Result

Search results for the GEO ID: GSE28274

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Title

Source name

Description

Characteristics

GSM699776

GPL570

Control1

MCF-7 cells

cell line: MCF-7

Gene expression data from control sample

Sample_geo_accession	GSM699776
Sample_status	Public on Apr 04 2011
Sample_submission_date	Mar 30 2011
Sample_last_update_date	Apr 04 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Drug activity testing: (a) 5 h equilibration with RM with and 8-min cycles (4 min exchange of medium and 4 min without flow); (b) drug incubation with freshly dissolved cisplatin at indicated concentration and the same 8-min cycles (4 min stop/ 4 min flow) for indicated time.
Sample_growth_protocol_ch1	Cells were first grown on BIONAS SC100 sensor chips in DMEM (pen/strep; 10% FCS) and incubated in a standard tissue culture incubator at 37 °C, 5% CO2, and 95% humidity for 24 h until 80–90% confluence. Sensor chips with cells were then transferred to Bionas 2500 workstation in which medium is continuously exchanged in 8-min cycles (4 min exchange of medium and 4 min without flow) during which metabolic parameters were measured. Running medium (RM) used during analysis was DMEM without carbonate buffer (PAN Cat. Nr. P03-0010), weakly buffered with 1 mM Hepes, reduced FCS (0.1%) and low glucose (1 g/l).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cell lysis for RNA extraction was done directly on biosensor at indicated time points, using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA quality was examined by agarose gel electrophoresis and concentration was determined by UV absorbance.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Labeled cRNA was prepared following the basic Affymetrix protocol with minor modifications. In short, double stranded cDNA was synthesized using a customary oligodT- T7 cDNA synthesis primer (Affymetrix, Santa Clara, CA, USA). The labeled antisense cRNA was generated using T7-RNA-polymerase (Enzo, Farmingdale, NY, USA) and biotin-labeled NTPs (Enzo). For fragmentation labeled cRNA was heated to 94° C for 35 min in the presence of 150 mM magnesium (Mg2+).
Sample_hyb_protocol	The Human GeneChip HG-U133 2.0 Plus was hybridized and analyzed in an Affymetrix workstation (fluidic-station and scanner). Primary data were obtained with the Affymetrix microarray suite.
Sample_scan_protocol	Affymetrix scaner and Microarray Suite Software Package.
Sample_data_processing	Primary data analysis was done with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Further analysis was done using normalized data, which were normalized using a rank based normalization algorithm (rank mean). Signal intensity obtained after rank based normalization (rank mean/quantile) of primary data obtained using dChip (Li C, Wong WH (2001) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 98:31-36).
Sample_platform_id	GPL570
Sample_contact_name	Stefan,,Wolfl
Sample_contact_email	wolfl@uni-hd.de
Sample_contact_laboratory	Bioanalytik
Sample_contact_department	IPMB, Biology
Sample_contact_institute	University Heidelberg
Sample_contact_address	Im Neuenheimer Feld 364
Sample_contact_city	Heidelberg
Sample_contact_zip/postal_code	D-69120
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM699nnn/GSM699776/suppl/GSM699776.CEL.gz
Sample_series_id	GSE28274
Sample_data_row_count	54675

GSM699777

GPL570

Control2

MCF-7 cells

cell line: MCF-7

Gene expression data from control sample

Sample_geo_accession	GSM699777
Sample_status	Public on Apr 04 2011
Sample_submission_date	Mar 30 2011
Sample_last_update_date	Apr 04 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Drug activity testing: (a) 5 h equilibration with RM with and 8-min cycles (4 min exchange of medium and 4 min without flow); (b) drug incubation with freshly dissolved cisplatin at indicated concentration and the same 8-min cycles (4 min stop/ 4 min flow) for indicated time.
Sample_growth_protocol_ch1	Cells were first grown on BIONAS SC100 sensor chips in DMEM (pen/strep; 10% FCS) and incubated in a standard tissue culture incubator at 37 °C, 5% CO2, and 95% humidity for 24 h until 80–90% confluence. Sensor chips with cells were then transferred to Bionas 2500 workstation in which medium is continuously exchanged in 8-min cycles (4 min exchange of medium and 4 min without flow) during which metabolic parameters were measured. Running medium (RM) used during analysis was DMEM without carbonate buffer (PAN Cat. Nr. P03-0010), weakly buffered with 1 mM Hepes, reduced FCS (0.1%) and low glucose (1 g/l).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cell lysis for RNA extraction was done directly on biosensor at indicated time points, using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA quality was examined by agarose gel electrophoresis and concentration was determined by UV absorbance.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Labeled cRNA was prepared following the basic Affymetrix protocol with minor modifications. In short, double stranded cDNA was synthesized using a customary oligodT- T7 cDNA synthesis primer (Affymetrix, Santa Clara, CA, USA). The labeled antisense cRNA was generated using T7-RNA-polymerase (Enzo, Farmingdale, NY, USA) and biotin-labeled NTPs (Enzo). For fragmentation labeled cRNA was heated to 94° C for 35 min in the presence of 150 mM magnesium (Mg2+).
Sample_hyb_protocol	The Human GeneChip HG-U133 2.0 Plus was hybridized and analyzed in an Affymetrix workstation (fluidic-station and scanner). Primary data were obtained with the Affymetrix microarray suite.
Sample_scan_protocol	Affymetrix scaner and Microarray Suite Software Package.
Sample_data_processing	Primary data analysis was done with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Further analysis was done using normalized data, which were normalized using a rank based normalization algorithm (rank mean). Signal intensity obtained after rank based normalization (rank mean/quantile) of primary data obtained using dChip (Li C, Wong WH (2001) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 98:31-36).
Sample_platform_id	GPL570
Sample_contact_name	Stefan,,Wolfl
Sample_contact_email	wolfl@uni-hd.de
Sample_contact_laboratory	Bioanalytik
Sample_contact_department	IPMB, Biology
Sample_contact_institute	University Heidelberg
Sample_contact_address	Im Neuenheimer Feld 364
Sample_contact_city	Heidelberg
Sample_contact_zip/postal_code	D-69120
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM699nnn/GSM699777/suppl/GSM699777.CEL.gz
Sample_series_id	GSE28274
Sample_data_row_count	54675

GSM699778

GPL570

Glycolysis_change1

MCF-7 cells

cell line: MCF-7

Gene expression data from cisplatin treatment

Sample_geo_accession	GSM699778
Sample_status	Public on Apr 04 2011
Sample_submission_date	Mar 30 2011
Sample_last_update_date	Apr 04 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Drug activity testing: (a) 5 h equilibration with RM with and 8-min cycles (4 min exchange of medium and 4 min without flow); (b) drug incubation with freshly dissolved cisplatin at indicated concentration and the same 8-min cycles (4 min stop/ 4 min flow) for indicated time.
Sample_growth_protocol_ch1	Cells were first grown on BIONAS SC100 sensor chips in DMEM (pen/strep; 10% FCS) and incubated in a standard tissue culture incubator at 37 °C, 5% CO2, and 95% humidity for 24 h until 80–90% confluence. Sensor chips with cells were then transferred to Bionas 2500 workstation in which medium is continuously exchanged in 8-min cycles (4 min exchange of medium and 4 min without flow) during which metabolic parameters were measured. Running medium (RM) used during analysis was DMEM without carbonate buffer (PAN Cat. Nr. P03-0010), weakly buffered with 1 mM Hepes, reduced FCS (0.1%) and low glucose (1 g/l).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cell lysis for RNA extraction was done directly on biosensor at indicated time points, using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA quality was examined by agarose gel electrophoresis and concentration was determined by UV absorbance.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Labeled cRNA was prepared following the basic Affymetrix protocol with minor modifications. In short, double stranded cDNA was synthesized using a customary oligodT- T7 cDNA synthesis primer (Affymetrix, Santa Clara, CA, USA). The labeled antisense cRNA was generated using T7-RNA-polymerase (Enzo, Farmingdale, NY, USA) and biotin-labeled NTPs (Enzo). For fragmentation labeled cRNA was heated to 94° C for 35 min in the presence of 150 mM magnesium (Mg2+).
Sample_hyb_protocol	The Human GeneChip HG-U133 2.0 Plus was hybridized and analyzed in an Affymetrix workstation (fluidic-station and scanner). Primary data were obtained with the Affymetrix microarray suite.
Sample_scan_protocol	Affymetrix scaner and Microarray Suite Software Package.
Sample_data_processing	Primary data analysis was done with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Further analysis was done using normalized data, which were normalized using a rank based normalization algorithm (rank mean). Signal intensity obtained after rank based normalization (rank mean/quantile) of primary data obtained using dChip (Li C, Wong WH (2001) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 98:31-36).
Sample_platform_id	GPL570
Sample_contact_name	Stefan,,Wolfl
Sample_contact_email	wolfl@uni-hd.de
Sample_contact_laboratory	Bioanalytik
Sample_contact_department	IPMB, Biology
Sample_contact_institute	University Heidelberg
Sample_contact_address	Im Neuenheimer Feld 364
Sample_contact_city	Heidelberg
Sample_contact_zip/postal_code	D-69120
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM699nnn/GSM699778/suppl/GSM699778.CEL.gz
Sample_series_id	GSE28274
Sample_data_row_count	54675

GSM699779

GPL570

Glycolysis_change2

MCF-7 cells

cell line: MCF-7

Gene expression data from cisplatin treatment

Sample_geo_accession	GSM699779
Sample_status	Public on Apr 04 2011
Sample_submission_date	Mar 30 2011
Sample_last_update_date	Apr 04 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Drug activity testing: (a) 5 h equilibration with RM with and 8-min cycles (4 min exchange of medium and 4 min without flow); (b) drug incubation with freshly dissolved cisplatin at indicated concentration and the same 8-min cycles (4 min stop/ 4 min flow) for indicated time.
Sample_growth_protocol_ch1	Cells were first grown on BIONAS SC100 sensor chips in DMEM (pen/strep; 10% FCS) and incubated in a standard tissue culture incubator at 37 °C, 5% CO2, and 95% humidity for 24 h until 80–90% confluence. Sensor chips with cells were then transferred to Bionas 2500 workstation in which medium is continuously exchanged in 8-min cycles (4 min exchange of medium and 4 min without flow) during which metabolic parameters were measured. Running medium (RM) used during analysis was DMEM without carbonate buffer (PAN Cat. Nr. P03-0010), weakly buffered with 1 mM Hepes, reduced FCS (0.1%) and low glucose (1 g/l).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cell lysis for RNA extraction was done directly on biosensor at indicated time points, using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA quality was examined by agarose gel electrophoresis and concentration was determined by UV absorbance.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Labeled cRNA was prepared following the basic Affymetrix protocol with minor modifications. In short, double stranded cDNA was synthesized using a customary oligodT- T7 cDNA synthesis primer (Affymetrix, Santa Clara, CA, USA). The labeled antisense cRNA was generated using T7-RNA-polymerase (Enzo, Farmingdale, NY, USA) and biotin-labeled NTPs (Enzo). For fragmentation labeled cRNA was heated to 94° C for 35 min in the presence of 150 mM magnesium (Mg2+).
Sample_hyb_protocol	The Human GeneChip HG-U133 2.0 Plus was hybridized and analyzed in an Affymetrix workstation (fluidic-station and scanner). Primary data were obtained with the Affymetrix microarray suite.
Sample_scan_protocol	Affymetrix scaner and Microarray Suite Software Package.
Sample_data_processing	Primary data analysis was done with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Further analysis was done using normalized data, which were normalized using a rank based normalization algorithm (rank mean). Signal intensity obtained after rank based normalization (rank mean/quantile) of primary data obtained using dChip (Li C, Wong WH (2001) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 98:31-36).
Sample_platform_id	GPL570
Sample_contact_name	Stefan,,Wolfl
Sample_contact_email	wolfl@uni-hd.de
Sample_contact_laboratory	Bioanalytik
Sample_contact_department	IPMB, Biology
Sample_contact_institute	University Heidelberg
Sample_contact_address	Im Neuenheimer Feld 364
Sample_contact_city	Heidelberg
Sample_contact_zip/postal_code	D-69120
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM699nnn/GSM699779/suppl/GSM699779.CEL.gz
Sample_series_id	GSE28274
Sample_data_row_count	54675

GSM699780

GPL570

Impedance_change1

MCF-7 cells

cell line: MCF-7

Gene expression data from cisplatin treatment

Sample_geo_accession	GSM699780
Sample_status	Public on Apr 04 2011
Sample_submission_date	Mar 30 2011
Sample_last_update_date	Apr 04 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Drug activity testing: (a) 5 h equilibration with RM with and 8-min cycles (4 min exchange of medium and 4 min without flow); (b) drug incubation with freshly dissolved cisplatin at indicated concentration and the same 8-min cycles (4 min stop/ 4 min flow) for indicated time.
Sample_growth_protocol_ch1	Cells were first grown on BIONAS SC100 sensor chips in DMEM (pen/strep; 10% FCS) and incubated in a standard tissue culture incubator at 37 °C, 5% CO2, and 95% humidity for 24 h until 80–90% confluence. Sensor chips with cells were then transferred to Bionas 2500 workstation in which medium is continuously exchanged in 8-min cycles (4 min exchange of medium and 4 min without flow) during which metabolic parameters were measured. Running medium (RM) used during analysis was DMEM without carbonate buffer (PAN Cat. Nr. P03-0010), weakly buffered with 1 mM Hepes, reduced FCS (0.1%) and low glucose (1 g/l).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cell lysis for RNA extraction was done directly on biosensor at indicated time points, using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA quality was examined by agarose gel electrophoresis and concentration was determined by UV absorbance.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Labeled cRNA was prepared following the basic Affymetrix protocol with minor modifications. In short, double stranded cDNA was synthesized using a customary oligodT- T7 cDNA synthesis primer (Affymetrix, Santa Clara, CA, USA). The labeled antisense cRNA was generated using T7-RNA-polymerase (Enzo, Farmingdale, NY, USA) and biotin-labeled NTPs (Enzo). For fragmentation labeled cRNA was heated to 94° C for 35 min in the presence of 150 mM magnesium (Mg2+).
Sample_hyb_protocol	The Human GeneChip HG-U133 2.0 Plus was hybridized and analyzed in an Affymetrix workstation (fluidic-station and scanner). Primary data were obtained with the Affymetrix microarray suite.
Sample_scan_protocol	Affymetrix scaner and Microarray Suite Software Package.
Sample_data_processing	Primary data analysis was done with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Further analysis was done using normalized data, which were normalized using a rank based normalization algorithm (rank mean). Signal intensity obtained after rank based normalization (rank mean/quantile) of primary data obtained using dChip (Li C, Wong WH (2001) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 98:31-36).
Sample_platform_id	GPL570
Sample_contact_name	Stefan,,Wolfl
Sample_contact_email	wolfl@uni-hd.de
Sample_contact_laboratory	Bioanalytik
Sample_contact_department	IPMB, Biology
Sample_contact_institute	University Heidelberg
Sample_contact_address	Im Neuenheimer Feld 364
Sample_contact_city	Heidelberg
Sample_contact_zip/postal_code	D-69120
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM699nnn/GSM699780/suppl/GSM699780.CEL.gz
Sample_series_id	GSE28274
Sample_data_row_count	54675

GSM699781

GPL570

Impedance_change2

MCF-7 cells

cell line: MCF-7

Gene expression data from cisplatin treatment

Sample_geo_accession	GSM699781
Sample_status	Public on Apr 04 2011
Sample_submission_date	Mar 30 2011
Sample_last_update_date	Apr 04 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Drug activity testing: (a) 5 h equilibration with RM with and 8-min cycles (4 min exchange of medium and 4 min without flow); (b) drug incubation with freshly dissolved cisplatin at indicated concentration and the same 8-min cycles (4 min stop/ 4 min flow) for indicated time.
Sample_growth_protocol_ch1	Cells were first grown on BIONAS SC100 sensor chips in DMEM (pen/strep; 10% FCS) and incubated in a standard tissue culture incubator at 37 °C, 5% CO2, and 95% humidity for 24 h until 80–90% confluence. Sensor chips with cells were then transferred to Bionas 2500 workstation in which medium is continuously exchanged in 8-min cycles (4 min exchange of medium and 4 min without flow) during which metabolic parameters were measured. Running medium (RM) used during analysis was DMEM without carbonate buffer (PAN Cat. Nr. P03-0010), weakly buffered with 1 mM Hepes, reduced FCS (0.1%) and low glucose (1 g/l).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cell lysis for RNA extraction was done directly on biosensor at indicated time points, using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA quality was examined by agarose gel electrophoresis and concentration was determined by UV absorbance.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Labeled cRNA was prepared following the basic Affymetrix protocol with minor modifications. In short, double stranded cDNA was synthesized using a customary oligodT- T7 cDNA synthesis primer (Affymetrix, Santa Clara, CA, USA). The labeled antisense cRNA was generated using T7-RNA-polymerase (Enzo, Farmingdale, NY, USA) and biotin-labeled NTPs (Enzo). For fragmentation labeled cRNA was heated to 94° C for 35 min in the presence of 150 mM magnesium (Mg2+).
Sample_hyb_protocol	The Human GeneChip HG-U133 2.0 Plus was hybridized and analyzed in an Affymetrix workstation (fluidic-station and scanner). Primary data were obtained with the Affymetrix microarray suite.
Sample_scan_protocol	Affymetrix scaner and Microarray Suite Software Package.
Sample_data_processing	Primary data analysis was done with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Further analysis was done using normalized data, which were normalized using a rank based normalization algorithm (rank mean). Signal intensity obtained after rank based normalization (rank mean/quantile) of primary data obtained using dChip (Li C, Wong WH (2001) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 98:31-36).
Sample_platform_id	GPL570
Sample_contact_name	Stefan,,Wolfl
Sample_contact_email	wolfl@uni-hd.de
Sample_contact_laboratory	Bioanalytik
Sample_contact_department	IPMB, Biology
Sample_contact_institute	University Heidelberg
Sample_contact_address	Im Neuenheimer Feld 364
Sample_contact_city	Heidelberg
Sample_contact_zip/postal_code	D-69120
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM699nnn/GSM699781/suppl/GSM699781.CEL.gz
Sample_series_id	GSE28274
Sample_data_row_count	54675

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