Search results for the GEO ID: GSE39042  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM954533 | GPL570 |
|
N_EPI_1
|
Cells + epirubicin 10 uM in normoxia
|
cell line: MDA-MB-231
|
Gene expression data from MDA-MB-231 cells
|
| Sample_geo_accession | GSM954533
| | Sample_status | Public on Jul 03 2012
| | Sample_submission_date | Jul 02 2012
| | Sample_last_update_date | Jul 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16 hours incubation in the presence of epirubicin 10 uM or paclitaxel 50 uM in medium without serum, under normoxia or hypoxia (1 % O2)
| | Sample_growth_protocol_ch1 | MDA-MB-231 were grown in RPMI1640 + 10 % fetal calf serum
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction kit (Invitrogen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Fragmented biotinylated cRNA and hybridization controls (Affymetrix) were hybridized on array followed by washing and staining steps according to the manufacturer’s procedures.
| | Sample_scan_protocol | GeneChip® Scanner 3000
| | Sample_data_processing | Probe-level data were normalized and gene expression summaries were computed for each probe set using GeneChip Robust Multichip Analysis (GC-RMA) on R 2.7. The data set was then filtered for low expression value and calls exhibiting values under an arbitrary threshold value of 8.84 (twice the value of the basal intensity) were considered ‘absent’ otherwise calls were considered ‘present’.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bertrand,,De Meulder
| | Sample_contact_email | bertrand.de.meulder@fundp.ac.be
| | Sample_contact_department | Biology
| | Sample_contact_institute | FUNDP
| | Sample_contact_address | Rue de Bruxelles, 61
| | Sample_contact_city | Namur
| | Sample_contact_state | Namur
| | Sample_contact_zip/postal_code | 500
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM954nnn/GSM954533/suppl/GSM954533_KM-ARN001.CEL.gz
| | Sample_series_id | GSE39042
| | Sample_data_row_count | 54675
| | |
|
GSM954534 | GPL570 |
|
H_EPI_1
|
Cells + epirubicin 10 uM in hypoxia
|
cell line: MDA-MB-231
|
Gene expression data from MDA-MB-231 cells
|
| Sample_geo_accession | GSM954534
| | Sample_status | Public on Jul 03 2012
| | Sample_submission_date | Jul 02 2012
| | Sample_last_update_date | Jul 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16 hours incubation in the presence of epirubicin 10 uM or paclitaxel 50 uM in medium without serum, under normoxia or hypoxia (1 % O2)
| | Sample_growth_protocol_ch1 | MDA-MB-231 were grown in RPMI1640 + 10 % fetal calf serum
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction kit (Invitrogen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Fragmented biotinylated cRNA and hybridization controls (Affymetrix) were hybridized on array followed by washing and staining steps according to the manufacturer’s procedures.
| | Sample_scan_protocol | GeneChip® Scanner 3000
| | Sample_data_processing | Probe-level data were normalized and gene expression summaries were computed for each probe set using GeneChip Robust Multichip Analysis (GC-RMA) on R 2.7. The data set was then filtered for low expression value and calls exhibiting values under an arbitrary threshold value of 8.84 (twice the value of the basal intensity) were considered ‘absent’ otherwise calls were considered ‘present’.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bertrand,,De Meulder
| | Sample_contact_email | bertrand.de.meulder@fundp.ac.be
| | Sample_contact_department | Biology
| | Sample_contact_institute | FUNDP
| | Sample_contact_address | Rue de Bruxelles, 61
| | Sample_contact_city | Namur
| | Sample_contact_state | Namur
| | Sample_contact_zip/postal_code | 500
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM954nnn/GSM954534/suppl/GSM954534_KM-ARN002.CEL.gz
| | Sample_series_id | GSE39042
| | Sample_data_row_count | 54675
| | |
|
GSM954535 | GPL570 |
|
N_CTL_1
|
Control cells in normoxia
|
cell line: MDA-MB-231
|
Gene expression data from MDA-MB-231 cells
|
| Sample_geo_accession | GSM954535
| | Sample_status | Public on Jul 03 2012
| | Sample_submission_date | Jul 02 2012
| | Sample_last_update_date | Jul 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16 hours incubation in the presence of epirubicin 10 uM or paclitaxel 50 uM in medium without serum, under normoxia or hypoxia (1 % O2)
| | Sample_growth_protocol_ch1 | MDA-MB-231 were grown in RPMI1640 + 10 % fetal calf serum
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction kit (Invitrogen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Fragmented biotinylated cRNA and hybridization controls (Affymetrix) were hybridized on array followed by washing and staining steps according to the manufacturer’s procedures.
| | Sample_scan_protocol | GeneChip® Scanner 3000
| | Sample_data_processing | Probe-level data were normalized and gene expression summaries were computed for each probe set using GeneChip Robust Multichip Analysis (GC-RMA) on R 2.7. The data set was then filtered for low expression value and calls exhibiting values under an arbitrary threshold value of 8.84 (twice the value of the basal intensity) were considered ‘absent’ otherwise calls were considered ‘present’.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bertrand,,De Meulder
| | Sample_contact_email | bertrand.de.meulder@fundp.ac.be
| | Sample_contact_department | Biology
| | Sample_contact_institute | FUNDP
| | Sample_contact_address | Rue de Bruxelles, 61
| | Sample_contact_city | Namur
| | Sample_contact_state | Namur
| | Sample_contact_zip/postal_code | 500
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM954nnn/GSM954535/suppl/GSM954535_KM-ARN003.CEL.gz
| | Sample_series_id | GSE39042
| | Sample_data_row_count | 54675
| | |
|
GSM954536 | GPL570 |
|
H_CTL_1
|
Control cells in hypoxia
|
cell line: MDA-MB-231
|
Gene expression data from MDA-MB-231 cells
|
| Sample_geo_accession | GSM954536
| | Sample_status | Public on Jul 03 2012
| | Sample_submission_date | Jul 02 2012
| | Sample_last_update_date | Jul 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16 hours incubation in the presence of epirubicin 10 uM or paclitaxel 50 uM in medium without serum, under normoxia or hypoxia (1 % O2)
| | Sample_growth_protocol_ch1 | MDA-MB-231 were grown in RPMI1640 + 10 % fetal calf serum
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction kit (Invitrogen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Fragmented biotinylated cRNA and hybridization controls (Affymetrix) were hybridized on array followed by washing and staining steps according to the manufacturer’s procedures.
| | Sample_scan_protocol | GeneChip® Scanner 3000
| | Sample_data_processing | Probe-level data were normalized and gene expression summaries were computed for each probe set using GeneChip Robust Multichip Analysis (GC-RMA) on R 2.7. The data set was then filtered for low expression value and calls exhibiting values under an arbitrary threshold value of 8.84 (twice the value of the basal intensity) were considered ‘absent’ otherwise calls were considered ‘present’.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bertrand,,De Meulder
| | Sample_contact_email | bertrand.de.meulder@fundp.ac.be
| | Sample_contact_department | Biology
| | Sample_contact_institute | FUNDP
| | Sample_contact_address | Rue de Bruxelles, 61
| | Sample_contact_city | Namur
| | Sample_contact_state | Namur
| | Sample_contact_zip/postal_code | 500
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM954nnn/GSM954536/suppl/GSM954536_KM-ARN004.CEL.gz
| | Sample_series_id | GSE39042
| | Sample_data_row_count | 54675
| | |
|
GSM954537 | GPL570 |
|
N_TAX_1
|
Cells + paclitaxel 50 uM in normoxia
|
cell line: MDA-MB-231
|
Gene expression data from MDA-MB-231 cells
|
| Sample_geo_accession | GSM954537
| | Sample_status | Public on Jul 03 2012
| | Sample_submission_date | Jul 02 2012
| | Sample_last_update_date | Jul 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16 hours incubation in the presence of epirubicin 10 uM or paclitaxel 50 uM in medium without serum, under normoxia or hypoxia (1 % O2)
| | Sample_growth_protocol_ch1 | MDA-MB-231 were grown in RPMI1640 + 10 % fetal calf serum
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction kit (Invitrogen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Fragmented biotinylated cRNA and hybridization controls (Affymetrix) were hybridized on array followed by washing and staining steps according to the manufacturer’s procedures.
| | Sample_scan_protocol | GeneChip® Scanner 3000
| | Sample_data_processing | Probe-level data were normalized and gene expression summaries were computed for each probe set using GeneChip Robust Multichip Analysis (GC-RMA) on R 2.7. The data set was then filtered for low expression value and calls exhibiting values under an arbitrary threshold value of 8.84 (twice the value of the basal intensity) were considered ‘absent’ otherwise calls were considered ‘present’.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bertrand,,De Meulder
| | Sample_contact_email | bertrand.de.meulder@fundp.ac.be
| | Sample_contact_department | Biology
| | Sample_contact_institute | FUNDP
| | Sample_contact_address | Rue de Bruxelles, 61
| | Sample_contact_city | Namur
| | Sample_contact_state | Namur
| | Sample_contact_zip/postal_code | 500
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM954nnn/GSM954537/suppl/GSM954537_KM-ARN005.CEL.gz
| | Sample_series_id | GSE39042
| | Sample_data_row_count | 54675
| | |
|
GSM954538 | GPL570 |
|
H_TAX_1
|
Cells + paclitaxel 50 uM in hypoxia
|
cell line: MDA-MB-231
|
Gene expression data from MDA-MB-231 cells
|
| Sample_geo_accession | GSM954538
| | Sample_status | Public on Jul 03 2012
| | Sample_submission_date | Jul 02 2012
| | Sample_last_update_date | Jul 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16 hours incubation in the presence of epirubicin 10 uM or paclitaxel 50 uM in medium without serum, under normoxia or hypoxia (1 % O2)
| | Sample_growth_protocol_ch1 | MDA-MB-231 were grown in RPMI1640 + 10 % fetal calf serum
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction kit (Invitrogen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Fragmented biotinylated cRNA and hybridization controls (Affymetrix) were hybridized on array followed by washing and staining steps according to the manufacturer’s procedures.
| | Sample_scan_protocol | GeneChip® Scanner 3000
| | Sample_data_processing | Probe-level data were normalized and gene expression summaries were computed for each probe set using GeneChip Robust Multichip Analysis (GC-RMA) on R 2.7. The data set was then filtered for low expression value and calls exhibiting values under an arbitrary threshold value of 8.84 (twice the value of the basal intensity) were considered ‘absent’ otherwise calls were considered ‘present’.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bertrand,,De Meulder
| | Sample_contact_email | bertrand.de.meulder@fundp.ac.be
| | Sample_contact_department | Biology
| | Sample_contact_institute | FUNDP
| | Sample_contact_address | Rue de Bruxelles, 61
| | Sample_contact_city | Namur
| | Sample_contact_state | Namur
| | Sample_contact_zip/postal_code | 500
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM954nnn/GSM954538/suppl/GSM954538_KM-ARN006.CEL.gz
| | Sample_series_id | GSE39042
| | Sample_data_row_count | 54675
| | |
|
GSM954539 | GPL570 |
|
N_EPI_2
|
Cells + epirubicin 10 uM in normoxia
|
cell line: MDA-MB-231
|
Gene expression data from MDA-MB-231 cells
|
| Sample_geo_accession | GSM954539
| | Sample_status | Public on Jul 03 2012
| | Sample_submission_date | Jul 02 2012
| | Sample_last_update_date | Jul 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16 hours incubation in the presence of epirubicin 10 uM or paclitaxel 50 uM in medium without serum, under normoxia or hypoxia (1 % O2)
| | Sample_growth_protocol_ch1 | MDA-MB-231 were grown in RPMI1640 + 10 % fetal calf serum
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction kit (Invitrogen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Fragmented biotinylated cRNA and hybridization controls (Affymetrix) were hybridized on array followed by washing and staining steps according to the manufacturer’s procedures.
| | Sample_scan_protocol | GeneChip® Scanner 3000
| | Sample_data_processing | Probe-level data were normalized and gene expression summaries were computed for each probe set using GeneChip Robust Multichip Analysis (GC-RMA) on R 2.7. The data set was then filtered for low expression value and calls exhibiting values under an arbitrary threshold value of 8.84 (twice the value of the basal intensity) were considered ‘absent’ otherwise calls were considered ‘present’.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bertrand,,De Meulder
| | Sample_contact_email | bertrand.de.meulder@fundp.ac.be
| | Sample_contact_department | Biology
| | Sample_contact_institute | FUNDP
| | Sample_contact_address | Rue de Bruxelles, 61
| | Sample_contact_city | Namur
| | Sample_contact_state | Namur
| | Sample_contact_zip/postal_code | 500
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM954nnn/GSM954539/suppl/GSM954539_KM-ARN007.CEL.gz
| | Sample_series_id | GSE39042
| | Sample_data_row_count | 54675
| | |
|
GSM954540 | GPL570 |
|
H_EPI_2
|
Cells + epirubicin 10 uM in hypoxia
|
cell line: MDA-MB-231
|
Gene expression data from MDA-MB-231 cells
|
| Sample_geo_accession | GSM954540
| | Sample_status | Public on Jul 03 2012
| | Sample_submission_date | Jul 02 2012
| | Sample_last_update_date | Jul 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16 hours incubation in the presence of epirubicin 10 uM or paclitaxel 50 uM in medium without serum, under normoxia or hypoxia (1 % O2)
| | Sample_growth_protocol_ch1 | MDA-MB-231 were grown in RPMI1640 + 10 % fetal calf serum
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction kit (Invitrogen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Fragmented biotinylated cRNA and hybridization controls (Affymetrix) were hybridized on array followed by washing and staining steps according to the manufacturer’s procedures.
| | Sample_scan_protocol | GeneChip® Scanner 3000
| | Sample_data_processing | Probe-level data were normalized and gene expression summaries were computed for each probe set using GeneChip Robust Multichip Analysis (GC-RMA) on R 2.7. The data set was then filtered for low expression value and calls exhibiting values under an arbitrary threshold value of 8.84 (twice the value of the basal intensity) were considered ‘absent’ otherwise calls were considered ‘present’.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bertrand,,De Meulder
| | Sample_contact_email | bertrand.de.meulder@fundp.ac.be
| | Sample_contact_department | Biology
| | Sample_contact_institute | FUNDP
| | Sample_contact_address | Rue de Bruxelles, 61
| | Sample_contact_city | Namur
| | Sample_contact_state | Namur
| | Sample_contact_zip/postal_code | 500
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM954nnn/GSM954540/suppl/GSM954540_KM-ARN008.CEL.gz
| | Sample_series_id | GSE39042
| | Sample_data_row_count | 54675
| | |
|
GSM954541 | GPL570 |
|
N_CTL_2
|
Control cells in normoxia
|
cell line: MDA-MB-231
|
Gene expression data from MDA-MB-231 cells
|
| Sample_geo_accession | GSM954541
| | Sample_status | Public on Jul 03 2012
| | Sample_submission_date | Jul 02 2012
| | Sample_last_update_date | Jul 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16 hours incubation in the presence of epirubicin 10 uM or paclitaxel 50 uM in medium without serum, under normoxia or hypoxia (1 % O2)
| | Sample_growth_protocol_ch1 | MDA-MB-231 were grown in RPMI1640 + 10 % fetal calf serum
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction kit (Invitrogen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Fragmented biotinylated cRNA and hybridization controls (Affymetrix) were hybridized on array followed by washing and staining steps according to the manufacturer’s procedures.
| | Sample_scan_protocol | GeneChip® Scanner 3000
| | Sample_data_processing | Probe-level data were normalized and gene expression summaries were computed for each probe set using GeneChip Robust Multichip Analysis (GC-RMA) on R 2.7. The data set was then filtered for low expression value and calls exhibiting values under an arbitrary threshold value of 8.84 (twice the value of the basal intensity) were considered ‘absent’ otherwise calls were considered ‘present’.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bertrand,,De Meulder
| | Sample_contact_email | bertrand.de.meulder@fundp.ac.be
| | Sample_contact_department | Biology
| | Sample_contact_institute | FUNDP
| | Sample_contact_address | Rue de Bruxelles, 61
| | Sample_contact_city | Namur
| | Sample_contact_state | Namur
| | Sample_contact_zip/postal_code | 500
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM954nnn/GSM954541/suppl/GSM954541_KM-ARN009.CEL.gz
| | Sample_series_id | GSE39042
| | Sample_data_row_count | 54675
| | |
|
GSM954542 | GPL570 |
|
H_CTL_2
|
Control cells in hypoxia
|
cell line: MDA-MB-231
|
Gene expression data from MDA-MB-231 cells
|
| Sample_geo_accession | GSM954542
| | Sample_status | Public on Jul 03 2012
| | Sample_submission_date | Jul 02 2012
| | Sample_last_update_date | Jul 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16 hours incubation in the presence of epirubicin 10 uM or paclitaxel 50 uM in medium without serum, under normoxia or hypoxia (1 % O2)
| | Sample_growth_protocol_ch1 | MDA-MB-231 were grown in RPMI1640 + 10 % fetal calf serum
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction kit (Invitrogen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Fragmented biotinylated cRNA and hybridization controls (Affymetrix) were hybridized on array followed by washing and staining steps according to the manufacturer’s procedures.
| | Sample_scan_protocol | GeneChip® Scanner 3000
| | Sample_data_processing | Probe-level data were normalized and gene expression summaries were computed for each probe set using GeneChip Robust Multichip Analysis (GC-RMA) on R 2.7. The data set was then filtered for low expression value and calls exhibiting values under an arbitrary threshold value of 8.84 (twice the value of the basal intensity) were considered ‘absent’ otherwise calls were considered ‘present’.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bertrand,,De Meulder
| | Sample_contact_email | bertrand.de.meulder@fundp.ac.be
| | Sample_contact_department | Biology
| | Sample_contact_institute | FUNDP
| | Sample_contact_address | Rue de Bruxelles, 61
| | Sample_contact_city | Namur
| | Sample_contact_state | Namur
| | Sample_contact_zip/postal_code | 500
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM954nnn/GSM954542/suppl/GSM954542_KM-ARN010.CEL.gz
| | Sample_series_id | GSE39042
| | Sample_data_row_count | 54675
| | |
|
GSM954543 | GPL570 |
|
N_TAX_2
|
Cells + paclitaxel 50 uM in normoxia
|
cell line: MDA-MB-231
|
Gene expression data from MDA-MB-231 cells
|
| Sample_geo_accession | GSM954543
| | Sample_status | Public on Jul 03 2012
| | Sample_submission_date | Jul 02 2012
| | Sample_last_update_date | Jul 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16 hours incubation in the presence of epirubicin 10 uM or paclitaxel 50 uM in medium without serum, under normoxia or hypoxia (1 % O2)
| | Sample_growth_protocol_ch1 | MDA-MB-231 were grown in RPMI1640 + 10 % fetal calf serum
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction kit (Invitrogen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Fragmented biotinylated cRNA and hybridization controls (Affymetrix) were hybridized on array followed by washing and staining steps according to the manufacturer’s procedures.
| | Sample_scan_protocol | GeneChip® Scanner 3000
| | Sample_data_processing | Probe-level data were normalized and gene expression summaries were computed for each probe set using GeneChip Robust Multichip Analysis (GC-RMA) on R 2.7. The data set was then filtered for low expression value and calls exhibiting values under an arbitrary threshold value of 8.84 (twice the value of the basal intensity) were considered ‘absent’ otherwise calls were considered ‘present’.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bertrand,,De Meulder
| | Sample_contact_email | bertrand.de.meulder@fundp.ac.be
| | Sample_contact_department | Biology
| | Sample_contact_institute | FUNDP
| | Sample_contact_address | Rue de Bruxelles, 61
| | Sample_contact_city | Namur
| | Sample_contact_state | Namur
| | Sample_contact_zip/postal_code | 500
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM954nnn/GSM954543/suppl/GSM954543_KM-ARN011.CEL.gz
| | Sample_series_id | GSE39042
| | Sample_data_row_count | 54675
| | |
|
GSM954544 | GPL570 |
|
H_TAX_2
|
Cells + paclitaxel 50 uM in hypoxia
|
cell line: MDA-MB-231
|
Gene expression data from MDA-MB-231 cells
|
| Sample_geo_accession | GSM954544
| | Sample_status | Public on Jul 03 2012
| | Sample_submission_date | Jul 02 2012
| | Sample_last_update_date | Jul 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16 hours incubation in the presence of epirubicin 10 uM or paclitaxel 50 uM in medium without serum, under normoxia or hypoxia (1 % O2)
| | Sample_growth_protocol_ch1 | MDA-MB-231 were grown in RPMI1640 + 10 % fetal calf serum
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction kit (Invitrogen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Fragmented biotinylated cRNA and hybridization controls (Affymetrix) were hybridized on array followed by washing and staining steps according to the manufacturer’s procedures.
| | Sample_scan_protocol | GeneChip® Scanner 3000
| | Sample_data_processing | Probe-level data were normalized and gene expression summaries were computed for each probe set using GeneChip Robust Multichip Analysis (GC-RMA) on R 2.7. The data set was then filtered for low expression value and calls exhibiting values under an arbitrary threshold value of 8.84 (twice the value of the basal intensity) were considered ‘absent’ otherwise calls were considered ‘present’.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bertrand,,De Meulder
| | Sample_contact_email | bertrand.de.meulder@fundp.ac.be
| | Sample_contact_department | Biology
| | Sample_contact_institute | FUNDP
| | Sample_contact_address | Rue de Bruxelles, 61
| | Sample_contact_city | Namur
| | Sample_contact_state | Namur
| | Sample_contact_zip/postal_code | 500
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM954nnn/GSM954544/suppl/GSM954544_KM-ARN012.CEL.gz
| | Sample_series_id | GSE39042
| | Sample_data_row_count | 54675
| | |
|
GSM954545 | GPL570 |
|
N_CTL_3
|
Cells + epirubicin 10 uM in normoxia
|
cell line: MDA-MB-231
|
Gene expression data from MDA-MB-231 cells
|
| Sample_geo_accession | GSM954545
| | Sample_status | Public on Jul 03 2012
| | Sample_submission_date | Jul 02 2012
| | Sample_last_update_date | Jul 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16 hours incubation in the presence of epirubicin 10 uM or paclitaxel 50 uM in medium without serum, under normoxia or hypoxia (1 % O2)
| | Sample_growth_protocol_ch1 | MDA-MB-231 were grown in RPMI1640 + 10 % fetal calf serum
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction kit (Invitrogen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Fragmented biotinylated cRNA and hybridization controls (Affymetrix) were hybridized on array followed by washing and staining steps according to the manufacturer’s procedures.
| | Sample_scan_protocol | GeneChip® Scanner 3000
| | Sample_data_processing | Probe-level data were normalized and gene expression summaries were computed for each probe set using GeneChip Robust Multichip Analysis (GC-RMA) on R 2.7. The data set was then filtered for low expression value and calls exhibiting values under an arbitrary threshold value of 8.84 (twice the value of the basal intensity) were considered ‘absent’ otherwise calls were considered ‘present’.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bertrand,,De Meulder
| | Sample_contact_email | bertrand.de.meulder@fundp.ac.be
| | Sample_contact_department | Biology
| | Sample_contact_institute | FUNDP
| | Sample_contact_address | Rue de Bruxelles, 61
| | Sample_contact_city | Namur
| | Sample_contact_state | Namur
| | Sample_contact_zip/postal_code | 500
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM954nnn/GSM954545/suppl/GSM954545_KM-ARN013.CEL.gz
| | Sample_series_id | GSE39042
| | Sample_data_row_count | 54675
| | |
|
GSM954546 | GPL570 |
|
H_CTL_3
|
Cells + epirubicin 10 uM in hypoxia
|
cell line: MDA-MB-231
|
Gene expression data from MDA-MB-231 cells
|
| Sample_geo_accession | GSM954546
| | Sample_status | Public on Jul 03 2012
| | Sample_submission_date | Jul 02 2012
| | Sample_last_update_date | Jul 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16 hours incubation in the presence of epirubicin 10 uM or paclitaxel 50 uM in medium without serum, under normoxia or hypoxia (1 % O2)
| | Sample_growth_protocol_ch1 | MDA-MB-231 were grown in RPMI1640 + 10 % fetal calf serum
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction kit (Invitrogen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Fragmented biotinylated cRNA and hybridization controls (Affymetrix) were hybridized on array followed by washing and staining steps according to the manufacturer’s procedures.
| | Sample_scan_protocol | GeneChip® Scanner 3000
| | Sample_data_processing | Probe-level data were normalized and gene expression summaries were computed for each probe set using GeneChip Robust Multichip Analysis (GC-RMA) on R 2.7. The data set was then filtered for low expression value and calls exhibiting values under an arbitrary threshold value of 8.84 (twice the value of the basal intensity) were considered ‘absent’ otherwise calls were considered ‘present’.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bertrand,,De Meulder
| | Sample_contact_email | bertrand.de.meulder@fundp.ac.be
| | Sample_contact_department | Biology
| | Sample_contact_institute | FUNDP
| | Sample_contact_address | Rue de Bruxelles, 61
| | Sample_contact_city | Namur
| | Sample_contact_state | Namur
| | Sample_contact_zip/postal_code | 500
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM954nnn/GSM954546/suppl/GSM954546_KM-ARN014.CEL.gz
| | Sample_series_id | GSE39042
| | Sample_data_row_count | 54675
| | |
|
GSM954547 | GPL570 |
|
N_TAX_3
|
Control cells in normoxia
|
cell line: MDA-MB-231
|
Gene expression data from MDA-MB-231 cells
|
| Sample_geo_accession | GSM954547
| | Sample_status | Public on Jul 03 2012
| | Sample_submission_date | Jul 02 2012
| | Sample_last_update_date | Jul 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16 hours incubation in the presence of epirubicin 10 uM or paclitaxel 50 uM in medium without serum, under normoxia or hypoxia (1 % O2)
| | Sample_growth_protocol_ch1 | MDA-MB-231 were grown in RPMI1640 + 10 % fetal calf serum
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction kit (Invitrogen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Fragmented biotinylated cRNA and hybridization controls (Affymetrix) were hybridized on array followed by washing and staining steps according to the manufacturer’s procedures.
| | Sample_scan_protocol | GeneChip® Scanner 3000
| | Sample_data_processing | Probe-level data were normalized and gene expression summaries were computed for each probe set using GeneChip Robust Multichip Analysis (GC-RMA) on R 2.7. The data set was then filtered for low expression value and calls exhibiting values under an arbitrary threshold value of 8.84 (twice the value of the basal intensity) were considered ‘absent’ otherwise calls were considered ‘present’.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bertrand,,De Meulder
| | Sample_contact_email | bertrand.de.meulder@fundp.ac.be
| | Sample_contact_department | Biology
| | Sample_contact_institute | FUNDP
| | Sample_contact_address | Rue de Bruxelles, 61
| | Sample_contact_city | Namur
| | Sample_contact_state | Namur
| | Sample_contact_zip/postal_code | 500
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM954nnn/GSM954547/suppl/GSM954547_KM-ARN015.CEL.gz
| | Sample_series_id | GSE39042
| | Sample_data_row_count | 54675
| | |
|
GSM954548 | GPL570 |
|
H_TAX_3
|
Control cells in hypoxia
|
cell line: MDA-MB-231
|
Gene expression data from MDA-MB-231 cells
|
| Sample_geo_accession | GSM954548
| | Sample_status | Public on Jul 03 2012
| | Sample_submission_date | Jul 02 2012
| | Sample_last_update_date | Jul 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16 hours incubation in the presence of epirubicin 10 uM or paclitaxel 50 uM in medium without serum, under normoxia or hypoxia (1 % O2)
| | Sample_growth_protocol_ch1 | MDA-MB-231 were grown in RPMI1640 + 10 % fetal calf serum
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction kit (Invitrogen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Fragmented biotinylated cRNA and hybridization controls (Affymetrix) were hybridized on array followed by washing and staining steps according to the manufacturer’s procedures.
| | Sample_scan_protocol | GeneChip® Scanner 3000
| | Sample_data_processing | Probe-level data were normalized and gene expression summaries were computed for each probe set using GeneChip Robust Multichip Analysis (GC-RMA) on R 2.7. The data set was then filtered for low expression value and calls exhibiting values under an arbitrary threshold value of 8.84 (twice the value of the basal intensity) were considered ‘absent’ otherwise calls were considered ‘present’.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bertrand,,De Meulder
| | Sample_contact_email | bertrand.de.meulder@fundp.ac.be
| | Sample_contact_department | Biology
| | Sample_contact_institute | FUNDP
| | Sample_contact_address | Rue de Bruxelles, 61
| | Sample_contact_city | Namur
| | Sample_contact_state | Namur
| | Sample_contact_zip/postal_code | 500
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM954nnn/GSM954548/suppl/GSM954548_KM-ARN016.CEL.gz
| | Sample_series_id | GSE39042
| | Sample_data_row_count | 54675
| | |
|
GSM954549 | GPL570 |
|
N_EPI_3
|
Cells + paclitaxel 50 uM in normoxia
|
cell line: MDA-MB-231
|
Gene expression data from MDA-MB-231 cells
|
| Sample_geo_accession | GSM954549
| | Sample_status | Public on Jul 03 2012
| | Sample_submission_date | Jul 02 2012
| | Sample_last_update_date | Jul 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16 hours incubation in the presence of epirubicin 10 uM or paclitaxel 50 uM in medium without serum, under normoxia or hypoxia (1 % O2)
| | Sample_growth_protocol_ch1 | MDA-MB-231 were grown in RPMI1640 + 10 % fetal calf serum
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction kit (Invitrogen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Fragmented biotinylated cRNA and hybridization controls (Affymetrix) were hybridized on array followed by washing and staining steps according to the manufacturer’s procedures.
| | Sample_scan_protocol | GeneChip® Scanner 3000
| | Sample_data_processing | Probe-level data were normalized and gene expression summaries were computed for each probe set using GeneChip Robust Multichip Analysis (GC-RMA) on R 2.7. The data set was then filtered for low expression value and calls exhibiting values under an arbitrary threshold value of 8.84 (twice the value of the basal intensity) were considered ‘absent’ otherwise calls were considered ‘present’.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bertrand,,De Meulder
| | Sample_contact_email | bertrand.de.meulder@fundp.ac.be
| | Sample_contact_department | Biology
| | Sample_contact_institute | FUNDP
| | Sample_contact_address | Rue de Bruxelles, 61
| | Sample_contact_city | Namur
| | Sample_contact_state | Namur
| | Sample_contact_zip/postal_code | 500
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM954nnn/GSM954549/suppl/GSM954549_KM-ARN017.CEL.gz
| | Sample_series_id | GSE39042
| | Sample_data_row_count | 54675
| | |
|
GSM954550 | GPL570 |
|
H_EPI_3
|
Cells + paclitaxel 50 uM in hypoxia
|
cell line: MDA-MB-231
|
Gene expression data from MDA-MB-231 cells
|
| Sample_geo_accession | GSM954550
| | Sample_status | Public on Jul 03 2012
| | Sample_submission_date | Jul 02 2012
| | Sample_last_update_date | Jul 03 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 16 hours incubation in the presence of epirubicin 10 uM or paclitaxel 50 uM in medium without serum, under normoxia or hypoxia (1 % O2)
| | Sample_growth_protocol_ch1 | MDA-MB-231 were grown in RPMI1640 + 10 % fetal calf serum
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction kit (Invitrogen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Fragmented biotinylated cRNA and hybridization controls (Affymetrix) were hybridized on array followed by washing and staining steps according to the manufacturer’s procedures.
| | Sample_scan_protocol | GeneChip® Scanner 3000
| | Sample_data_processing | Probe-level data were normalized and gene expression summaries were computed for each probe set using GeneChip Robust Multichip Analysis (GC-RMA) on R 2.7. The data set was then filtered for low expression value and calls exhibiting values under an arbitrary threshold value of 8.84 (twice the value of the basal intensity) were considered ‘absent’ otherwise calls were considered ‘present’.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bertrand,,De Meulder
| | Sample_contact_email | bertrand.de.meulder@fundp.ac.be
| | Sample_contact_department | Biology
| | Sample_contact_institute | FUNDP
| | Sample_contact_address | Rue de Bruxelles, 61
| | Sample_contact_city | Namur
| | Sample_contact_state | Namur
| | Sample_contact_zip/postal_code | 500
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM954nnn/GSM954550/suppl/GSM954550_KM-ARN018.CEL.gz
| | Sample_series_id | GSE39042
| | 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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