Search results for the GEO ID: GSE46493  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1131226 | GPL570 |
|
U2OS No Treatment, Replicate 1
|
U2OS No Treatment
|
cell line: U2OS
cell type: osteosarcoma
agent: No Treatment (control for Doxorubicin-treated cells)
|
U2OS No Treatment control 24 hr, control for Doxorubicin-treated cells
|
| Sample_geo_accession | GSM1131226
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Apr 30 2013
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | for No Treatment: none; Doxorubicin: 0.6 ug/ml Doxorubicin for 24 hrs; DMSO; 0.1% DMSO for 24 hrs; Nutlin: 10 uM Nutlin-3 for 24 hrs
| | Sample_growth_protocol_ch1 | U2OS expressing endogenous wild-type p53 was maintained in McCoy's 5A medium supplemented with 10% fetal calf serum and 1% Penicillin/Streptomycin at 37ºCin 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from U2OS cells was extracted using the RNeasy Midi kit with DNAse treatment according to the manufacturer's protocol (Qiagen). Quantity and quality was determined by Nanodrop ND1000 and Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol.
| | Sample_hyb_protocol | 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.
| | Sample_scan_protocol | Arrays were scanned in an Affymetrix Scanner 3000.
| | Sample_data_processing | data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files..
| | Sample_platform_id | GPL570
| | Sample_contact_name | NIEHS,,Microarray Core
| | Sample_contact_email | microarray@niehs.nih.gov, liuliw@niehs.nih.gov
| | Sample_contact_laboratory | Microarray Core
| | Sample_contact_department | DIR
| | Sample_contact_institute | NIEHS
| | Sample_contact_address | 111 T.W. Alexander Drive
| | Sample_contact_city | RTP
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131226/suppl/GSM1131226_11448_U2OS_No_Treatment_Rep_1_HG-U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131226/suppl/GSM1131226_11448_U2OS_No_Treatment_Rep_1_HG-U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE46493
| | Sample_series_id | GSE46642
| | Sample_data_row_count | 54675
| | |
|
GSM1131227 | GPL570 |
|
U2OS No Treatment, Replicate 2
|
U2OS No Treatment
|
cell line: U2OS
cell type: osteosarcoma
agent: No Treatment (control for Doxorubicin-treated cells)
|
U2OS No Treatment control 24 hr, control for Doxorubicin-treated cells
|
| Sample_geo_accession | GSM1131227
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Apr 30 2013
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | for No Treatment: none; Doxorubicin: 0.6 ug/ml Doxorubicin for 24 hrs; DMSO; 0.1% DMSO for 24 hrs; Nutlin: 10 uM Nutlin-3 for 24 hrs
| | Sample_growth_protocol_ch1 | U2OS expressing endogenous wild-type p53 was maintained in McCoy's 5A medium supplemented with 10% fetal calf serum and 1% Penicillin/Streptomycin at 37ºCin 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from U2OS cells was extracted using the RNeasy Midi kit with DNAse treatment according to the manufacturer's protocol (Qiagen). Quantity and quality was determined by Nanodrop ND1000 and Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol.
| | Sample_hyb_protocol | 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.
| | Sample_scan_protocol | Arrays were scanned in an Affymetrix Scanner 3000.
| | Sample_data_processing | data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files..
| | Sample_platform_id | GPL570
| | Sample_contact_name | NIEHS,,Microarray Core
| | Sample_contact_email | microarray@niehs.nih.gov, liuliw@niehs.nih.gov
| | Sample_contact_laboratory | Microarray Core
| | Sample_contact_department | DIR
| | Sample_contact_institute | NIEHS
| | Sample_contact_address | 111 T.W. Alexander Drive
| | Sample_contact_city | RTP
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131227/suppl/GSM1131227_11449_U2OS_No_Treatment_Rep_2_HG-U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131227/suppl/GSM1131227_11449_U2OS_No_Treatment_Rep_2_HG-U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE46493
| | Sample_series_id | GSE46642
| | Sample_data_row_count | 54675
| | |
|
GSM1131228 | GPL570 |
|
U2OS No Treatment, Replicate 3
|
U2OS No Treatment
|
cell line: U2OS
cell type: osteosarcoma
agent: No Treatment (control for Doxorubicin-treated cells)
|
U2OS No Treatment control 24 hr, control for Doxorubicin-treated cells
|
| Sample_geo_accession | GSM1131228
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Apr 30 2013
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | for No Treatment: none; Doxorubicin: 0.6 ug/ml Doxorubicin for 24 hrs; DMSO; 0.1% DMSO for 24 hrs; Nutlin: 10 uM Nutlin-3 for 24 hrs
| | Sample_growth_protocol_ch1 | U2OS expressing endogenous wild-type p53 was maintained in McCoy's 5A medium supplemented with 10% fetal calf serum and 1% Penicillin/Streptomycin at 37ºCin 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from U2OS cells was extracted using the RNeasy Midi kit with DNAse treatment according to the manufacturer's protocol (Qiagen). Quantity and quality was determined by Nanodrop ND1000 and Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol.
| | Sample_hyb_protocol | 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.
| | Sample_scan_protocol | Arrays were scanned in an Affymetrix Scanner 3000.
| | Sample_data_processing | data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files..
| | Sample_platform_id | GPL570
| | Sample_contact_name | NIEHS,,Microarray Core
| | Sample_contact_email | microarray@niehs.nih.gov, liuliw@niehs.nih.gov
| | Sample_contact_laboratory | Microarray Core
| | Sample_contact_department | DIR
| | Sample_contact_institute | NIEHS
| | Sample_contact_address | 111 T.W. Alexander Drive
| | Sample_contact_city | RTP
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131228/suppl/GSM1131228_11450_U2OS_No_Treatment_Rep_3_HG-U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131228/suppl/GSM1131228_11450_U2OS_No_Treatment_Rep_3_HG-U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE46493
| | Sample_series_id | GSE46642
| | Sample_data_row_count | 54675
| | |
|
GSM1131229 | GPL570 |
|
U2OS Doxorubicin treated, Replicate 1
|
U2OS Doxorubicin treated
|
cell line: U2OS
cell type: osteosarcoma
agent: Doxorubicin
|
U2OS cells treated with 0.6 ug/ml Doxorubicin for 24 hr
|
| Sample_geo_accession | GSM1131229
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Apr 30 2013
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | for No Treatment: none; Doxorubicin: 0.6 ug/ml Doxorubicin for 24 hrs; DMSO; 0.1% DMSO for 24 hrs; Nutlin: 10 uM Nutlin-3 for 24 hrs
| | Sample_growth_protocol_ch1 | U2OS expressing endogenous wild-type p53 was maintained in McCoy's 5A medium supplemented with 10% fetal calf serum and 1% Penicillin/Streptomycin at 37ºCin 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from U2OS cells was extracted using the RNeasy Midi kit with DNAse treatment according to the manufacturer's protocol (Qiagen). Quantity and quality was determined by Nanodrop ND1000 and Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol.
| | Sample_hyb_protocol | 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.
| | Sample_scan_protocol | Arrays were scanned in an Affymetrix Scanner 3000.
| | Sample_data_processing | data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files..
| | Sample_platform_id | GPL570
| | Sample_contact_name | NIEHS,,Microarray Core
| | Sample_contact_email | microarray@niehs.nih.gov, liuliw@niehs.nih.gov
| | Sample_contact_laboratory | Microarray Core
| | Sample_contact_department | DIR
| | Sample_contact_institute | NIEHS
| | Sample_contact_address | 111 T.W. Alexander Drive
| | Sample_contact_city | RTP
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131229/suppl/GSM1131229_11454_U2OS_Doxo_Rep_1_HG-U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131229/suppl/GSM1131229_11454_U2OS_Doxo_Rep_1_HG-U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE46493
| | Sample_series_id | GSE46642
| | Sample_data_row_count | 54675
| | |
|
GSM1131230 | GPL570 |
|
U2OS Doxorubicin treated, Replicate 2
|
U2OS Doxorubicin treated
|
cell line: U2OS
cell type: osteosarcoma
agent: Doxorubicin
|
U2OS cells treated with 0.6 ug/ml Doxorubicin for 24 hr
|
| Sample_geo_accession | GSM1131230
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Apr 30 2013
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | for No Treatment: none; Doxorubicin: 0.6 ug/ml Doxorubicin for 24 hrs; DMSO; 0.1% DMSO for 24 hrs; Nutlin: 10 uM Nutlin-3 for 24 hrs
| | Sample_growth_protocol_ch1 | U2OS expressing endogenous wild-type p53 was maintained in McCoy's 5A medium supplemented with 10% fetal calf serum and 1% Penicillin/Streptomycin at 37ºCin 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from U2OS cells was extracted using the RNeasy Midi kit with DNAse treatment according to the manufacturer's protocol (Qiagen). Quantity and quality was determined by Nanodrop ND1000 and Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol.
| | Sample_hyb_protocol | 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.
| | Sample_scan_protocol | Arrays were scanned in an Affymetrix Scanner 3000.
| | Sample_data_processing | data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files..
| | Sample_platform_id | GPL570
| | Sample_contact_name | NIEHS,,Microarray Core
| | Sample_contact_email | microarray@niehs.nih.gov, liuliw@niehs.nih.gov
| | Sample_contact_laboratory | Microarray Core
| | Sample_contact_department | DIR
| | Sample_contact_institute | NIEHS
| | Sample_contact_address | 111 T.W. Alexander Drive
| | Sample_contact_city | RTP
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131230/suppl/GSM1131230_11455_U2OS_Doxo_Rep_2_HG-U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131230/suppl/GSM1131230_11455_U2OS_Doxo_Rep_2_HG-U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE46493
| | Sample_series_id | GSE46642
| | Sample_data_row_count | 54675
| | |
|
GSM1131231 | GPL570 |
|
U2OS Doxorubicin treated, Replicate 3
|
U2OS Doxorubicin treated
|
cell line: U2OS
cell type: osteosarcoma
agent: Doxorubicin
|
U2OS cells treated with 0.6 ug/ml Doxorubicin for 24 hr
|
| Sample_geo_accession | GSM1131231
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Apr 30 2013
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | for No Treatment: none; Doxorubicin: 0.6 ug/ml Doxorubicin for 24 hrs; DMSO; 0.1% DMSO for 24 hrs; Nutlin: 10 uM Nutlin-3 for 24 hrs
| | Sample_growth_protocol_ch1 | U2OS expressing endogenous wild-type p53 was maintained in McCoy's 5A medium supplemented with 10% fetal calf serum and 1% Penicillin/Streptomycin at 37ºCin 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from U2OS cells was extracted using the RNeasy Midi kit with DNAse treatment according to the manufacturer's protocol (Qiagen). Quantity and quality was determined by Nanodrop ND1000 and Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol.
| | Sample_hyb_protocol | 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.
| | Sample_scan_protocol | Arrays were scanned in an Affymetrix Scanner 3000.
| | Sample_data_processing | data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files..
| | Sample_platform_id | GPL570
| | Sample_contact_name | NIEHS,,Microarray Core
| | Sample_contact_email | microarray@niehs.nih.gov, liuliw@niehs.nih.gov
| | Sample_contact_laboratory | Microarray Core
| | Sample_contact_department | DIR
| | Sample_contact_institute | NIEHS
| | Sample_contact_address | 111 T.W. Alexander Drive
| | Sample_contact_city | RTP
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131231/suppl/GSM1131231_11456_U2OS_Doxo_Rep_3_HG-U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131231/suppl/GSM1131231_11456_U2OS_Doxo_Rep_3_HG-U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE46493
| | Sample_series_id | GSE46642
| | Sample_data_row_count | 54675
| | |
|
GSM1131232 | GPL570 |
|
U2OS DMSO treated, Replicate 1
|
U2OS DMSO treated
|
cell line: U2OS
cell type: osteosarcoma
agent: DMSO (control for Nutlin-treated cells)
|
U2OS cells treated with 0.1% DMSO for 24 hr, control for Nutlin-treated cells
|
| Sample_geo_accession | GSM1131232
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Apr 30 2013
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | for No Treatment: none; Doxorubicin: 0.6 ug/ml Doxorubicin for 24 hrs; DMSO; 0.1% DMSO for 24 hrs; Nutlin: 10 uM Nutlin-3 for 24 hrs
| | Sample_growth_protocol_ch1 | U2OS expressing endogenous wild-type p53 was maintained in McCoy's 5A medium supplemented with 10% fetal calf serum and 1% Penicillin/Streptomycin at 37ºCin 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from U2OS cells was extracted using the RNeasy Midi kit with DNAse treatment according to the manufacturer's protocol (Qiagen). Quantity and quality was determined by Nanodrop ND1000 and Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol.
| | Sample_hyb_protocol | 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.
| | Sample_scan_protocol | Arrays were scanned in an Affymetrix Scanner 3000.
| | Sample_data_processing | data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files..
| | Sample_platform_id | GPL570
| | Sample_contact_name | NIEHS,,Microarray Core
| | Sample_contact_email | microarray@niehs.nih.gov, liuliw@niehs.nih.gov
| | Sample_contact_laboratory | Microarray Core
| | Sample_contact_department | DIR
| | Sample_contact_institute | NIEHS
| | Sample_contact_address | 111 T.W. Alexander Drive
| | Sample_contact_city | RTP
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131232/suppl/GSM1131232_10509_614_DMSO_Rep_1_HG-U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131232/suppl/GSM1131232_10509_614_DMSO_Rep_1_HG-U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE46493
| | Sample_series_id | GSE46642
| | Sample_data_row_count | 54675
| | |
|
GSM1131233 | GPL570 |
|
U2OS DMSO treated, Replicate 2
|
U2OS DMSO treated
|
cell line: U2OS
cell type: osteosarcoma
agent: DMSO (control for Nutlin-treated cells)
|
U2OS cells treated with 0.1% DMSO for 24 hr, control for Nutlin-treated cells
|
| Sample_geo_accession | GSM1131233
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Apr 30 2013
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | for No Treatment: none; Doxorubicin: 0.6 ug/ml Doxorubicin for 24 hrs; DMSO; 0.1% DMSO for 24 hrs; Nutlin: 10 uM Nutlin-3 for 24 hrs
| | Sample_growth_protocol_ch1 | U2OS expressing endogenous wild-type p53 was maintained in McCoy's 5A medium supplemented with 10% fetal calf serum and 1% Penicillin/Streptomycin at 37ºCin 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from U2OS cells was extracted using the RNeasy Midi kit with DNAse treatment according to the manufacturer's protocol (Qiagen). Quantity and quality was determined by Nanodrop ND1000 and Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol.
| | Sample_hyb_protocol | 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.
| | Sample_scan_protocol | Arrays were scanned in an Affymetrix Scanner 3000.
| | Sample_data_processing | data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files..
| | Sample_platform_id | GPL570
| | Sample_contact_name | NIEHS,,Microarray Core
| | Sample_contact_email | microarray@niehs.nih.gov, liuliw@niehs.nih.gov
| | Sample_contact_laboratory | Microarray Core
| | Sample_contact_department | DIR
| | Sample_contact_institute | NIEHS
| | Sample_contact_address | 111 T.W. Alexander Drive
| | Sample_contact_city | RTP
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131233/suppl/GSM1131233_10510_614_DMSO_Rep_2_HG-U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131233/suppl/GSM1131233_10510_614_DMSO_Rep_2_HG-U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE46493
| | Sample_series_id | GSE46642
| | Sample_data_row_count | 54675
| | |
|
GSM1131234 | GPL570 |
|
U2OS DMSO treated, Replicate 3
|
U2OS DMSO treated
|
cell line: U2OS
cell type: osteosarcoma
agent: DMSO (control for Nutlin-treated cells)
|
U2OS cells treated with 0.1% DMSO for 24 hr, control for Nutlin-treated cells
|
| Sample_geo_accession | GSM1131234
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Apr 30 2013
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | for No Treatment: none; Doxorubicin: 0.6 ug/ml Doxorubicin for 24 hrs; DMSO; 0.1% DMSO for 24 hrs; Nutlin: 10 uM Nutlin-3 for 24 hrs
| | Sample_growth_protocol_ch1 | U2OS expressing endogenous wild-type p53 was maintained in McCoy's 5A medium supplemented with 10% fetal calf serum and 1% Penicillin/Streptomycin at 37ºCin 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from U2OS cells was extracted using the RNeasy Midi kit with DNAse treatment according to the manufacturer's protocol (Qiagen). Quantity and quality was determined by Nanodrop ND1000 and Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol.
| | Sample_hyb_protocol | 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.
| | Sample_scan_protocol | Arrays were scanned in an Affymetrix Scanner 3000.
| | Sample_data_processing | data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files..
| | Sample_platform_id | GPL570
| | Sample_contact_name | NIEHS,,Microarray Core
| | Sample_contact_email | microarray@niehs.nih.gov, liuliw@niehs.nih.gov
| | Sample_contact_laboratory | Microarray Core
| | Sample_contact_department | DIR
| | Sample_contact_institute | NIEHS
| | Sample_contact_address | 111 T.W. Alexander Drive
| | Sample_contact_city | RTP
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131234/suppl/GSM1131234_10511_614_DMSO_Rep_3_HG-U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131234/suppl/GSM1131234_10511_614_DMSO_Rep_3_HG-U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE46493
| | Sample_series_id | GSE46642
| | Sample_data_row_count | 54675
| | |
|
GSM1131235 | GPL570 |
|
U2OS Nutlin-3 treated, Replicate 1
|
U2OS Nutlin-3 treated
|
cell line: U2OS
cell type: osteosarcoma
agent: Nutlin-3
|
U2OS cells treated with 10 uM Nutlin-3 for 24 hr
|
| Sample_geo_accession | GSM1131235
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Apr 30 2013
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | for No Treatment: none; Doxorubicin: 0.6 ug/ml Doxorubicin for 24 hrs; DMSO; 0.1% DMSO for 24 hrs; Nutlin: 10 uM Nutlin-3 for 24 hrs
| | Sample_growth_protocol_ch1 | U2OS expressing endogenous wild-type p53 was maintained in McCoy's 5A medium supplemented with 10% fetal calf serum and 1% Penicillin/Streptomycin at 37ºCin 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from U2OS cells was extracted using the RNeasy Midi kit with DNAse treatment according to the manufacturer's protocol (Qiagen). Quantity and quality was determined by Nanodrop ND1000 and Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol.
| | Sample_hyb_protocol | 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.
| | Sample_scan_protocol | Arrays were scanned in an Affymetrix Scanner 3000.
| | Sample_data_processing | data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files..
| | Sample_platform_id | GPL570
| | Sample_contact_name | NIEHS,,Microarray Core
| | Sample_contact_email | microarray@niehs.nih.gov, liuliw@niehs.nih.gov
| | Sample_contact_laboratory | Microarray Core
| | Sample_contact_department | DIR
| | Sample_contact_institute | NIEHS
| | Sample_contact_address | 111 T.W. Alexander Drive
| | Sample_contact_city | RTP
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131235/suppl/GSM1131235_10515_614_Nutlin_Rep_1_HG-U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131235/suppl/GSM1131235_10515_614_Nutlin_Rep_1_HG-U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE46493
| | Sample_series_id | GSE46642
| | Sample_data_row_count | 54675
| | |
|
GSM1131236 | GPL570 |
|
U2OS Nutlin-3 treated, Replicate 2
|
U2OS Nutlin-3 treated
|
cell line: U2OS
cell type: osteosarcoma
agent: Nutlin-3
|
U2OS cells treated with 10 uM Nutlin-3 for 24 hr
|
| Sample_geo_accession | GSM1131236
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Apr 30 2013
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | for No Treatment: none; Doxorubicin: 0.6 ug/ml Doxorubicin for 24 hrs; DMSO; 0.1% DMSO for 24 hrs; Nutlin: 10 uM Nutlin-3 for 24 hrs
| | Sample_growth_protocol_ch1 | U2OS expressing endogenous wild-type p53 was maintained in McCoy's 5A medium supplemented with 10% fetal calf serum and 1% Penicillin/Streptomycin at 37ºCin 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from U2OS cells was extracted using the RNeasy Midi kit with DNAse treatment according to the manufacturer's protocol (Qiagen). Quantity and quality was determined by Nanodrop ND1000 and Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol.
| | Sample_hyb_protocol | 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.
| | Sample_scan_protocol | Arrays were scanned in an Affymetrix Scanner 3000.
| | Sample_data_processing | data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files..
| | Sample_platform_id | GPL570
| | Sample_contact_name | NIEHS,,Microarray Core
| | Sample_contact_email | microarray@niehs.nih.gov, liuliw@niehs.nih.gov
| | Sample_contact_laboratory | Microarray Core
| | Sample_contact_department | DIR
| | Sample_contact_institute | NIEHS
| | Sample_contact_address | 111 T.W. Alexander Drive
| | Sample_contact_city | RTP
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131236/suppl/GSM1131236_10516_614_Nutlin_Rep_2_HG-U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131236/suppl/GSM1131236_10516_614_Nutlin_Rep_2_HG-U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE46493
| | Sample_series_id | GSE46642
| | Sample_data_row_count | 54675
| | |
|
GSM1131237 | GPL570 |
|
U2OS Nutlin-3 treated, Replicate 3
|
U2OS Nutlin-3 treated
|
cell line: U2OS
cell type: osteosarcoma
agent: Nutlin-3
|
U2OS cells treated with 10 uM Nutlin-3 for 24 hr
|
| Sample_geo_accession | GSM1131237
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Apr 30 2013
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | for No Treatment: none; Doxorubicin: 0.6 ug/ml Doxorubicin for 24 hrs; DMSO; 0.1% DMSO for 24 hrs; Nutlin: 10 uM Nutlin-3 for 24 hrs
| | Sample_growth_protocol_ch1 | U2OS expressing endogenous wild-type p53 was maintained in McCoy's 5A medium supplemented with 10% fetal calf serum and 1% Penicillin/Streptomycin at 37ºCin 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from U2OS cells was extracted using the RNeasy Midi kit with DNAse treatment according to the manufacturer's protocol (Qiagen). Quantity and quality was determined by Nanodrop ND1000 and Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol.
| | Sample_hyb_protocol | 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.
| | Sample_scan_protocol | Arrays were scanned in an Affymetrix Scanner 3000.
| | Sample_data_processing | data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files..
| | Sample_platform_id | GPL570
| | Sample_contact_name | NIEHS,,Microarray Core
| | Sample_contact_email | microarray@niehs.nih.gov, liuliw@niehs.nih.gov
| | Sample_contact_laboratory | Microarray Core
| | Sample_contact_department | DIR
| | Sample_contact_institute | NIEHS
| | Sample_contact_address | 111 T.W. Alexander Drive
| | Sample_contact_city | RTP
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27709
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131237/suppl/GSM1131237_10517_614_Nutlin_Rep_3_HG-U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1131nnn/GSM1131237/suppl/GSM1131237_10517_614_Nutlin_Rep_3_HG-U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE46493
| | Sample_series_id | GSE46642
| | Sample_data_row_count | 54675
| | |
|
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
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