Search results for the GEO ID: GSE26538  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM652414 | GPL1261 |
|
Liver_normal_1
|
Liver_normal
|
strain: B6C3F1
tissue: Liver
|
control
|
| Sample_geo_accession | GSM652414
| | Sample_status | Public on Jun 07 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Jun 08 2011
| | 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).
| | 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/GSM652nnn/GSM652414/suppl/GSM652414_8349_473_CTL_Rep1_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652414/suppl/GSM652414_8349_473_CTL_Rep1_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE26538
| | Sample_series_id | GSE29813
| | Sample_data_row_count | 45101
| | |
|
GSM652415 | GPL1261 |
|
Liver_normal_2
|
Liver_normal
|
strain: B6C3F1
tissue: Liver
|
control
|
| Sample_geo_accession | GSM652415
| | Sample_status | Public on Jun 07 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Jun 08 2011
| | 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).
| | 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/GSM652nnn/GSM652415/suppl/GSM652415_8350_473_CTL_Rep2_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652415/suppl/GSM652415_8350_473_CTL_Rep2_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE26538
| | Sample_series_id | GSE29813
| | Sample_data_row_count | 45101
| | |
|
GSM652416 | GPL1261 |
|
Liver_normal_3
|
Liver_normal
|
strain: B6C3F1
tissue: Liver
|
control
|
| Sample_geo_accession | GSM652416
| | Sample_status | Public on Jun 07 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Jun 08 2011
| | 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).
| | 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/GSM652nnn/GSM652416/suppl/GSM652416_8351_473_CTL_Rep3_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652416/suppl/GSM652416_8351_473_CTL_Rep3_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE26538
| | Sample_series_id | GSE29813
| | Sample_data_row_count | 45101
| | |
|
GSM652417 | GPL1261 |
|
Liver_normal_4
|
Liver_normal
|
strain: B6C3F1
tissue: Liver
|
control
|
| Sample_geo_accession | GSM652417
| | Sample_status | Public on Jun 07 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Jun 08 2011
| | 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).
| | 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/GSM652nnn/GSM652417/suppl/GSM652417_8352_473_CTL_Rep4_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652417/suppl/GSM652417_8352_473_CTL_Rep4_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE26538
| | Sample_series_id | GSE29813
| | Sample_data_row_count | 45101
| | |
|
GSM652418 | GPL1261 |
|
Liver_normal_5
|
Liver_normal
|
strain: B6C3F1
tissue: Liver
|
control
|
| Sample_geo_accession | GSM652418
| | Sample_status | Public on Jun 07 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Jun 08 2011
| | 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).
| | 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/GSM652nnn/GSM652418/suppl/GSM652418_8353_473_CTL_Rep5_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652418/suppl/GSM652418_8353_473_CTL_Rep5_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE26538
| | Sample_series_id | GSE29813
| | Sample_data_row_count | 45101
| | |
|
GSM652419 | GPL1261 |
|
Liver_normal_6
|
Liver_normal
|
strain: B6C3F1
tissue: Liver
|
control
|
| Sample_geo_accession | GSM652419
| | Sample_status | Public on Jun 07 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Jun 08 2011
| | 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).
| | 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/GSM652nnn/GSM652419/suppl/GSM652419_8354_473_CTL_Rep6_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652419/suppl/GSM652419_8354_473_CTL_Rep6_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE26538
| | Sample_series_id | GSE29813
| | Sample_data_row_count | 45101
| | |
|
GSM652420 | GPL1261 |
|
Liver_HCC_1
|
Liver_HCC
|
strain: B6C3F1
tissue: Liver
|
spontaneous tumor
|
| Sample_geo_accession | GSM652420
| | Sample_status | Public on Jun 07 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Jun 08 2011
| | 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).
| | 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/GSM652nnn/GSM652420/suppl/GSM652420_8355_473_SPONT_Rep1_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652420/suppl/GSM652420_8355_473_SPONT_Rep1_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE26538
| | Sample_series_id | GSE29813
| | Sample_data_row_count | 45101
| | |
|
GSM652421 | GPL1261 |
|
Liver_HCC_2
|
Liver_HCC
|
strain: B6C3F1
tissue: Liver
|
spontaneous tumor
|
| Sample_geo_accession | GSM652421
| | Sample_status | Public on Jun 07 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Jun 08 2011
| | 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).
| | 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/GSM652nnn/GSM652421/suppl/GSM652421_8356_473_SPONT_Rep2_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652421/suppl/GSM652421_8356_473_SPONT_Rep2_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE26538
| | Sample_series_id | GSE29813
| | Sample_data_row_count | 45101
| | |
|
GSM652422 | GPL1261 |
|
Liver_HCC_3
|
Liver_HCC
|
strain: B6C3F1
tissue: Liver
|
spontaneous tumor
|
| Sample_geo_accession | GSM652422
| | Sample_status | Public on Jun 07 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Jun 08 2011
| | 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).
| | 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/GSM652nnn/GSM652422/suppl/GSM652422_8357_473_SPONT_Rep3_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652422/suppl/GSM652422_8357_473_SPONT_Rep3_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE26538
| | Sample_series_id | GSE29813
| | Sample_data_row_count | 45101
| | |
|
GSM652423 | GPL1261 |
|
Liver_HCC_4
|
Liver_HCC
|
strain: B6C3F1
tissue: Liver
|
spontaneous tumor
|
| Sample_geo_accession | GSM652423
| | Sample_status | Public on Jun 07 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Jun 08 2011
| | 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).
| | 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/GSM652nnn/GSM652423/suppl/GSM652423_8358_473_SPONT_Rep4_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652423/suppl/GSM652423_8358_473_SPONT_Rep4_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE26538
| | Sample_series_id | GSE29813
| | Sample_data_row_count | 45101
| | |
|
GSM652424 | GPL1261 |
|
Liver_HCC_5
|
Liver_HCC
|
strain: B6C3F1
tissue: Liver
|
spontaneous tumor
|
| Sample_geo_accession | GSM652424
| | Sample_status | Public on Jun 07 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Jun 08 2011
| | 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).
| | 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/GSM652nnn/GSM652424/suppl/GSM652424_8359_473_SPONT_Rep5_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652424/suppl/GSM652424_8359_473_SPONT_Rep5_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE26538
| | Sample_series_id | GSE29813
| | Sample_data_row_count | 45101
| | |
|
GSM652425 | GPL1261 |
|
Liver_HCC_6
|
Liver_HCC
|
strain: B6C3F1
tissue: Liver
|
spontaneous tumor
|
| Sample_geo_accession | GSM652425
| | Sample_status | Public on Jun 07 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | Jun 08 2011
| | 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).
| | 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/GSM652nnn/GSM652425/suppl/GSM652425_8360_473_SPONT_Rep6_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652425/suppl/GSM652425_8360_473_SPONT_Rep6_Mouse430_2_.mas5.CHP.gz
| | Sample_series_id | GSE26538
| | Sample_series_id | GSE29813
| | Sample_data_row_count | 45101
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
