Search results for the GEO ID: GSE17661  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM440879 | GPL1355 |
|
WB-F344, Control, Rep1
|
WB-F344 cells, Vehicle Control
|
rapamycin response: Sensitive
doubling time: 42h
tumorigenic: No
|
Normal diploid rat liver epithelial cell line derived from adult male Fischer rat
|
| Sample_geo_accession | GSM440879
| | Sample_status | Public on Sep 20 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Sep 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | 10^6 cells were plated per 100mm plate and allowed to attach overnight. Cells were treated with 50nM Rapamycin or DMSO vehicle for 24 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in DMEM/F-12 containing 10% fetal bovine serum, 2mM L-glutamine and 0.1% antibiotic-antimycotic solution. Cells were cultured at 37°C with 5.0% carbon dioxide.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturers instructions. RNA was further purified using the Uneasy kit (Qiagen). RNA quality was evaluated using the Agilent Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 5 ug of total RNA using the one cycle target kit from Affymetrix according to the manufacturer's instructions.
| | Sample_hyb_protocol | Fragmented cRNA (10 ug) was hybridized for 16 hour at 45°C on a Affymetrix GeneChip Rat Genome 230 2.0 array. Arrays were washed using the Affymetrix fluidics station and stained with strepavidinphycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was analyzed using GeneSpring GX 7.3 (Agilent Technologies). Microarray fluorescence signals were normalized using Robust Multiarray Average (RMA). For gene expression comparisons, genes with expression values less than 100 or fold change less than 1.2 were excluded from further statistical analyses. A two-sample t-test using p-value cut-off of 0.05 with multiple test correction (Benjamini and Hochberg false discovery rate) was applied for each gene to determine if the gene were differentially expressed in the pair wise comparisons. Triplicate control and rapamycin samples from each cell line were used in these comparisons.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jennifer,Ann,Sanders
| | Sample_contact_email | Jennifer_Sanders@brown.edu
| | Sample_contact_department | Pediatric Endocrinology
| | Sample_contact_institute | Rhode Island Hospital
| | Sample_contact_address | 593 Eddy Street
| | Sample_contact_city | Providence
| | Sample_contact_state | RI
| | Sample_contact_zip/postal_code | 02903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440879/suppl/GSM440879.CEL.gz
| | Sample_series_id | GSE17661
| | Sample_series_id | GSE17677
| | Sample_data_row_count | 31099
| | |
|
GSM440880 | GPL1355 |
|
WB-F344, Control, Rep2
|
WB-F344 cells, Vehicle Control
|
rapamycin response: Sensitive
doubling time: 42h
tumorigenic: No
|
Normal diploid rat liver epithelial cell line derived from adult male Fischer rat
|
| Sample_geo_accession | GSM440880
| | Sample_status | Public on Sep 20 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Sep 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | 10^6 cells were plated per 100mm plate and allowed to attach overnight. Cells were treated with 50nM Rapamycin or DMSO vehicle for 24 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in DMEM/F-12 containing 10% fetal bovine serum, 2mM L-glutamine and 0.1% antibiotic-antimycotic solution. Cells were cultured at 37°C with 5.0% carbon dioxide.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturers instructions. RNA was further purified using the Uneasy kit (Qiagen). RNA quality was evaluated using the Agilent Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 5 ug of total RNA using the one cycle target kit from Affymetrix according to the manufacturer's instructions.
| | Sample_hyb_protocol | Fragmented cRNA (10 ug) was hybridized for 16 hour at 45°C on a Affymetrix GeneChip Rat Genome 230 2.0 array. Arrays were washed using the Affymetrix fluidics station and stained with strepavidinphycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was analyzed using GeneSpring GX 7.3 (Agilent Technologies). Microarray fluorescence signals were normalized using Robust Multiarray Average (RMA). For gene expression comparisons, genes with expression values less than 100 or fold change less than 1.2 were excluded from further statistical analyses. A two-sample t-test using p-value cut-off of 0.05 with multiple test correction (Benjamini and Hochberg false discovery rate) was applied for each gene to determine if the gene were differentially expressed in the pair wise comparisons. Triplicate control and rapamycin samples from each cell line were used in these comparisons.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jennifer,Ann,Sanders
| | Sample_contact_email | Jennifer_Sanders@brown.edu
| | Sample_contact_department | Pediatric Endocrinology
| | Sample_contact_institute | Rhode Island Hospital
| | Sample_contact_address | 593 Eddy Street
| | Sample_contact_city | Providence
| | Sample_contact_state | RI
| | Sample_contact_zip/postal_code | 02903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440880/suppl/GSM440880.CEL.gz
| | Sample_series_id | GSE17661
| | Sample_series_id | GSE17677
| | Sample_data_row_count | 31099
| | |
|
GSM440881 | GPL1355 |
|
WB-F344, Control, Rep3
|
WB-F344 cells, Vehicle Control
|
rapamycin response: Sensitive
doubling time: 42h
tumorigenic: No
|
Normal diploid rat liver epithelial cell line derived from adult male Fischer rat
|
| Sample_geo_accession | GSM440881
| | Sample_status | Public on Sep 20 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Sep 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | 10^6 cells were plated per 100mm plate and allowed to attach overnight. Cells were treated with 50nM Rapamycin or DMSO vehicle for 24 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in DMEM/F-12 containing 10% fetal bovine serum, 2mM L-glutamine and 0.1% antibiotic-antimycotic solution. Cells were cultured at 37°C with 5.0% carbon dioxide.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturers instructions. RNA was further purified using the Uneasy kit (Qiagen). RNA quality was evaluated using the Agilent Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 5 ug of total RNA using the one cycle target kit from Affymetrix according to the manufacturer's instructions.
| | Sample_hyb_protocol | Fragmented cRNA (10 ug) was hybridized for 16 hour at 45°C on a Affymetrix GeneChip Rat Genome 230 2.0 array. Arrays were washed using the Affymetrix fluidics station and stained with strepavidinphycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was analyzed using GeneSpring GX 7.3 (Agilent Technologies). Microarray fluorescence signals were normalized using Robust Multiarray Average (RMA). For gene expression comparisons, genes with expression values less than 100 or fold change less than 1.2 were excluded from further statistical analyses. A two-sample t-test using p-value cut-off of 0.05 with multiple test correction (Benjamini and Hochberg false discovery rate) was applied for each gene to determine if the gene were differentially expressed in the pair wise comparisons. Triplicate control and rapamycin samples from each cell line were used in these comparisons.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jennifer,Ann,Sanders
| | Sample_contact_email | Jennifer_Sanders@brown.edu
| | Sample_contact_department | Pediatric Endocrinology
| | Sample_contact_institute | Rhode Island Hospital
| | Sample_contact_address | 593 Eddy Street
| | Sample_contact_city | Providence
| | Sample_contact_state | RI
| | Sample_contact_zip/postal_code | 02903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440881/suppl/GSM440881.CEL.gz
| | Sample_series_id | GSE17661
| | Sample_series_id | GSE17677
| | Sample_data_row_count | 31099
| | |
|
GSM440882 | GPL1355 |
|
WB-F344, Rapamycin, Rep1
|
WB-F344 cells, 50nM Rapamycin
|
rapamycin response: Sensitive
doubling time: 42h
tumorigenic: No
|
Normal diploid rat liver epithelial cell line derived from adult male Fischer rat
|
| Sample_geo_accession | GSM440882
| | Sample_status | Public on Sep 20 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Sep 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | 10^6 cells were plated per 100mm plate and allowed to attach overnight. Cells were treated with 50nM Rapamycin or DMSO vehicle for 24 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in DMEM/F-12 containing 10% fetal bovine serum, 2mM L-glutamine and 0.1% antibiotic-antimycotic solution. Cells were cultured at 37°C with 5.0% carbon dioxide.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturers instructions. RNA was further purified using the Uneasy kit (Qiagen). RNA quality was evaluated using the Agilent Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 5 ug of total RNA using the one cycle target kit from Affymetrix according to the manufacturer's instructions.
| | Sample_hyb_protocol | Fragmented cRNA (10 ug) was hybridized for 16 hour at 45°C on a Affymetrix GeneChip Rat Genome 230 2.0 array. Arrays were washed using the Affymetrix fluidics station and stained with strepavidinphycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was analyzed using GeneSpring GX 7.3 (Agilent Technologies). Microarray fluorescence signals were normalized using Robust Multiarray Average (RMA). For gene expression comparisons, genes with expression values less than 100 or fold change less than 1.2 were excluded from further statistical analyses. A two-sample t-test using p-value cut-off of 0.05 with multiple test correction (Benjamini and Hochberg false discovery rate) was applied for each gene to determine if the gene were differentially expressed in the pair wise comparisons. Triplicate control and rapamycin samples from each cell line were used in these comparisons.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jennifer,Ann,Sanders
| | Sample_contact_email | Jennifer_Sanders@brown.edu
| | Sample_contact_department | Pediatric Endocrinology
| | Sample_contact_institute | Rhode Island Hospital
| | Sample_contact_address | 593 Eddy Street
| | Sample_contact_city | Providence
| | Sample_contact_state | RI
| | Sample_contact_zip/postal_code | 02903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440882/suppl/GSM440882.CEL.gz
| | Sample_series_id | GSE17661
| | Sample_series_id | GSE17677
| | Sample_data_row_count | 31099
| | |
|
GSM440883 | GPL1355 |
|
WB-F344, Rapamycin, Rep2
|
WB-F344 cells, 50nM Rapamycin
|
rapamycin response: Sensitive
doubling time: 42h
tumorigenic: No
|
Normal diploid rat liver epithelial cell line derived from adult male Fischer rat
|
| Sample_geo_accession | GSM440883
| | Sample_status | Public on Sep 20 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Sep 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | 10^6 cells were plated per 100mm plate and allowed to attach overnight. Cells were treated with 50nM Rapamycin or DMSO vehicle for 24 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in DMEM/F-12 containing 10% fetal bovine serum, 2mM L-glutamine and 0.1% antibiotic-antimycotic solution. Cells were cultured at 37°C with 5.0% carbon dioxide.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturers instructions. RNA was further purified using the Uneasy kit (Qiagen). RNA quality was evaluated using the Agilent Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 5 ug of total RNA using the one cycle target kit from Affymetrix according to the manufacturer's instructions.
| | Sample_hyb_protocol | Fragmented cRNA (10 ug) was hybridized for 16 hour at 45°C on a Affymetrix GeneChip Rat Genome 230 2.0 array. Arrays were washed using the Affymetrix fluidics station and stained with strepavidinphycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was analyzed using GeneSpring GX 7.3 (Agilent Technologies). Microarray fluorescence signals were normalized using Robust Multiarray Average (RMA). For gene expression comparisons, genes with expression values less than 100 or fold change less than 1.2 were excluded from further statistical analyses. A two-sample t-test using p-value cut-off of 0.05 with multiple test correction (Benjamini and Hochberg false discovery rate) was applied for each gene to determine if the gene were differentially expressed in the pair wise comparisons. Triplicate control and rapamycin samples from each cell line were used in these comparisons.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jennifer,Ann,Sanders
| | Sample_contact_email | Jennifer_Sanders@brown.edu
| | Sample_contact_department | Pediatric Endocrinology
| | Sample_contact_institute | Rhode Island Hospital
| | Sample_contact_address | 593 Eddy Street
| | Sample_contact_city | Providence
| | Sample_contact_state | RI
| | Sample_contact_zip/postal_code | 02903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440883/suppl/GSM440883.CEL.gz
| | Sample_series_id | GSE17661
| | Sample_series_id | GSE17677
| | Sample_data_row_count | 31099
| | |
|
GSM440884 | GPL1355 |
|
WB-F344, Rapamycin, Rep3
|
WB-F344 cells, 50nM Rapamycin
|
rapamycin response: Sensitive
doubling time: 42h
tumorigenic: No
|
Normal diploid rat liver epithelial cell line derived from adult male Fischer rat
|
| Sample_geo_accession | GSM440884
| | Sample_status | Public on Sep 20 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Sep 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | 10^6 cells were plated per 100mm plate and allowed to attach overnight. Cells were treated with 50nM Rapamycin or DMSO vehicle for 24 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in DMEM/F-12 containing 10% fetal bovine serum, 2mM L-glutamine and 0.1% antibiotic-antimycotic solution. Cells were cultured at 37°C with 5.0% carbon dioxide.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturers instructions. RNA was further purified using the Uneasy kit (Qiagen). RNA quality was evaluated using the Agilent Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 5 ug of total RNA using the one cycle target kit from Affymetrix according to the manufacturer's instructions.
| | Sample_hyb_protocol | Fragmented cRNA (10 ug) was hybridized for 16 hour at 45°C on a Affymetrix GeneChip Rat Genome 230 2.0 array. Arrays were washed using the Affymetrix fluidics station and stained with strepavidinphycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was analyzed using GeneSpring GX 7.3 (Agilent Technologies). Microarray fluorescence signals were normalized using Robust Multiarray Average (RMA). For gene expression comparisons, genes with expression values less than 100 or fold change less than 1.2 were excluded from further statistical analyses. A two-sample t-test using p-value cut-off of 0.05 with multiple test correction (Benjamini and Hochberg false discovery rate) was applied for each gene to determine if the gene were differentially expressed in the pair wise comparisons. Triplicate control and rapamycin samples from each cell line were used in these comparisons.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jennifer,Ann,Sanders
| | Sample_contact_email | Jennifer_Sanders@brown.edu
| | Sample_contact_department | Pediatric Endocrinology
| | Sample_contact_institute | Rhode Island Hospital
| | Sample_contact_address | 593 Eddy Street
| | Sample_contact_city | Providence
| | Sample_contact_state | RI
| | Sample_contact_zip/postal_code | 02903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440884/suppl/GSM440884.CEL.gz
| | Sample_series_id | GSE17661
| | Sample_series_id | GSE17677
| | Sample_data_row_count | 31099
| | |
|
GSM440885 | GPL1355 |
|
WB311, Control, Rep1
|
WB311 cells, Vehicle Control
|
rapamycin response: Resistant
doubling time: 15.5h
tumorigenic: Yes
|
Spontaneously derived from WB-F344 cell line
|
| Sample_geo_accession | GSM440885
| | Sample_status | Public on Sep 20 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Sep 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | 10^6 cells were plated per 100mm plate and allowed to attach overnight. Cells were treated with 50nM Rapamycin or DMSO vehicle for 24 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in DMEM/F-12 containing 10% fetal bovine serum, 2mM L-glutamine and 0.1% antibiotic-antimycotic solution. Cells were cultured at 37°C with 5.0% carbon dioxide.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturers instructions. RNA was further purified using the Uneasy kit (Qiagen). RNA quality was evaluated using the Agilent Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 5 ug of total RNA using the one cycle target kit from Affymetrix according to the manufacturer's instructions.
| | Sample_hyb_protocol | Fragmented cRNA (10 ug) was hybridized for 16 hour at 45°C on a Affymetrix GeneChip Rat Genome 230 2.0 array. Arrays were washed using the Affymetrix fluidics station and stained with strepavidinphycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was analyzed using GeneSpring GX 7.3 (Agilent Technologies). Microarray fluorescence signals were normalized using Robust Multiarray Average (RMA). For gene expression comparisons, genes with expression values less than 100 or fold change less than 1.2 were excluded from further statistical analyses. A two-sample t-test using p-value cut-off of 0.05 with multiple test correction (Benjamini and Hochberg false discovery rate) was applied for each gene to determine if the gene were differentially expressed in the pair wise comparisons. Triplicate control and rapamycin samples from each cell line were used in these comparisons.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jennifer,Ann,Sanders
| | Sample_contact_email | Jennifer_Sanders@brown.edu
| | Sample_contact_department | Pediatric Endocrinology
| | Sample_contact_institute | Rhode Island Hospital
| | Sample_contact_address | 593 Eddy Street
| | Sample_contact_city | Providence
| | Sample_contact_state | RI
| | Sample_contact_zip/postal_code | 02903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440885/suppl/GSM440885.CEL.gz
| | Sample_series_id | GSE17661
| | Sample_series_id | GSE17677
| | Sample_data_row_count | 31099
| | |
|
GSM440886 | GPL1355 |
|
WB311, Control, Rep2
|
WB311 cells, Vehicle Control
|
rapamycin response: Resistant
doubling time: 15.5h
tumorigenic: Yes
|
Spontaneously derived from WB-F344 cell line
|
| Sample_geo_accession | GSM440886
| | Sample_status | Public on Sep 20 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Sep 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | 10^6 cells were plated per 100mm plate and allowed to attach overnight. Cells were treated with 50nM Rapamycin or DMSO vehicle for 24 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in DMEM/F-12 containing 10% fetal bovine serum, 2mM L-glutamine and 0.1% antibiotic-antimycotic solution. Cells were cultured at 37°C with 5.0% carbon dioxide.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturers instructions. RNA was further purified using the Uneasy kit (Qiagen). RNA quality was evaluated using the Agilent Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 5 ug of total RNA using the one cycle target kit from Affymetrix according to the manufacturer's instructions.
| | Sample_hyb_protocol | Fragmented cRNA (10 ug) was hybridized for 16 hour at 45°C on a Affymetrix GeneChip Rat Genome 230 2.0 array. Arrays were washed using the Affymetrix fluidics station and stained with strepavidinphycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was analyzed using GeneSpring GX 7.3 (Agilent Technologies). Microarray fluorescence signals were normalized using Robust Multiarray Average (RMA). For gene expression comparisons, genes with expression values less than 100 or fold change less than 1.2 were excluded from further statistical analyses. A two-sample t-test using p-value cut-off of 0.05 with multiple test correction (Benjamini and Hochberg false discovery rate) was applied for each gene to determine if the gene were differentially expressed in the pair wise comparisons. Triplicate control and rapamycin samples from each cell line were used in these comparisons.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jennifer,Ann,Sanders
| | Sample_contact_email | Jennifer_Sanders@brown.edu
| | Sample_contact_department | Pediatric Endocrinology
| | Sample_contact_institute | Rhode Island Hospital
| | Sample_contact_address | 593 Eddy Street
| | Sample_contact_city | Providence
| | Sample_contact_state | RI
| | Sample_contact_zip/postal_code | 02903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440886/suppl/GSM440886.CEL.gz
| | Sample_series_id | GSE17661
| | Sample_series_id | GSE17677
| | Sample_data_row_count | 31099
| | |
|
GSM440887 | GPL1355 |
|
WB311, Control, Rep3
|
WB311 cells, Vehicle Control
|
rapamycin response: Resistant
doubling time: 15.5h
tumorigenic: Yes
|
Spontaneously derived from WB-F344 cell line
|
| Sample_geo_accession | GSM440887
| | Sample_status | Public on Sep 20 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Sep 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | 10^6 cells were plated per 100mm plate and allowed to attach overnight. Cells were treated with 50nM Rapamycin or DMSO vehicle for 24 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in DMEM/F-12 containing 10% fetal bovine serum, 2mM L-glutamine and 0.1% antibiotic-antimycotic solution. Cells were cultured at 37°C with 5.0% carbon dioxide.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturers instructions. RNA was further purified using the Uneasy kit (Qiagen). RNA quality was evaluated using the Agilent Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 5 ug of total RNA using the one cycle target kit from Affymetrix according to the manufacturer's instructions.
| | Sample_hyb_protocol | Fragmented cRNA (10 ug) was hybridized for 16 hour at 45°C on a Affymetrix GeneChip Rat Genome 230 2.0 array. Arrays were washed using the Affymetrix fluidics station and stained with strepavidinphycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was analyzed using GeneSpring GX 7.3 (Agilent Technologies). Microarray fluorescence signals were normalized using Robust Multiarray Average (RMA). For gene expression comparisons, genes with expression values less than 100 or fold change less than 1.2 were excluded from further statistical analyses. A two-sample t-test using p-value cut-off of 0.05 with multiple test correction (Benjamini and Hochberg false discovery rate) was applied for each gene to determine if the gene were differentially expressed in the pair wise comparisons. Triplicate control and rapamycin samples from each cell line were used in these comparisons.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jennifer,Ann,Sanders
| | Sample_contact_email | Jennifer_Sanders@brown.edu
| | Sample_contact_department | Pediatric Endocrinology
| | Sample_contact_institute | Rhode Island Hospital
| | Sample_contact_address | 593 Eddy Street
| | Sample_contact_city | Providence
| | Sample_contact_state | RI
| | Sample_contact_zip/postal_code | 02903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440887/suppl/GSM440887.CEL.gz
| | Sample_series_id | GSE17661
| | Sample_series_id | GSE17677
| | Sample_data_row_count | 31099
| | |
|
GSM440888 | GPL1355 |
|
WB311, Rapamycin, Rep1
|
WB311 cells, 50nM Rapamycin
|
rapamycin response: Resistant
doubling time: 15.5h
tumorigenic: Yes
|
Spontaneously derived from WB-F344 cell line
|
| Sample_geo_accession | GSM440888
| | Sample_status | Public on Sep 20 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Sep 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | 10^6 cells were plated per 100mm plate and allowed to attach overnight. Cells were treated with 50nM Rapamycin or DMSO vehicle for 24 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in DMEM/F-12 containing 10% fetal bovine serum, 2mM L-glutamine and 0.1% antibiotic-antimycotic solution. Cells were cultured at 37°C with 5.0% carbon dioxide.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturers instructions. RNA was further purified using the Uneasy kit (Qiagen). RNA quality was evaluated using the Agilent Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 5 ug of total RNA using the one cycle target kit from Affymetrix according to the manufacturer's instructions.
| | Sample_hyb_protocol | Fragmented cRNA (10 ug) was hybridized for 16 hour at 45°C on a Affymetrix GeneChip Rat Genome 230 2.0 array. Arrays were washed using the Affymetrix fluidics station and stained with strepavidinphycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was analyzed using GeneSpring GX 7.3 (Agilent Technologies). Microarray fluorescence signals were normalized using Robust Multiarray Average (RMA). For gene expression comparisons, genes with expression values less than 100 or fold change less than 1.2 were excluded from further statistical analyses. A two-sample t-test using p-value cut-off of 0.05 with multiple test correction (Benjamini and Hochberg false discovery rate) was applied for each gene to determine if the gene were differentially expressed in the pair wise comparisons. Triplicate control and rapamycin samples from each cell line were used in these comparisons.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jennifer,Ann,Sanders
| | Sample_contact_email | Jennifer_Sanders@brown.edu
| | Sample_contact_department | Pediatric Endocrinology
| | Sample_contact_institute | Rhode Island Hospital
| | Sample_contact_address | 593 Eddy Street
| | Sample_contact_city | Providence
| | Sample_contact_state | RI
| | Sample_contact_zip/postal_code | 02903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440888/suppl/GSM440888.CEL.gz
| | Sample_series_id | GSE17661
| | Sample_series_id | GSE17677
| | Sample_data_row_count | 31099
| | |
|
GSM440889 | GPL1355 |
|
WB311, Rapamycin, Rep2
|
WB311 cells, 50nM Rapamycin
|
rapamycin response: Resistant
doubling time: 15.5h
tumorigenic: Yes
|
Spontaneously derived from WB-F344 cell line
|
| Sample_geo_accession | GSM440889
| | Sample_status | Public on Sep 20 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Sep 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | 10^6 cells were plated per 100mm plate and allowed to attach overnight. Cells were treated with 50nM Rapamycin or DMSO vehicle for 24 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in DMEM/F-12 containing 10% fetal bovine serum, 2mM L-glutamine and 0.1% antibiotic-antimycotic solution. Cells were cultured at 37°C with 5.0% carbon dioxide.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturers instructions. RNA was further purified using the Uneasy kit (Qiagen). RNA quality was evaluated using the Agilent Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 5 ug of total RNA using the one cycle target kit from Affymetrix according to the manufacturer's instructions.
| | Sample_hyb_protocol | Fragmented cRNA (10 ug) was hybridized for 16 hour at 45°C on a Affymetrix GeneChip Rat Genome 230 2.0 array. Arrays were washed using the Affymetrix fluidics station and stained with strepavidinphycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was analyzed using GeneSpring GX 7.3 (Agilent Technologies). Microarray fluorescence signals were normalized using Robust Multiarray Average (RMA). For gene expression comparisons, genes with expression values less than 100 or fold change less than 1.2 were excluded from further statistical analyses. A two-sample t-test using p-value cut-off of 0.05 with multiple test correction (Benjamini and Hochberg false discovery rate) was applied for each gene to determine if the gene were differentially expressed in the pair wise comparisons. Triplicate control and rapamycin samples from each cell line were used in these comparisons.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jennifer,Ann,Sanders
| | Sample_contact_email | Jennifer_Sanders@brown.edu
| | Sample_contact_department | Pediatric Endocrinology
| | Sample_contact_institute | Rhode Island Hospital
| | Sample_contact_address | 593 Eddy Street
| | Sample_contact_city | Providence
| | Sample_contact_state | RI
| | Sample_contact_zip/postal_code | 02903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440889/suppl/GSM440889.CEL.gz
| | Sample_series_id | GSE17661
| | Sample_series_id | GSE17677
| | Sample_data_row_count | 31099
| | |
|
GSM440890 | GPL1355 |
|
WB311, Rapamycin, Rep3
|
WB311 cells, 50nM Rapamycin
|
rapamycin response: Resistant
doubling time: 15.5h
tumorigenic: Yes
|
Spontaneously derived from WB-F344 cell line
|
| Sample_geo_accession | GSM440890
| | Sample_status | Public on Sep 20 2009
| | Sample_submission_date | Aug 14 2009
| | Sample_last_update_date | Sep 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | 10^6 cells were plated per 100mm plate and allowed to attach overnight. Cells were treated with 50nM Rapamycin or DMSO vehicle for 24 hours.
| | Sample_growth_protocol_ch1 | Cells were cultured in DMEM/F-12 containing 10% fetal bovine serum, 2mM L-glutamine and 0.1% antibiotic-antimycotic solution. Cells were cultured at 37°C with 5.0% carbon dioxide.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturers instructions. RNA was further purified using the Uneasy kit (Qiagen). RNA quality was evaluated using the Agilent Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 5 ug of total RNA using the one cycle target kit from Affymetrix according to the manufacturer's instructions.
| | Sample_hyb_protocol | Fragmented cRNA (10 ug) was hybridized for 16 hour at 45°C on a Affymetrix GeneChip Rat Genome 230 2.0 array. Arrays were washed using the Affymetrix fluidics station and stained with strepavidinphycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was analyzed using GeneSpring GX 7.3 (Agilent Technologies). Microarray fluorescence signals were normalized using Robust Multiarray Average (RMA). For gene expression comparisons, genes with expression values less than 100 or fold change less than 1.2 were excluded from further statistical analyses. A two-sample t-test using p-value cut-off of 0.05 with multiple test correction (Benjamini and Hochberg false discovery rate) was applied for each gene to determine if the gene were differentially expressed in the pair wise comparisons. Triplicate control and rapamycin samples from each cell line were used in these comparisons.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Jennifer,Ann,Sanders
| | Sample_contact_email | Jennifer_Sanders@brown.edu
| | Sample_contact_department | Pediatric Endocrinology
| | Sample_contact_institute | Rhode Island Hospital
| | Sample_contact_address | 593 Eddy Street
| | Sample_contact_city | Providence
| | Sample_contact_state | RI
| | Sample_contact_zip/postal_code | 02903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM440nnn/GSM440890/suppl/GSM440890.CEL.gz
| | Sample_series_id | GSE17661
| | Sample_series_id | GSE17677
| | Sample_data_row_count | 31099
| | |
|
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| Select GSMs and click on "Add groups" |
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