Search results for the GEO ID: GSE19638 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM490029 | GPL570 |
|
MCF7 untreated cells, rep1
|
MCF7, untreated
|
cell line: MCF7
cell type: adenocarcinoma mammary cells
treatment: untreated
|
Gene expression data from MCF7 untreated.
|
Sample_geo_accession | GSM490029
| Sample_status | Public on Jul 14 2010
| Sample_submission_date | Dec 23 2009
| Sample_last_update_date | Jul 09 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | After 24 hours, cells were treated with the different compounds at a dose equal to 5 times the IC50 for 6 hours and collected using Qiagen lysis buffer RLT (Qiagen cat no. 79216).
| Sample_growth_protocol_ch1 | MCF7 (human adenocarcinoma mammary) from ECACC were seeded in T-75 tissue culture flasks (Corning), 25.000 cells/cm2 in RPMI 1640 (Gibco), pH 7.4, 10% FBS (EUROCLONE Australia-USDA approved, cat. ECSO170D, lot.EUS003383), 2mM L-Glutamine (Gibco), 1x Penicillin-Streptomycin (Gibco) and maintained in 5% CO2 at 37°C with 96% relative humidity.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen Rneasy kit (Qiagen cat. no. 74104), starting from total cell lysates.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotin-labeled, fragmented cRNA probes were prepared starting from 1.5 µg of total RNA per replicate sample, using the ‘One-Cycle Target Labeling and Control Reagents’ (Affymetrix, Santa Clara, CA) according to the protocols included in the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com).
| Sample_hyb_protocol | Samples were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays and processed as per manufacturer’s instructions using ‘GeneChip® Hybridization, Wash, and Stain Kit’ components (Affymetrix, Santa Clara, CA).
| Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000.
| Sample_data_processing | Scanned images were first inspected for quality control (QC) using a variety of built-in QC tools from the Bioconductor package [www.bioconductor.org] of R, the open source environment for statistical analysis. Feature intensity values from scanned arrays were normalised and reduced to expression summaries using MAS5 implemented in the R statistical environment.
| Sample_platform_id | GPL570
| Sample_contact_name | Roberta,,Bosotti
| Sample_contact_email | roberta.bosotti@nervianoms.com
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Biotechnology
| Sample_contact_institute | Nerviano Medical Sciences srl
| Sample_contact_address | viale Pasteur,10
| Sample_contact_city | Nerviano
| Sample_contact_state | MI
| Sample_contact_zip/postal_code | 20014
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.nervianoms.com/cont/en/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM490nnn/GSM490029/suppl/GSM490029.CEL.gz
| Sample_series_id | GSE18552
| Sample_series_id | GSE19638
| Sample_data_row_count | 54675
| |
|
GSM490030 | GPL570 |
|
MCF7 untreated cells, rep2
|
MCF7, untreated
|
cell line: MCF7
cell type: adenocarcinoma mammary cells
treatment: untreated
|
Gene expression data from MCF7 untreated.
|
Sample_geo_accession | GSM490030
| Sample_status | Public on Jul 14 2010
| Sample_submission_date | Dec 23 2009
| Sample_last_update_date | Jul 09 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | After 24 hours, cells were treated with the different compounds at a dose equal to 5 times the IC50 for 6 hours and collected using Qiagen lysis buffer RLT (Qiagen cat no. 79216).
| Sample_growth_protocol_ch1 | MCF7 (human adenocarcinoma mammary) from ECACC were seeded in T-75 tissue culture flasks (Corning), 25.000 cells/cm2 in RPMI 1640 (Gibco), pH 7.4, 10% FBS (EUROCLONE Australia-USDA approved, cat. ECSO170D, lot.EUS003383), 2mM L-Glutamine (Gibco), 1x Penicillin-Streptomycin (Gibco) and maintained in 5% CO2 at 37°C with 96% relative humidity.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen Rneasy kit (Qiagen cat. no. 74104), starting from total cell lysates.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotin-labeled, fragmented cRNA probes were prepared starting from 1.5 µg of total RNA per replicate sample, using the ‘One-Cycle Target Labeling and Control Reagents’ (Affymetrix, Santa Clara, CA) according to the protocols included in the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com).
| Sample_hyb_protocol | Samples were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays and processed as per manufacturer’s instructions using ‘GeneChip® Hybridization, Wash, and Stain Kit’ components (Affymetrix, Santa Clara, CA).
| Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000.
| Sample_data_processing | Scanned images were first inspected for quality control (QC) using a variety of built-in QC tools from the Bioconductor package [www.bioconductor.org] of R, the open source environment for statistical analysis. Feature intensity values from scanned arrays were normalised and reduced to expression summaries using MAS5 implemented in the R statistical environment.
| Sample_platform_id | GPL570
| Sample_contact_name | Roberta,,Bosotti
| Sample_contact_email | roberta.bosotti@nervianoms.com
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Biotechnology
| Sample_contact_institute | Nerviano Medical Sciences srl
| Sample_contact_address | viale Pasteur,10
| Sample_contact_city | Nerviano
| Sample_contact_state | MI
| Sample_contact_zip/postal_code | 20014
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.nervianoms.com/cont/en/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM490nnn/GSM490030/suppl/GSM490030.CEL.gz
| Sample_series_id | GSE18552
| Sample_series_id | GSE19638
| Sample_data_row_count | 54675
| |
|
GSM490031 | GPL570 |
|
MCF7 treated with 17AAG, rep1
|
MCF7, 17AAG
|
cell line: MCF7
cell type: adenocarcinoma mammary cells
treatment: 17AAG
|
Gene expression data from MCF7 treated with 17AAG.
|
Sample_geo_accession | GSM490031
| Sample_status | Public on Jul 14 2010
| Sample_submission_date | Dec 23 2009
| Sample_last_update_date | Jul 09 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | After 24 hours, cells were treated with the different compounds at a dose equal to 5 times the IC50 for 6 hours and collected using Qiagen lysis buffer RLT (Qiagen cat no. 79216).
| Sample_growth_protocol_ch1 | MCF7 (human adenocarcinoma mammary) from ECACC were seeded in T-75 tissue culture flasks (Corning), 25.000 cells/cm2 in RPMI 1640 (Gibco), pH 7.4, 10% FBS (EUROCLONE Australia-USDA approved, cat. ECSO170D, lot.EUS003383), 2mM L-Glutamine (Gibco), 1x Penicillin-Streptomycin (Gibco) and maintained in 5% CO2 at 37°C with 96% relative humidity.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen Rneasy kit (Qiagen cat. no. 74104), starting from total cell lysates.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotin-labeled, fragmented cRNA probes were prepared starting from 1.5 µg of total RNA per replicate sample, using the ‘One-Cycle Target Labeling and Control Reagents’ (Affymetrix, Santa Clara, CA) according to the protocols included in the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com).
| Sample_hyb_protocol | Samples were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays and processed as per manufacturer’s instructions using ‘GeneChip® Hybridization, Wash, and Stain Kit’ components (Affymetrix, Santa Clara, CA).
| Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000.
| Sample_data_processing | Scanned images were first inspected for quality control (QC) using a variety of built-in QC tools from the Bioconductor package [www.bioconductor.org] of R, the open source environment for statistical analysis. Feature intensity values from scanned arrays were normalised and reduced to expression summaries using MAS5 implemented in the R statistical environment.
| Sample_platform_id | GPL570
| Sample_contact_name | Roberta,,Bosotti
| Sample_contact_email | roberta.bosotti@nervianoms.com
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Biotechnology
| Sample_contact_institute | Nerviano Medical Sciences srl
| Sample_contact_address | viale Pasteur,10
| Sample_contact_city | Nerviano
| Sample_contact_state | MI
| Sample_contact_zip/postal_code | 20014
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.nervianoms.com/cont/en/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM490nnn/GSM490031/suppl/GSM490031.CEL.gz
| Sample_series_id | GSE18552
| Sample_series_id | GSE19638
| Sample_data_row_count | 54675
| |
|
GSM490032 | GPL570 |
|
MCF7 treated with 17AAG, rep2
|
MCF7, 17AAG
|
cell line: MCF7
cell type: adenocarcinoma mammary cells
treatment: 17AAG
|
Gene expression data from MCF7 treated with 17AAG.
|
Sample_geo_accession | GSM490032
| Sample_status | Public on Jul 14 2010
| Sample_submission_date | Dec 23 2009
| Sample_last_update_date | Jul 09 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | After 24 hours, cells were treated with the different compounds at a dose equal to 5 times the IC50 for 6 hours and collected using Qiagen lysis buffer RLT (Qiagen cat no. 79216).
| Sample_growth_protocol_ch1 | MCF7 (human adenocarcinoma mammary) from ECACC were seeded in T-75 tissue culture flasks (Corning), 25.000 cells/cm2 in RPMI 1640 (Gibco), pH 7.4, 10% FBS (EUROCLONE Australia-USDA approved, cat. ECSO170D, lot.EUS003383), 2mM L-Glutamine (Gibco), 1x Penicillin-Streptomycin (Gibco) and maintained in 5% CO2 at 37°C with 96% relative humidity.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen Rneasy kit (Qiagen cat. no. 74104), starting from total cell lysates.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotin-labeled, fragmented cRNA probes were prepared starting from 1.5 µg of total RNA per replicate sample, using the ‘One-Cycle Target Labeling and Control Reagents’ (Affymetrix, Santa Clara, CA) according to the protocols included in the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com).
| Sample_hyb_protocol | Samples were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays and processed as per manufacturer’s instructions using ‘GeneChip® Hybridization, Wash, and Stain Kit’ components (Affymetrix, Santa Clara, CA).
| Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000.
| Sample_data_processing | Scanned images were first inspected for quality control (QC) using a variety of built-in QC tools from the Bioconductor package [www.bioconductor.org] of R, the open source environment for statistical analysis. Feature intensity values from scanned arrays were normalised and reduced to expression summaries using MAS5 implemented in the R statistical environment.
| Sample_platform_id | GPL570
| Sample_contact_name | Roberta,,Bosotti
| Sample_contact_email | roberta.bosotti@nervianoms.com
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Biotechnology
| Sample_contact_institute | Nerviano Medical Sciences srl
| Sample_contact_address | viale Pasteur,10
| Sample_contact_city | Nerviano
| Sample_contact_state | MI
| Sample_contact_zip/postal_code | 20014
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.nervianoms.com/cont/en/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM490nnn/GSM490032/suppl/GSM490032.CEL.gz
| Sample_series_id | GSE18552
| Sample_series_id | GSE19638
| Sample_data_row_count | 54675
| |
|
GSM490033 | GPL570 |
|
MCF7 treated with AUY922, rep1
|
MCF7, AUY922
|
cell line: MCF7
cell type: adenocarcinoma mammary cells
treatment: AUY922
|
Gene expression data from MCF7 treated with AUY922.
|
Sample_geo_accession | GSM490033
| Sample_status | Public on Jul 14 2010
| Sample_submission_date | Dec 23 2009
| Sample_last_update_date | Jul 09 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | After 24 hours, cells were treated with the different compounds at a dose equal to 5 times the IC50 for 6 hours and collected using Qiagen lysis buffer RLT (Qiagen cat no. 79216).
| Sample_growth_protocol_ch1 | MCF7 (human adenocarcinoma mammary) from ECACC were seeded in T-75 tissue culture flasks (Corning), 25.000 cells/cm2 in RPMI 1640 (Gibco), pH 7.4, 10% FBS (EUROCLONE Australia-USDA approved, cat. ECSO170D, lot.EUS003383), 2mM L-Glutamine (Gibco), 1x Penicillin-Streptomycin (Gibco) and maintained in 5% CO2 at 37°C with 96% relative humidity.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen Rneasy kit (Qiagen cat. no. 74104), starting from total cell lysates.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotin-labeled, fragmented cRNA probes were prepared starting from 1.5 µg of total RNA per replicate sample, using the ‘One-Cycle Target Labeling and Control Reagents’ (Affymetrix, Santa Clara, CA) according to the protocols included in the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com).
| Sample_hyb_protocol | Samples were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays and processed as per manufacturer’s instructions using ‘GeneChip® Hybridization, Wash, and Stain Kit’ components (Affymetrix, Santa Clara, CA).
| Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000.
| Sample_data_processing | Scanned images were first inspected for quality control (QC) using a variety of built-in QC tools from the Bioconductor package [www.bioconductor.org] of R, the open source environment for statistical analysis. Feature intensity values from scanned arrays were normalised and reduced to expression summaries using MAS5 implemented in the R statistical environment.
| Sample_platform_id | GPL570
| Sample_contact_name | Roberta,,Bosotti
| Sample_contact_email | roberta.bosotti@nervianoms.com
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Biotechnology
| Sample_contact_institute | Nerviano Medical Sciences srl
| Sample_contact_address | viale Pasteur,10
| Sample_contact_city | Nerviano
| Sample_contact_state | MI
| Sample_contact_zip/postal_code | 20014
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.nervianoms.com/cont/en/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM490nnn/GSM490033/suppl/GSM490033.CEL.gz
| Sample_series_id | GSE18552
| Sample_series_id | GSE19638
| Sample_data_row_count | 54675
| |
|
GSM490034 | GPL570 |
|
MCF7 treated with AUY922, rep2
|
MCF7, AUY922
|
cell line: MCF7
cell type: adenocarcinoma mammary cells
treatment: AUY922
|
Gene expression data from MCF7 treated with AUY922.
|
Sample_geo_accession | GSM490034
| Sample_status | Public on Jul 14 2010
| Sample_submission_date | Dec 23 2009
| Sample_last_update_date | Jul 09 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | After 24 hours, cells were treated with the different compounds at a dose equal to 5 times the IC50 for 6 hours and collected using Qiagen lysis buffer RLT (Qiagen cat no. 79216).
| Sample_growth_protocol_ch1 | MCF7 (human adenocarcinoma mammary) from ECACC were seeded in T-75 tissue culture flasks (Corning), 25.000 cells/cm2 in RPMI 1640 (Gibco), pH 7.4, 10% FBS (EUROCLONE Australia-USDA approved, cat. ECSO170D, lot.EUS003383), 2mM L-Glutamine (Gibco), 1x Penicillin-Streptomycin (Gibco) and maintained in 5% CO2 at 37°C with 96% relative humidity.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen Rneasy kit (Qiagen cat. no. 74104), starting from total cell lysates.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotin-labeled, fragmented cRNA probes were prepared starting from 1.5 µg of total RNA per replicate sample, using the ‘One-Cycle Target Labeling and Control Reagents’ (Affymetrix, Santa Clara, CA) according to the protocols included in the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com).
| Sample_hyb_protocol | Samples were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays and processed as per manufacturer’s instructions using ‘GeneChip® Hybridization, Wash, and Stain Kit’ components (Affymetrix, Santa Clara, CA).
| Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000.
| Sample_data_processing | Scanned images were first inspected for quality control (QC) using a variety of built-in QC tools from the Bioconductor package [www.bioconductor.org] of R, the open source environment for statistical analysis. Feature intensity values from scanned arrays were normalised and reduced to expression summaries using MAS5 implemented in the R statistical environment.
| Sample_platform_id | GPL570
| Sample_contact_name | Roberta,,Bosotti
| Sample_contact_email | roberta.bosotti@nervianoms.com
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Biotechnology
| Sample_contact_institute | Nerviano Medical Sciences srl
| Sample_contact_address | viale Pasteur,10
| Sample_contact_city | Nerviano
| Sample_contact_state | MI
| Sample_contact_zip/postal_code | 20014
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.nervianoms.com/cont/en/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM490nnn/GSM490034/suppl/GSM490034.CEL.gz
| Sample_series_id | GSE18552
| Sample_series_id | GSE19638
| Sample_data_row_count | 54675
| |
|
GSM490035 | GPL570 |
|
MCF7 treated with CDK-887, rep1
|
MCF7, CDK-887
|
cell line: MCF7
cell type: adenocarcinoma mammary cells
treatment: CDK-887
|
Gene expression data from MCF7 treated with CDK-887.
|
Sample_geo_accession | GSM490035
| Sample_status | Public on Jul 14 2010
| Sample_submission_date | Dec 23 2009
| Sample_last_update_date | Jul 09 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | After 24 hours, cells were treated with the different compounds at a dose equal to 5 times the IC50 for 6 hours and collected using Qiagen lysis buffer RLT (Qiagen cat no. 79216).
| Sample_growth_protocol_ch1 | MCF7 (human adenocarcinoma mammary) from ECACC were seeded in T-75 tissue culture flasks (Corning), 25.000 cells/cm2 in RPMI 1640 (Gibco), pH 7.4, 10% FBS (EUROCLONE Australia-USDA approved, cat. ECSO170D, lot.EUS003383), 2mM L-Glutamine (Gibco), 1x Penicillin-Streptomycin (Gibco) and maintained in 5% CO2 at 37°C with 96% relative humidity.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen Rneasy kit (Qiagen cat. no. 74104), starting from total cell lysates.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotin-labeled, fragmented cRNA probes were prepared starting from 1.5 µg of total RNA per replicate sample, using the ‘One-Cycle Target Labeling and Control Reagents’ (Affymetrix, Santa Clara, CA) according to the protocols included in the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com).
| Sample_hyb_protocol | Samples were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays and processed as per manufacturer’s instructions using ‘GeneChip® Hybridization, Wash, and Stain Kit’ components (Affymetrix, Santa Clara, CA).
| Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000.
| Sample_data_processing | Scanned images were first inspected for quality control (QC) using a variety of built-in QC tools from the Bioconductor package [www.bioconductor.org] of R, the open source environment for statistical analysis. Feature intensity values from scanned arrays were normalised and reduced to expression summaries using MAS5 implemented in the R statistical environment.
| Sample_platform_id | GPL570
| Sample_contact_name | Roberta,,Bosotti
| Sample_contact_email | roberta.bosotti@nervianoms.com
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Biotechnology
| Sample_contact_institute | Nerviano Medical Sciences srl
| Sample_contact_address | viale Pasteur,10
| Sample_contact_city | Nerviano
| Sample_contact_state | MI
| Sample_contact_zip/postal_code | 20014
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.nervianoms.com/cont/en/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM490nnn/GSM490035/suppl/GSM490035.CEL.gz
| Sample_series_id | GSE18552
| Sample_series_id | GSE19638
| Sample_data_row_count | 54675
| |
|
GSM490036 | GPL570 |
|
MCF7 treated with CDK-887, rep2
|
MCF7, CDK-887
|
cell line: MCF7
cell type: adenocarcinoma mammary cells
treatment: CDK-887
|
Gene expression data from MCF7 treated with CDK-887.
|
Sample_geo_accession | GSM490036
| Sample_status | Public on Jul 14 2010
| Sample_submission_date | Dec 23 2009
| Sample_last_update_date | Jul 09 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | After 24 hours, cells were treated with the different compounds at a dose equal to 5 times the IC50 for 6 hours and collected using Qiagen lysis buffer RLT (Qiagen cat no. 79216).
| Sample_growth_protocol_ch1 | MCF7 (human adenocarcinoma mammary) from ECACC were seeded in T-75 tissue culture flasks (Corning), 25.000 cells/cm2 in RPMI 1640 (Gibco), pH 7.4, 10% FBS (EUROCLONE Australia-USDA approved, cat. ECSO170D, lot.EUS003383), 2mM L-Glutamine (Gibco), 1x Penicillin-Streptomycin (Gibco) and maintained in 5% CO2 at 37°C with 96% relative humidity.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen Rneasy kit (Qiagen cat. no. 74104), starting from total cell lysates.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotin-labeled, fragmented cRNA probes were prepared starting from 1.5 µg of total RNA per replicate sample, using the ‘One-Cycle Target Labeling and Control Reagents’ (Affymetrix, Santa Clara, CA) according to the protocols included in the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com).
| Sample_hyb_protocol | Samples were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays and processed as per manufacturer’s instructions using ‘GeneChip® Hybridization, Wash, and Stain Kit’ components (Affymetrix, Santa Clara, CA).
| Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000.
| Sample_data_processing | Scanned images were first inspected for quality control (QC) using a variety of built-in QC tools from the Bioconductor package [www.bioconductor.org] of R, the open source environment for statistical analysis. Feature intensity values from scanned arrays were normalised and reduced to expression summaries using MAS5 implemented in the R statistical environment.
| Sample_platform_id | GPL570
| Sample_contact_name | Roberta,,Bosotti
| Sample_contact_email | roberta.bosotti@nervianoms.com
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Biotechnology
| Sample_contact_institute | Nerviano Medical Sciences srl
| Sample_contact_address | viale Pasteur,10
| Sample_contact_city | Nerviano
| Sample_contact_state | MI
| Sample_contact_zip/postal_code | 20014
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.nervianoms.com/cont/en/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM490nnn/GSM490036/suppl/GSM490036.CEL.gz
| Sample_series_id | GSE18552
| Sample_series_id | GSE19638
| Sample_data_row_count | 54675
| |
|
GSM490037 | GPL570 |
|
MCF7 treated with doxo, rep1
|
MCF7, doxo
|
cell line: MCF7
cell type: adenocarcinoma mammary cells
treatment: doxorubicin
|
Gene expression data from MCF7 treated with doxo.
|
Sample_geo_accession | GSM490037
| Sample_status | Public on Jul 14 2010
| Sample_submission_date | Dec 23 2009
| Sample_last_update_date | Jul 09 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | After 24 hours, cells were treated with the different compounds at a dose equal to 5 times the IC50 for 6 hours and collected using Qiagen lysis buffer RLT (Qiagen cat no. 79216).
| Sample_growth_protocol_ch1 | MCF7 (human adenocarcinoma mammary) from ECACC were seeded in T-75 tissue culture flasks (Corning), 25.000 cells/cm2 in RPMI 1640 (Gibco), pH 7.4, 10% FBS (EUROCLONE Australia-USDA approved, cat. ECSO170D, lot.EUS003383), 2mM L-Glutamine (Gibco), 1x Penicillin-Streptomycin (Gibco) and maintained in 5% CO2 at 37°C with 96% relative humidity.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen Rneasy kit (Qiagen cat. no. 74104), starting from total cell lysates.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotin-labeled, fragmented cRNA probes were prepared starting from 1.5 µg of total RNA per replicate sample, using the ‘One-Cycle Target Labeling and Control Reagents’ (Affymetrix, Santa Clara, CA) according to the protocols included in the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com).
| Sample_hyb_protocol | Samples were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays and processed as per manufacturer’s instructions using ‘GeneChip® Hybridization, Wash, and Stain Kit’ components (Affymetrix, Santa Clara, CA).
| Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000.
| Sample_data_processing | Scanned images were first inspected for quality control (QC) using a variety of built-in QC tools from the Bioconductor package [www.bioconductor.org] of R, the open source environment for statistical analysis. Feature intensity values from scanned arrays were normalised and reduced to expression summaries using MAS5 implemented in the R statistical environment.
| Sample_platform_id | GPL570
| Sample_contact_name | Roberta,,Bosotti
| Sample_contact_email | roberta.bosotti@nervianoms.com
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Biotechnology
| Sample_contact_institute | Nerviano Medical Sciences srl
| Sample_contact_address | viale Pasteur,10
| Sample_contact_city | Nerviano
| Sample_contact_state | MI
| Sample_contact_zip/postal_code | 20014
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.nervianoms.com/cont/en/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM490nnn/GSM490037/suppl/GSM490037.CEL.gz
| Sample_series_id | GSE18552
| Sample_series_id | GSE19638
| Sample_data_row_count | 54675
| |
|
GSM490038 | GPL570 |
|
MCF7 treated with doxo, rep2
|
MCF7, doxo
|
cell line: MCF7
cell type: adenocarcinoma mammary cells
treatment: doxorubicin
|
Gene expression data from MCF7 treated with doxo.
|
Sample_geo_accession | GSM490038
| Sample_status | Public on Jul 14 2010
| Sample_submission_date | Dec 23 2009
| Sample_last_update_date | Jul 09 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | After 24 hours, cells were treated with the different compounds at a dose equal to 5 times the IC50 for 6 hours and collected using Qiagen lysis buffer RLT (Qiagen cat no. 79216).
| Sample_growth_protocol_ch1 | MCF7 (human adenocarcinoma mammary) from ECACC were seeded in T-75 tissue culture flasks (Corning), 25.000 cells/cm2 in RPMI 1640 (Gibco), pH 7.4, 10% FBS (EUROCLONE Australia-USDA approved, cat. ECSO170D, lot.EUS003383), 2mM L-Glutamine (Gibco), 1x Penicillin-Streptomycin (Gibco) and maintained in 5% CO2 at 37°C with 96% relative humidity.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen Rneasy kit (Qiagen cat. no. 74104), starting from total cell lysates.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotin-labeled, fragmented cRNA probes were prepared starting from 1.5 µg of total RNA per replicate sample, using the ‘One-Cycle Target Labeling and Control Reagents’ (Affymetrix, Santa Clara, CA) according to the protocols included in the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com).
| Sample_hyb_protocol | Samples were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays and processed as per manufacturer’s instructions using ‘GeneChip® Hybridization, Wash, and Stain Kit’ components (Affymetrix, Santa Clara, CA).
| Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000.
| Sample_data_processing | Scanned images were first inspected for quality control (QC) using a variety of built-in QC tools from the Bioconductor package [www.bioconductor.org] of R, the open source environment for statistical analysis. Feature intensity values from scanned arrays were normalised and reduced to expression summaries using MAS5 implemented in the R statistical environment.
| Sample_platform_id | GPL570
| Sample_contact_name | Roberta,,Bosotti
| Sample_contact_email | roberta.bosotti@nervianoms.com
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Biotechnology
| Sample_contact_institute | Nerviano Medical Sciences srl
| Sample_contact_address | viale Pasteur,10
| Sample_contact_city | Nerviano
| Sample_contact_state | MI
| Sample_contact_zip/postal_code | 20014
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.nervianoms.com/cont/en/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM490nnn/GSM490038/suppl/GSM490038.CEL.gz
| Sample_series_id | GSE18552
| Sample_series_id | GSE19638
| Sample_data_row_count | 54675
| |
|
GSM490039 | GPL570 |
|
MCF7 treated with E973, rep1
|
MCF7, E973
|
cell line: MCF7
cell type: adenocarcinoma mammary cells
treatment: E973
|
Gene expression data from MCF7 treated with E973.
|
Sample_geo_accession | GSM490039
| Sample_status | Public on Jul 14 2010
| Sample_submission_date | Dec 23 2009
| Sample_last_update_date | Jul 09 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | After 24 hours, cells were treated with the different compounds at a dose equal to 5 times the IC50 for 6 hours and collected using Qiagen lysis buffer RLT (Qiagen cat no. 79216).
| Sample_growth_protocol_ch1 | MCF7 (human adenocarcinoma mammary) from ECACC were seeded in T-75 tissue culture flasks (Corning), 25.000 cells/cm2 in RPMI 1640 (Gibco), pH 7.4, 10% FBS (EUROCLONE Australia-USDA approved, cat. ECSO170D, lot.EUS003383), 2mM L-Glutamine (Gibco), 1x Penicillin-Streptomycin (Gibco) and maintained in 5% CO2 at 37°C with 96% relative humidity.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen Rneasy kit (Qiagen cat. no. 74104), starting from total cell lysates.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotin-labeled, fragmented cRNA probes were prepared starting from 1.5 µg of total RNA per replicate sample, using the ‘One-Cycle Target Labeling and Control Reagents’ (Affymetrix, Santa Clara, CA) according to the protocols included in the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com).
| Sample_hyb_protocol | Samples were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays and processed as per manufacturer’s instructions using ‘GeneChip® Hybridization, Wash, and Stain Kit’ components (Affymetrix, Santa Clara, CA).
| Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000.
| Sample_data_processing | Scanned images were first inspected for quality control (QC) using a variety of built-in QC tools from the Bioconductor package [www.bioconductor.org] of R, the open source environment for statistical analysis. Feature intensity values from scanned arrays were normalised and reduced to expression summaries using MAS5 implemented in the R statistical environment.
| Sample_platform_id | GPL570
| Sample_contact_name | Roberta,,Bosotti
| Sample_contact_email | roberta.bosotti@nervianoms.com
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Biotechnology
| Sample_contact_institute | Nerviano Medical Sciences srl
| Sample_contact_address | viale Pasteur,10
| Sample_contact_city | Nerviano
| Sample_contact_state | MI
| Sample_contact_zip/postal_code | 20014
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.nervianoms.com/cont/en/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM490nnn/GSM490039/suppl/GSM490039.CEL.gz
| Sample_series_id | GSE18552
| Sample_series_id | GSE19638
| Sample_data_row_count | 54675
| |
|
GSM490040 | GPL570 |
|
MCF7 treated with E973, rep2
|
MCF7, E973
|
cell line: MCF7
cell type: adenocarcinoma mammary cells
treatment: E973
|
Gene expression data from MCF7 treated with E973.
|
Sample_geo_accession | GSM490040
| Sample_status | Public on Jul 14 2010
| Sample_submission_date | Dec 23 2009
| Sample_last_update_date | Jul 09 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | After 24 hours, cells were treated with the different compounds at a dose equal to 5 times the IC50 for 6 hours and collected using Qiagen lysis buffer RLT (Qiagen cat no. 79216).
| Sample_growth_protocol_ch1 | MCF7 (human adenocarcinoma mammary) from ECACC were seeded in T-75 tissue culture flasks (Corning), 25.000 cells/cm2 in RPMI 1640 (Gibco), pH 7.4, 10% FBS (EUROCLONE Australia-USDA approved, cat. ECSO170D, lot.EUS003383), 2mM L-Glutamine (Gibco), 1x Penicillin-Streptomycin (Gibco) and maintained in 5% CO2 at 37°C with 96% relative humidity.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen Rneasy kit (Qiagen cat. no. 74104), starting from total cell lysates.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotin-labeled, fragmented cRNA probes were prepared starting from 1.5 µg of total RNA per replicate sample, using the ‘One-Cycle Target Labeling and Control Reagents’ (Affymetrix, Santa Clara, CA) according to the protocols included in the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com).
| Sample_hyb_protocol | Samples were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays and processed as per manufacturer’s instructions using ‘GeneChip® Hybridization, Wash, and Stain Kit’ components (Affymetrix, Santa Clara, CA).
| Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000.
| Sample_data_processing | Scanned images were first inspected for quality control (QC) using a variety of built-in QC tools from the Bioconductor package [www.bioconductor.org] of R, the open source environment for statistical analysis. Feature intensity values from scanned arrays were normalised and reduced to expression summaries using MAS5 implemented in the R statistical environment.
| Sample_platform_id | GPL570
| Sample_contact_name | Roberta,,Bosotti
| Sample_contact_email | roberta.bosotti@nervianoms.com
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Biotechnology
| Sample_contact_institute | Nerviano Medical Sciences srl
| Sample_contact_address | viale Pasteur,10
| Sample_contact_city | Nerviano
| Sample_contact_state | MI
| Sample_contact_zip/postal_code | 20014
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.nervianoms.com/cont/en/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM490nnn/GSM490040/suppl/GSM490040.CEL.gz
| Sample_series_id | GSE18552
| Sample_series_id | GSE19638
| Sample_data_row_count | 54675
| |
|
GSM490041 | GPL570 |
|
MCF7 treated with SN38, rep1
|
MCF7, SN38
|
cell line: MCF7
cell type: adenocarcinoma mammary cells
treatment: SN38
|
Gene expression data from MCF7 treated with SN38.
|
Sample_geo_accession | GSM490041
| Sample_status | Public on Jul 14 2010
| Sample_submission_date | Dec 23 2009
| Sample_last_update_date | Jul 09 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | After 24 hours, cells were treated with the different compounds at a dose equal to 5 times the IC50 for 6 hours and collected using Qiagen lysis buffer RLT (Qiagen cat no. 79216).
| Sample_growth_protocol_ch1 | MCF7 (human adenocarcinoma mammary) from ECACC were seeded in T-75 tissue culture flasks (Corning), 25.000 cells/cm2 in RPMI 1640 (Gibco), pH 7.4, 10% FBS (EUROCLONE Australia-USDA approved, cat. ECSO170D, lot.EUS003383), 2mM L-Glutamine (Gibco), 1x Penicillin-Streptomycin (Gibco) and maintained in 5% CO2 at 37°C with 96% relative humidity.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen Rneasy kit (Qiagen cat. no. 74104), starting from total cell lysates.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotin-labeled, fragmented cRNA probes were prepared starting from 1.5 µg of total RNA per replicate sample, using the ‘One-Cycle Target Labeling and Control Reagents’ (Affymetrix, Santa Clara, CA) according to the protocols included in the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com).
| Sample_hyb_protocol | Samples were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays and processed as per manufacturer’s instructions using ‘GeneChip® Hybridization, Wash, and Stain Kit’ components (Affymetrix, Santa Clara, CA).
| Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000.
| Sample_data_processing | Scanned images were first inspected for quality control (QC) using a variety of built-in QC tools from the Bioconductor package [www.bioconductor.org] of R, the open source environment for statistical analysis. Feature intensity values from scanned arrays were normalised and reduced to expression summaries using MAS5 implemented in the R statistical environment.
| Sample_platform_id | GPL570
| Sample_contact_name | Roberta,,Bosotti
| Sample_contact_email | roberta.bosotti@nervianoms.com
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Biotechnology
| Sample_contact_institute | Nerviano Medical Sciences srl
| Sample_contact_address | viale Pasteur,10
| Sample_contact_city | Nerviano
| Sample_contact_state | MI
| Sample_contact_zip/postal_code | 20014
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.nervianoms.com/cont/en/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM490nnn/GSM490041/suppl/GSM490041.CEL.gz
| Sample_series_id | GSE18552
| Sample_series_id | GSE19638
| Sample_data_row_count | 54675
| |
|
GSM490042 | GPL570 |
|
MCF7 treated with SN38, rep2
|
MCF7, SN38
|
cell line: MCF7
cell type: adenocarcinoma mammary cells
treatment: SN38
|
Gene expression data from MCF7 treated with SN38.
|
Sample_geo_accession | GSM490042
| Sample_status | Public on Jul 14 2010
| Sample_submission_date | Dec 23 2009
| Sample_last_update_date | Jul 09 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | After 24 hours, cells were treated with the different compounds at a dose equal to 5 times the IC50 for 6 hours and collected using Qiagen lysis buffer RLT (Qiagen cat no. 79216).
| Sample_growth_protocol_ch1 | MCF7 (human adenocarcinoma mammary) from ECACC were seeded in T-75 tissue culture flasks (Corning), 25.000 cells/cm2 in RPMI 1640 (Gibco), pH 7.4, 10% FBS (EUROCLONE Australia-USDA approved, cat. ECSO170D, lot.EUS003383), 2mM L-Glutamine (Gibco), 1x Penicillin-Streptomycin (Gibco) and maintained in 5% CO2 at 37°C with 96% relative humidity.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Qiagen Rneasy kit (Qiagen cat. no. 74104), starting from total cell lysates.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotin-labeled, fragmented cRNA probes were prepared starting from 1.5 µg of total RNA per replicate sample, using the ‘One-Cycle Target Labeling and Control Reagents’ (Affymetrix, Santa Clara, CA) according to the protocols included in the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com).
| Sample_hyb_protocol | Samples were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays and processed as per manufacturer’s instructions using ‘GeneChip® Hybridization, Wash, and Stain Kit’ components (Affymetrix, Santa Clara, CA).
| Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000.
| Sample_data_processing | Scanned images were first inspected for quality control (QC) using a variety of built-in QC tools from the Bioconductor package [www.bioconductor.org] of R, the open source environment for statistical analysis. Feature intensity values from scanned arrays were normalised and reduced to expression summaries using MAS5 implemented in the R statistical environment.
| Sample_platform_id | GPL570
| Sample_contact_name | Roberta,,Bosotti
| Sample_contact_email | roberta.bosotti@nervianoms.com
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Biotechnology
| Sample_contact_institute | Nerviano Medical Sciences srl
| Sample_contact_address | viale Pasteur,10
| Sample_contact_city | Nerviano
| Sample_contact_state | MI
| Sample_contact_zip/postal_code | 20014
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.nervianoms.com/cont/en/
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM490nnn/GSM490042/suppl/GSM490042.CEL.gz
| Sample_series_id | GSE18552
| Sample_series_id | GSE19638
| Sample_data_row_count | 54675
| |
|
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Select GSMs and click on "Add groups" |
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