contact_institute | Beth Israel Deaconess Medical Center
| | Sample_contact_address | 330 Brookline Avenue RN 380F
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508879/suppl/GSM508879_CL_HET1.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508879/suppl/GSM508879_CL_HET1.CHP.gz
| | Sample_series_id | GSE20299
| | Sample_data_row_count | 22716
| | |
|
GSM508880 | GPL8759 |
|
CL_Spdef_HET2 Mice
|
Colon
|
tissue: Colon
strain: C57BL/6
|
Colon sample from Spdef heterzygous mice
|
| Sample_geo_accession | GSM508880
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | Feb 12 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | None
| | Sample_growth_protocol_ch1 | 16 week old mice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Flash frozen samples (–80°C) were homogenized. RNA was isolated using TRIzol Reagent (Invitrogen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For transcriptional profiling, total RNA was converted into cRNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA) and hybridized to Affymetrix HT Mouse Genome 430 microarrays.
| | Sample_hyb_protocol | All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays. The HT_MG-430A Array plate consists of 24 single MG-430A arrays arranged into standard SBS 24 well plate format. All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.
| | Sample_scan_protocol | HT Plate Scanner
| | Sample_data_processing | The data were extracted with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL8759
| | Sample_contact_name | BIDMC ,,Genomics
| | Sample_contact_email | mbhasin@bidmc.harvard.edu
| | Sample_contact_phone | 617 735 2509
| | Sample_contact_fax | 6177352510
| | Sample_contact_institute | Beth Israel Deaconess Medical Center
| | Sample_contact_address | 330 Brookline Avenue RN 380F
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508880/suppl/GSM508880_CL_HET2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508880/suppl/GSM508880_CL_HET2.CHP.gz
| | Sample_series_id | GSE20299
| | Sample_data_row_count | 22716
| | |
|
GSM508881 | GPL8759 |
|
CL_Spdef_KN1 Mice
|
Colon
|
tissue: Colon
strain: C57BL/6
|
Colon sample from Spdef knockout mice
|
| Sample_geo_accession | GSM508881
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | Feb 12 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | None
| | Sample_growth_protocol_ch1 | 16 week old mice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Flash frozen samples (–80°C) were homogenized. RNA was isolated using TRIzol Reagent (Invitrogen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For transcriptional profiling, total RNA was converted into cRNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA) and hybridized to Affymetrix HT Mouse Genome 430 microarrays.
| | Sample_hyb_protocol | All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays. The HT_MG-430A Array plate consists of 24 single MG-430A arrays arranged into standard SBS 24 well plate format. All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.
| | Sample_scan_protocol | HT Plate Scanner
| | Sample_data_processing | The data were extracted with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL8759
| | Sample_contact_name | BIDMC ,,Genomics
| | Sample_contact_email | mbhasin@bidmc.harvard.edu
| | Sample_contact_phone | 617 735 2509
| | Sample_contact_fax | 6177352510
| | Sample_contact_institute | Beth Israel Deaconess Medical Center
| | Sample_contact_address | 330 Brookline Avenue RN 380F
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508881/suppl/GSM508881_CL_Spdef_KN1.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508881/suppl/GSM508881_CL_Spdef_KN1.CHP.gz
| | Sample_series_id | GSE20299
| | Sample_data_row_count | 22716
| | |
|
GSM508882 | GPL8759 |
|
CL_Spdef_KN2 Mice
|
Colon
|
tissue: Colon
strain: C57BL/6
|
Colon sample from Spdef knockout mice
|
| Sample_geo_accession | GSM508882
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | Feb 12 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | None
| | Sample_growth_protocol_ch1 | 16 week old mice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Flash frozen samples (–80°C) were homogenized. RNA was isolated using TRIzol Reagent (Invitrogen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For transcriptional profiling, total RNA was converted into cRNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA) and hybridized to Affymetrix HT Mouse Genome 430 microarrays.
| | Sample_hyb_protocol | All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays. The HT_MG-430A Array plate consists of 24 single MG-430A arrays arranged into standard SBS 24 well plate format. All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.
| | Sample_scan_protocol | HT Plate Scanner
| | Sample_data_processing | The data were extracted with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
| | Sample_platform_id | GPL8759
| | Sample_contact_name | BIDMC ,,Genomics
| | Sample_contact_email | mbhasin@bidmc.harvard.edu
| | Sample_contact_phone | 617 735 2509
| | Sample_contact_fax | 6177352510
| | Sample_contact_institute | Beth Israel Deaconess Medical Center
| | Sample_contact_address | 330 Brookline Avenue RN 380F
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508882/suppl/GSM508882_CL_Spdef_KN2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM508nnn/GSM508882/suppl/GSM508882_CL_Spdef_KN2.CHP.gz
| | Sample_series_id | GSE20299
| | Sample_data_row_count | 22716
| | |
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