Search results for the GEO ID: GSE31013  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM768525 | GPL1261 |
|
Lung_normal_1
|
Normal lung
|
age: 2-year-old
disease state: Normal
strain: B6C3F1
|
Control lung
|
| Sample_geo_accession | GSM768525
| | Sample_status | Public on Jun 22 2012
| | Sample_submission_date | Jul 28 2011
| | Sample_last_update_date | Jun 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | NA; no treatment was performed.
| | Sample_growth_protocol_ch1 | NA; tumors and tissue collected from B6C3F1 mice on 2-year National Toxicology Program bioassay.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Invitrogen PureLink Mini kit (Invitrogen cat# 12183-018A). Frozen tissue samples were lysed and homogenized in TRIzol reagent using a rotor-stator homogenizer. RNA isolation was performed according to the mini kit protocol. On column DNase treatment was performed using the Invitrogen PureLink DNase kit (Invitrogen cat# 12185-010) to purify the RNA samples. RNA concentration and 260/280 ratio were measured on a bioanalyzer (Agilent Technologies). RNA quality was checked on Embi Tec Precast RNA gels (Embec cat# GE-6010). Samples were aliquoted and stored at -80C.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One μg of total RNA was amplified as directed in the Affymetrix One-Cycle cDNA Synthesis protocol.
| | Sample_hyb_protocol | 15 μg of amplified biotin-cRNAs 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.
| | 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 | GPL1261
| | 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/GSM768nnn/GSM768525/suppl/GSM768525_8678_496_Control_Rep1_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM768nnn/GSM768525/suppl/GSM768525_8678_496_Control_Rep1_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE31013
| | Sample_data_row_count | 45101
| | |
|
GSM768526 | GPL1261 |
|
Lung_normal_2
|
Normal lung
|
age: 2-year-old
disease state: Normal
strain: B6C3F1
|
Control lung
|
| Sample_geo_accession | GSM768526
| | Sample_status | Public on Jun 22 2012
| | Sample_submission_date | Jul 28 2011
| | Sample_last_update_date | Jun 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | NA; no treatment was performed.
| | Sample_growth_protocol_ch1 | NA; tumors and tissue collected from B6C3F1 mice on 2-year National Toxicology Program bioassay.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Invitrogen PureLink Mini kit (Invitrogen cat# 12183-018A). Frozen tissue samples were lysed and homogenized in TRIzol reagent using a rotor-stator homogenizer. RNA isolation was performed according to the mini kit protocol. On column DNase treatment was performed using the Invitrogen PureLink DNase kit (Invitrogen cat# 12185-010) to purify the RNA samples. RNA concentration and 260/280 ratio were measured on a bioanalyzer (Agilent Technologies). RNA quality was checked on Embi Tec Precast RNA gels (Embec cat# GE-6010). Samples were aliquoted and stored at -80C.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One μg of total RNA was amplified as directed in the Affymetrix One-Cycle cDNA Synthesis protocol.
| | Sample_hyb_protocol | 15 μg of amplified biotin-cRNAs 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.
| | 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 | GPL1261
| | 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/GSM768nnn/GSM768526/suppl/GSM768526_8679_496_Control_Rep2_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM768nnn/GSM768526/suppl/GSM768526_8679_496_Control_Rep2_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE31013
| | Sample_data_row_count | 45101
| | |
|
GSM768527 | GPL1261 |
|
Lung_normal_3
|
Normal lung
|
age: 2-year-old
disease state: Normal
strain: B6C3F1
|
Control lung
|
| Sample_geo_accession | GSM768527
| | Sample_status | Public on Jun 22 2012
| | Sample_submission_date | Jul 28 2011
| | Sample_last_update_date | Jun 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | NA; no treatment was performed.
| | Sample_growth_protocol_ch1 | NA; tumors and tissue collected from B6C3F1 mice on 2-year National Toxicology Program bioassay.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Invitrogen PureLink Mini kit (Invitrogen cat# 12183-018A). Frozen tissue samples were lysed and homogenized in TRIzol reagent using a rotor-stator homogenizer. RNA isolation was performed according to the mini kit protocol. On column DNase treatment was performed using the Invitrogen PureLink DNase kit (Invitrogen cat# 12185-010) to purify the RNA samples. RNA concentration and 260/280 ratio were measured on a bioanalyzer (Agilent Technologies). RNA quality was checked on Embi Tec Precast RNA gels (Embec cat# GE-6010). Samples were aliquoted and stored at -80C.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One μg of total RNA was amplified as directed in the Affymetrix One-Cycle cDNA Synthesis protocol.
| | Sample_hyb_protocol | 15 μg of amplified biotin-cRNAs 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.
| | 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 | GPL1261
| | 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/GSM768nnn/GSM768527/suppl/GSM768527_8680_496_Control_Rep3_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM768nnn/GSM768527/suppl/GSM768527_8680_496_Control_Rep3_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE31013
| | Sample_data_row_count | 45101
| | |
|
GSM768528 | GPL1261 |
|
Lung_normal_4
|
Normal lung
|
age: 2-year-old
disease state: Normal
strain: B6C3F1
|
Control lung
|
| Sample_geo_accession | GSM768528
| | Sample_status | Public on Jun 22 2012
| | Sample_submission_date | Jul 28 2011
| | Sample_last_update_date | Jun 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | NA; no treatment was performed.
| | Sample_growth_protocol_ch1 | NA; tumors and tissue collected from B6C3F1 mice on 2-year National Toxicology Program bioassay.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Invitrogen PureLink Mini kit (Invitrogen cat# 12183-018A). Frozen tissue samples were lysed and homogenized in TRIzol reagent using a rotor-stator homogenizer. RNA isolation was performed according to the mini kit protocol. On column DNase treatment was performed using the Invitrogen PureLink DNase kit (Invitrogen cat# 12185-010) to purify the RNA samples. RNA concentration and 260/280 ratio were measured on a bioanalyzer (Agilent Technologies). RNA quality was checked on Embi Tec Precast RNA gels (Embec cat# GE-6010). Samples were aliquoted and stored at -80C.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One μg of total RNA was amplified as directed in the Affymetrix One-Cycle cDNA Synthesis protocol.
| | Sample_hyb_protocol | 15 μg of amplified biotin-cRNAs 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.
| | 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 | GPL1261
| | 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/GSM768nnn/GSM768528/suppl/GSM768528_8681_496_Control_Rep4_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM768nnn/GSM768528/suppl/GSM768528_8681_496_Control_Rep4_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE31013
| | Sample_data_row_count | 45101
| | |
|
GSM768529 | GPL1261 |
|
Lung_normal_5
|
Normal lung
|
age: 2-year-old
disease state: Normal
strain: B6C3F1
|
Control lung
|
| Sample_geo_accession | GSM768529
| | Sample_status | Public on Jun 22 2012
| | Sample_submission_date | Jul 28 2011
| | Sample_last_update_date | Jun 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | NA; no treatment was performed.
| | Sample_growth_protocol_ch1 | NA; tumors and tissue collected from B6C3F1 mice on 2-year National Toxicology Program bioassay.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Invitrogen PureLink Mini kit (Invitrogen cat# 12183-018A). Frozen tissue samples were lysed and homogenized in TRIzol reagent using a rotor-stator homogenizer. RNA isolation was performed according to the mini kit protocol. On column DNase treatment was performed using the Invitrogen PureLink DNase kit (Invitrogen cat# 12185-010) to purify the RNA samples. RNA concentration and 260/280 ratio were measured on a bioanalyzer (Agilent Technologies). RNA quality was checked on Embi Tec Precast RNA gels (Embec cat# GE-6010). Samples were aliquoted and stored at -80C.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One μg of total RNA was amplified as directed in the Affymetrix One-Cycle cDNA Synthesis protocol.
| | Sample_hyb_protocol | 15 μg of amplified biotin-cRNAs 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.
| | 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 | GPL1261
| | 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/GSM768nnn/GSM768529/suppl/GSM768529_8682_496_Control_Rep5_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM768nnn/GSM768529/suppl/GSM768529_8682_496_Control_Rep5_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE31013
| | Sample_data_row_count | 45101
| | |
|
GSM768530 | GPL1261 |
|
Lung_normal_6
|
Normal lung
|
age: 2-year-old
disease state: Normal
strain: B6C3F1
|
Control lung
|
| Sample_geo_accession | GSM768530
| | Sample_status | Public on Jun 22 2012
| | Sample_submission_date | Jul 28 2011
| | Sample_last_update_date | Jun 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | NA; no treatment was performed.
| | Sample_growth_protocol_ch1 | NA; tumors and tissue collected from B6C3F1 mice on 2-year National Toxicology Program bioassay.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Invitrogen PureLink Mini kit (Invitrogen cat# 12183-018A). Frozen tissue samples were lysed and homogenized in TRIzol reagent using a rotor-stator homogenizer. RNA isolation was performed according to the mini kit protocol. On column DNase treatment was performed using the Invitrogen PureLink DNase kit (Invitrogen cat# 12185-010) to purify the RNA samples. RNA concentration and 260/280 ratio were measured on a bioanalyzer (Agilent Technologies). RNA quality was checked on Embi Tec Precast RNA gels (Embec cat# GE-6010). Samples were aliquoted and stored at -80C.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One μg of total RNA was amplified as directed in the Affymetrix One-Cycle cDNA Synthesis protocol.
| | Sample_hyb_protocol | 15 μg of amplified biotin-cRNAs 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.
| | 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 | GPL1261
| | 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/GSM768nnn/GSM768530/suppl/GSM768530_8683_496_Control_Rep6_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM768nnn/GSM768530/suppl/GSM768530_8683_496_Control_Rep6_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE31013
| | Sample_data_row_count | 45101
| | |
|
GSM768531 | GPL1261 |
|
Spontaneous_lung_tumor_1
|
Spontaneous lung tumor
|
age: 2-year-old
disease state: Spontaneous lung tumor
strain: B6C3F1
|
Spontaneous Lung tumor in untreated animals
|
| Sample_geo_accession | GSM768531
| | Sample_status | Public on Jun 22 2012
| | Sample_submission_date | Jul 28 2011
| | Sample_last_update_date | Jun 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | NA; no treatment was performed.
| | Sample_growth_protocol_ch1 | NA; tumors and tissue collected from B6C3F1 mice on 2-year National Toxicology Program bioassay.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Invitrogen PureLink Mini kit (Invitrogen cat# 12183-018A). Frozen tissue samples were lysed and homogenized in TRIzol reagent using a rotor-stator homogenizer. RNA isolation was performed according to the mini kit protocol. On column DNase treatment was performed using the Invitrogen PureLink DNase kit (Invitrogen cat# 12185-010) to purify the RNA samples. RNA concentration and 260/280 ratio were measured on a bioanalyzer (Agilent Technologies). RNA quality was checked on Embi Tec Precast RNA gels (Embec cat# GE-6010). Samples were aliquoted and stored at -80C.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One μg of total RNA was amplified as directed in the Affymetrix One-Cycle cDNA Synthesis protocol.
| | Sample_hyb_protocol | 15 μg of amplified biotin-cRNAs 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.
| | 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 | GPL1261
| | 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/GSM768nnn/GSM768531/suppl/GSM768531_8672_496_Spont_Rep1_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM768nnn/GSM768531/suppl/GSM768531_8672_496_Spont_Rep1_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE31013
| | Sample_data_row_count | 45101
| | |
|
GSM768532 | GPL1261 |
|
Spontaneous_lung_tumor_2
|
Spontaneous lung tumor
|
age: 2-year-old
disease state: Spontaneous lung tumor
strain: B6C3F1
|
Spontaneous Lung tumor in untreated animals
|
| Sample_geo_accession | GSM768532
| | Sample_status | Public on Jun 22 2012
| | Sample_submission_date | Jul 28 2011
| | Sample_last_update_date | Jun 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | NA; no treatment was performed.
| | Sample_growth_protocol_ch1 | NA; tumors and tissue collected from B6C3F1 mice on 2-year National Toxicology Program bioassay.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Invitrogen PureLink Mini kit (Invitrogen cat# 12183-018A). Frozen tissue samples were lysed and homogenized in TRIzol reagent using a rotor-stator homogenizer. RNA isolation was performed according to the mini kit protocol. On column DNase treatment was performed using the Invitrogen PureLink DNase kit (Invitrogen cat# 12185-010) to purify the RNA samples. RNA concentration and 260/280 ratio were measured on a bioanalyzer (Agilent Technologies). RNA quality was checked on Embi Tec Precast RNA gels (Embec cat# GE-6010). Samples were aliquoted and stored at -80C.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One μg of total RNA was amplified as directed in the Affymetrix One-Cycle cDNA Synthesis protocol.
| | Sample_hyb_protocol | 15 μg of amplified biotin-cRNAs 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.
| | 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 | GPL1261
| | 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/GSM768nnn/GSM768532/suppl/GSM768532_8673_496_Spont_Rep2_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM768nnn/GSM768532/suppl/GSM768532_8673_496_Spont_Rep2_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE31013
| | Sample_data_row_count | 45101
| | |
|
GSM768533 | GPL1261 |
|
Spontaneous_lung_tumor_3
|
Spontaneous lung tumor
|
age: 2-year-old
disease state: Spontaneous lung tumor
strain: B6C3F1
|
Spontaneous Lung tumor in untreated animals
|
| Sample_geo_accession | GSM768533
| | Sample_status | Public on Jun 22 2012
| | Sample_submission_date | Jul 28 2011
| | Sample_last_update_date | Jun 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | NA; no treatment was performed.
| | Sample_growth_protocol_ch1 | NA; tumors and tissue collected from B6C3F1 mice on 2-year National Toxicology Program bioassay.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Invitrogen PureLink Mini kit (Invitrogen cat# 12183-018A). Frozen tissue samples were lysed and homogenized in TRIzol reagent using a rotor-stator homogenizer. RNA isolation was performed according to the mini kit protocol. On column DNase treatment was performed using the Invitrogen PureLink DNase kit (Invitrogen cat# 12185-010) to purify the RNA samples. RNA concentration and 260/280 ratio were measured on a bioanalyzer (Agilent Technologies). RNA quality was checked on Embi Tec Precast RNA gels (Embec cat# GE-6010). Samples were aliquoted and stored at -80C.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One μg of total RNA was amplified as directed in the Affymetrix One-Cycle cDNA Synthesis protocol.
| | Sample_hyb_protocol | 15 μg of amplified biotin-cRNAs 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.
| | 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 | GPL1261
| | 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/GSM768nnn/GSM768533/suppl/GSM768533_8674_496_Spont_Rep3_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM768nnn/GSM768533/suppl/GSM768533_8674_496_Spont_Rep3_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE31013
| | Sample_data_row_count | 45101
| | |
|
GSM768534 | GPL1261 |
|
Spontaneous_lung_tumor_4
|
Spontaneous lung tumor
|
age: 2-year-old
disease state: Spontaneous lung tumor
strain: B6C3F1
|
Spontaneous Lung tumor in untreated animals
|
| Sample_geo_accession | GSM768534
| | Sample_status | Public on Jun 22 2012
| | Sample_submission_date | Jul 28 2011
| | Sample_last_update_date | Jun 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | NA; no treatment was performed.
| | Sample_growth_protocol_ch1 | NA; tumors and tissue collected from B6C3F1 mice on 2-year National Toxicology Program bioassay.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Invitrogen PureLink Mini kit (Invitrogen cat# 12183-018A). Frozen tissue samples were lysed and homogenized in TRIzol reagent using a rotor-stator homogenizer. RNA isolation was performed according to the mini kit protocol. On column DNase treatment was performed using the Invitrogen PureLink DNase kit (Invitrogen cat# 12185-010) to purify the RNA samples. RNA concentration and 260/280 ratio were measured on a bioanalyzer (Agilent Technologies). RNA quality was checked on Embi Tec Precast RNA gels (Embec cat# GE-6010). Samples were aliquoted and stored at -80C.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One μg of total RNA was amplified as directed in the Affymetrix One-Cycle cDNA Synthesis protocol.
| | Sample_hyb_protocol | 15 μg of amplified biotin-cRNAs 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.
| | 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 | GPL1261
| | 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/GSM768nnn/GSM768534/suppl/GSM768534_8675_496_Spont_Rep4_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM768nnn/GSM768534/suppl/GSM768534_8675_496_Spont_Rep4_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE31013
| | Sample_data_row_count | 45101
| | |
|
GSM768535 | GPL1261 |
|
Spontaneous_lung_tumor_5
|
Spontaneous lung tumor
|
age: 2-year-old
disease state: Spontaneous lung tumor
strain: B6C3F1
|
Spontaneous Lung tumor in untreated animals
|
| Sample_geo_accession | GSM768535
| | Sample_status | Public on Jun 22 2012
| | Sample_submission_date | Jul 28 2011
| | Sample_last_update_date | Jun 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | NA; no treatment was performed.
| | Sample_growth_protocol_ch1 | NA; tumors and tissue collected from B6C3F1 mice on 2-year National Toxicology Program bioassay.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Invitrogen PureLink Mini kit (Invitrogen cat# 12183-018A). Frozen tissue samples were lysed and homogenized in TRIzol reagent using a rotor-stator homogenizer. RNA isolation was performed according to the mini kit protocol. On column DNase treatment was performed using the Invitrogen PureLink DNase kit (Invitrogen cat# 12185-010) to purify the RNA samples. RNA concentration and 260/280 ratio were measured on a bioanalyzer (Agilent Technologies). RNA quality was checked on Embi Tec Precast RNA gels (Embec cat# GE-6010). Samples were aliquoted and stored at -80C.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One μg of total RNA was amplified as directed in the Affymetrix One-Cycle cDNA Synthesis protocol.
| | Sample_hyb_protocol | 15 μg of amplified biotin-cRNAs 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.
| | 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 | GPL1261
| | 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/GSM768nnn/GSM768535/suppl/GSM768535_8676_496_Spont_Rep5_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM768nnn/GSM768535/suppl/GSM768535_8676_496_Spont_Rep5_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE31013
| | Sample_data_row_count | 45101
| | |
|
GSM768536 | GPL1261 |
|
Spontaneous_lung_tumor_6
|
Spontaneous lung tumor
|
age: 2-year-old
disease state: Spontaneous lung tumor
strain: B6C3F1
|
Spontaneous Lung tumor in untreated animals
|
| Sample_geo_accession | GSM768536
| | Sample_status | Public on Jun 22 2012
| | Sample_submission_date | Jul 28 2011
| | Sample_last_update_date | Jun 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | NA; no treatment was performed.
| | Sample_growth_protocol_ch1 | NA; tumors and tissue collected from B6C3F1 mice on 2-year National Toxicology Program bioassay.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Invitrogen PureLink Mini kit (Invitrogen cat# 12183-018A). Frozen tissue samples were lysed and homogenized in TRIzol reagent using a rotor-stator homogenizer. RNA isolation was performed according to the mini kit protocol. On column DNase treatment was performed using the Invitrogen PureLink DNase kit (Invitrogen cat# 12185-010) to purify the RNA samples. RNA concentration and 260/280 ratio were measured on a bioanalyzer (Agilent Technologies). RNA quality was checked on Embi Tec Precast RNA gels (Embec cat# GE-6010). Samples were aliquoted and stored at -80C.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One μg of total RNA was amplified as directed in the Affymetrix One-Cycle cDNA Synthesis protocol.
| | Sample_hyb_protocol | 15 μg of amplified biotin-cRNAs 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.
| | 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 | GPL1261
| | 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/GSM768nnn/GSM768536/suppl/GSM768536_8677_496_Spont_Rep6_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM768nnn/GSM768536/suppl/GSM768536_8677_496_Spont_Rep6_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE31013
| | Sample_data_row_count | 45101
| | |
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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" |
Enter the group name here: |
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