Search results for the GEO ID: GSE31246  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM774585 | GPL1261 |
|
A2C12 non-SP cells biological replicate 1
|
A2C12 non-SP cells
|
background strain: C57BL/6
cell line: A2C12
cell fraction: non-SP
treatment: none
|
lung tumour cell line from a c-myc/c-raf double transgenic mouse model
|
| Sample_geo_accession | GSM774585
| | Sample_status | Public on Aug 08 2012
| | Sample_submission_date | Aug 08 2011
| | Sample_last_update_date | Aug 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were treated with a monoclonal anti-mouse EpCAM antibody at concentrations of 100 µg/ml for 48 h. Subsequently, 10^6 cells/ml were resuspended in warm DMEM containing 2% FCS and 10 mmol/l HEPES buffer (Sigma-Aldrich, Munich, Germany). Hoechst 33342 dye was added to a final concentration of 5 µg/ml in the presence or absence of reserpine (50 µmol/l; Sigma-Aldrich, Munich, Germany) and incubated at 37°C for 90 min with gentle shaking. Afterwards, the cells were centrifuged at 4°C and resuspended in ice-cold Hank's balanced salt solution (HBSS, Invitrogen, Karlsruhe, Germany) containing 2% FCS and 10 mmol/l HEPES. Viable cells were visualized by propidium iodide staining (Invitrogen, Karlsruhe, Germany) and was added to a final concentration of 2 µg/ml. The cells were filtered by a 40 µm cell strainer to obtain a single cell suspension before sorting. Analyses and sorting were carried out on a FACSAria cytometer (Becton Dickinson, Heidelberg, Germany). Emissions of Hoechst 33342 (Hoechst-red and Hoechst-blue) were detected using 695/40 nm band-pass and 450/40 nm band-pass filters, respectively.
| | Sample_growth_protocol_ch1 | Cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM; PAA, Cölbe, Germany) supplemented with 10% foetal calf serum, 2 mmol/l L-glutamine, 100 units/ml streptomycin and 100 µg/ml penicillin in a humidified atmosphere containing 5% CO2 at 37°C. Cells were plated in 96well microtiter plates at a density of 5000 cells/well 24 h prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA-extraction was done with the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA (200 ng) was used to generate biotin-labelled cRNA (10 µg) by means of GeneChip 3' IVT Express Kit (Affymetrix). Sample processing was performed exactly as described by the microarray manufacturer (Affymetrix). Quality control of cRNA was performed using a bioanalyzer (Agilent 2001 Biosizing; Agilent Technologies, Böblingen, Germany).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome-430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized with the Robust Microarray Averaging (RMA) algorithm. Following experimental normalization signals < 50 were defined as background. Expression values were calculated as the ratio of non-stimulated (control) and anti-EpCAM stimulated SP vs. non-SP signals. Gene expression that was at least 25% increased or decreased in replicate experiments was considered as differentially expressed.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas,,Krüwel
| | Sample_contact_institute | Fraunhofer Institute for Toxicology and Experimental Medicine
| | Sample_contact_address | Nikolai-Fuchs-Str. 1
| | Sample_contact_city | Hannover
| | Sample_contact_zip/postal_code | 30625
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774585/suppl/GSM774585_A2C12_nonSP_2_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774585/suppl/GSM774585_A2C12_nonSP_2_Mouse430_2_.rma.chp.gz
| | Sample_series_id | GSE31246
| | Sample_series_id | GSE31317
| | Sample_data_row_count | 45101
| | |
|
GSM774586 | GPL1261 |
|
A2C12 non-SP cells biological replicate 2
|
A2C12 non-SP cells
|
background strain: C57BL/6
cell line: A2C12
cell fraction: non-SP
treatment: none
|
lung tumour cell line from a c-myc/c-raf double transgenic mouse model
|
| Sample_geo_accession | GSM774586
| | Sample_status | Public on Aug 08 2012
| | Sample_submission_date | Aug 08 2011
| | Sample_last_update_date | Aug 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were treated with a monoclonal anti-mouse EpCAM antibody at concentrations of 100 µg/ml for 48 h. Subsequently, 10^6 cells/ml were resuspended in warm DMEM containing 2% FCS and 10 mmol/l HEPES buffer (Sigma-Aldrich, Munich, Germany). Hoechst 33342 dye was added to a final concentration of 5 µg/ml in the presence or absence of reserpine (50 µmol/l; Sigma-Aldrich, Munich, Germany) and incubated at 37°C for 90 min with gentle shaking. Afterwards, the cells were centrifuged at 4°C and resuspended in ice-cold Hank's balanced salt solution (HBSS, Invitrogen, Karlsruhe, Germany) containing 2% FCS and 10 mmol/l HEPES. Viable cells were visualized by propidium iodide staining (Invitrogen, Karlsruhe, Germany) and was added to a final concentration of 2 µg/ml. The cells were filtered by a 40 µm cell strainer to obtain a single cell suspension before sorting. Analyses and sorting were carried out on a FACSAria cytometer (Becton Dickinson, Heidelberg, Germany). Emissions of Hoechst 33342 (Hoechst-red and Hoechst-blue) were detected using 695/40 nm band-pass and 450/40 nm band-pass filters, respectively.
| | Sample_growth_protocol_ch1 | Cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM; PAA, Cölbe, Germany) supplemented with 10% foetal calf serum, 2 mmol/l L-glutamine, 100 units/ml streptomycin and 100 µg/ml penicillin in a humidified atmosphere containing 5% CO2 at 37°C. Cells were plated in 96well microtiter plates at a density of 5000 cells/well 24 h prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA-extraction was done with the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA (200 ng) was used to generate biotin-labelled cRNA (10 µg) by means of GeneChip 3' IVT Express Kit (Affymetrix). Sample processing was performed exactly as described by the microarray manufacturer (Affymetrix). Quality control of cRNA was performed using a bioanalyzer (Agilent 2001 Biosizing; Agilent Technologies, Böblingen, Germany).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome-430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized with the Robust Microarray Averaging (RMA) algorithm. Following experimental normalization signals < 50 were defined as background. Expression values were calculated as the ratio of non-stimulated (control) and anti-EpCAM stimulated SP vs. non-SP signals. Gene expression that was at least 25% increased or decreased in replicate experiments was considered as differentially expressed.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas,,Krüwel
| | Sample_contact_institute | Fraunhofer Institute for Toxicology and Experimental Medicine
| | Sample_contact_address | Nikolai-Fuchs-Str. 1
| | Sample_contact_city | Hannover
| | Sample_contact_zip/postal_code | 30625
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774586/suppl/GSM774586_A2C12_nonSP_3_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774586/suppl/GSM774586_A2C12_nonSP_3_Mouse430_2_.rma.chp.gz
| | Sample_series_id | GSE31246
| | Sample_series_id | GSE31317
| | Sample_data_row_count | 45101
| | |
|
GSM774587 | GPL1261 |
|
A2C12 non-SP cells biological replicate 3
|
A2C12 non-SP cells
|
background strain: C57BL/6
cell line: A2C12
cell fraction: non-SP
treatment: none
|
lung tumour cell line from a c-myc/c-raf double transgenic mouse model
|
| Sample_geo_accession | GSM774587
| | Sample_status | Public on Aug 08 2012
| | Sample_submission_date | Aug 08 2011
| | Sample_last_update_date | Aug 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were treated with a monoclonal anti-mouse EpCAM antibody at concentrations of 100 µg/ml for 48 h. Subsequently, 10^6 cells/ml were resuspended in warm DMEM containing 2% FCS and 10 mmol/l HEPES buffer (Sigma-Aldrich, Munich, Germany). Hoechst 33342 dye was added to a final concentration of 5 µg/ml in the presence or absence of reserpine (50 µmol/l; Sigma-Aldrich, Munich, Germany) and incubated at 37°C for 90 min with gentle shaking. Afterwards, the cells were centrifuged at 4°C and resuspended in ice-cold Hank's balanced salt solution (HBSS, Invitrogen, Karlsruhe, Germany) containing 2% FCS and 10 mmol/l HEPES. Viable cells were visualized by propidium iodide staining (Invitrogen, Karlsruhe, Germany) and was added to a final concentration of 2 µg/ml. The cells were filtered by a 40 µm cell strainer to obtain a single cell suspension before sorting. Analyses and sorting were carried out on a FACSAria cytometer (Becton Dickinson, Heidelberg, Germany). Emissions of Hoechst 33342 (Hoechst-red and Hoechst-blue) were detected using 695/40 nm band-pass and 450/40 nm band-pass filters, respectively.
| | Sample_growth_protocol_ch1 | Cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM; PAA, Cölbe, Germany) supplemented with 10% foetal calf serum, 2 mmol/l L-glutamine, 100 units/ml streptomycin and 100 µg/ml penicillin in a humidified atmosphere containing 5% CO2 at 37°C. Cells were plated in 96well microtiter plates at a density of 5000 cells/well 24 h prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA-extraction was done with the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA (200 ng) was used to generate biotin-labelled cRNA (10 µg) by means of GeneChip 3' IVT Express Kit (Affymetrix). Sample processing was performed exactly as described by the microarray manufacturer (Affymetrix). Quality control of cRNA was performed using a bioanalyzer (Agilent 2001 Biosizing; Agilent Technologies, Böblingen, Germany).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome-430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized with the Robust Microarray Averaging (RMA) algorithm. Following experimental normalization signals < 50 were defined as background. Expression values were calculated as the ratio of non-stimulated (control) and anti-EpCAM stimulated SP vs. non-SP signals. Gene expression that was at least 25% increased or decreased in replicate experiments was considered as differentially expressed.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas,,Krüwel
| | Sample_contact_institute | Fraunhofer Institute for Toxicology and Experimental Medicine
| | Sample_contact_address | Nikolai-Fuchs-Str. 1
| | Sample_contact_city | Hannover
| | Sample_contact_zip/postal_code | 30625
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774587/suppl/GSM774587_A2C12_nonSP_4_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774587/suppl/GSM774587_A2C12_nonSP_4_Mouse430_2_.rma.chp.gz
| | Sample_series_id | GSE31246
| | Sample_series_id | GSE31317
| | Sample_data_row_count | 45101
| | |
|
GSM774588 | GPL1261 |
|
A2C12 anti-EpCAM treated non-SP cells biological replicate 1
|
A2C12 anti-EpCAM treated non-SP cells
|
background strain: C57BL/6
cell line: A2C12
cell fraction: non-SP
treatment: anti-EpCAM
|
lung tumour cell line from a c-myc/c-raf double transgenic mouse model
|
| Sample_geo_accession | GSM774588
| | Sample_status | Public on Aug 08 2012
| | Sample_submission_date | Aug 08 2011
| | Sample_last_update_date | Aug 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were treated with a monoclonal anti-mouse EpCAM antibody at concentrations of 100 µg/ml for 48 h. Subsequently, 10^6 cells/ml were resuspended in warm DMEM containing 2% FCS and 10 mmol/l HEPES buffer (Sigma-Aldrich, Munich, Germany). Hoechst 33342 dye was added to a final concentration of 5 µg/ml in the presence or absence of reserpine (50 µmol/l; Sigma-Aldrich, Munich, Germany) and incubated at 37°C for 90 min with gentle shaking. Afterwards, the cells were centrifuged at 4°C and resuspended in ice-cold Hank's balanced salt solution (HBSS, Invitrogen, Karlsruhe, Germany) containing 2% FCS and 10 mmol/l HEPES. Viable cells were visualized by propidium iodide staining (Invitrogen, Karlsruhe, Germany) and was added to a final concentration of 2 µg/ml. The cells were filtered by a 40 µm cell strainer to obtain a single cell suspension before sorting. Analyses and sorting were carried out on a FACSAria cytometer (Becton Dickinson, Heidelberg, Germany). Emissions of Hoechst 33342 (Hoechst-red and Hoechst-blue) were detected using 695/40 nm band-pass and 450/40 nm band-pass filters, respectively.
| | Sample_growth_protocol_ch1 | Cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM; PAA, Cölbe, Germany) supplemented with 10% foetal calf serum, 2 mmol/l L-glutamine, 100 units/ml streptomycin and 100 µg/ml penicillin in a humidified atmosphere containing 5% CO2 at 37°C. Cells were plated in 96well microtiter plates at a density of 5000 cells/well 24 h prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA-extraction was done with the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA (200 ng) was used to generate biotin-labelled cRNA (10 µg) by means of GeneChip 3' IVT Express Kit (Affymetrix). Sample processing was performed exactly as described by the microarray manufacturer (Affymetrix). Quality control of cRNA was performed using a bioanalyzer (Agilent 2001 Biosizing; Agilent Technologies, Böblingen, Germany).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome-430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized with the Robust Microarray Averaging (RMA) algorithm. Following experimental normalization signals < 50 were defined as background. Expression values were calculated as the ratio of non-stimulated (control) and anti-EpCAM stimulated SP vs. non-SP signals. Gene expression that was at least 25% increased or decreased in replicate experiments was considered as differentially expressed.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas,,Krüwel
| | Sample_contact_institute | Fraunhofer Institute for Toxicology and Experimental Medicine
| | Sample_contact_address | Nikolai-Fuchs-Str. 1
| | Sample_contact_city | Hannover
| | Sample_contact_zip/postal_code | 30625
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774588/suppl/GSM774588_A2C12_nonSP_EpCAM_1_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774588/suppl/GSM774588_A2C12_nonSP_EpCAM_1_Mouse430_2_.rma.chp.gz
| | Sample_series_id | GSE31246
| | Sample_series_id | GSE31317
| | Sample_data_row_count | 45101
| | |
|
GSM774589 | GPL1261 |
|
A2C12 anti-EpCAM treated non-SP cells biological replicate 2
|
A2C12 anti-EpCAM treated non-SP cells
|
background strain: C57BL/6
cell line: A2C12
cell fraction: non-SP
treatment: anti-EpCAM
|
lung tumour cell line from a c-myc/c-raf double transgenic mouse model
|
| Sample_geo_accession | GSM774589
| | Sample_status | Public on Aug 08 2012
| | Sample_submission_date | Aug 08 2011
| | Sample_last_update_date | Aug 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were treated with a monoclonal anti-mouse EpCAM antibody at concentrations of 100 µg/ml for 48 h. Subsequently, 10^6 cells/ml were resuspended in warm DMEM containing 2% FCS and 10 mmol/l HEPES buffer (Sigma-Aldrich, Munich, Germany). Hoechst 33342 dye was added to a final concentration of 5 µg/ml in the presence or absence of reserpine (50 µmol/l; Sigma-Aldrich, Munich, Germany) and incubated at 37°C for 90 min with gentle shaking. Afterwards, the cells were centrifuged at 4°C and resuspended in ice-cold Hank's balanced salt solution (HBSS, Invitrogen, Karlsruhe, Germany) containing 2% FCS and 10 mmol/l HEPES. Viable cells were visualized by propidium iodide staining (Invitrogen, Karlsruhe, Germany) and was added to a final concentration of 2 µg/ml. The cells were filtered by a 40 µm cell strainer to obtain a single cell suspension before sorting. Analyses and sorting were carried out on a FACSAria cytometer (Becton Dickinson, Heidelberg, Germany). Emissions of Hoechst 33342 (Hoechst-red and Hoechst-blue) were detected using 695/40 nm band-pass and 450/40 nm band-pass filters, respectively.
| | Sample_growth_protocol_ch1 | Cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM; PAA, Cölbe, Germany) supplemented with 10% foetal calf serum, 2 mmol/l L-glutamine, 100 units/ml streptomycin and 100 µg/ml penicillin in a humidified atmosphere containing 5% CO2 at 37°C. Cells were plated in 96well microtiter plates at a density of 5000 cells/well 24 h prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA-extraction was done with the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA (200 ng) was used to generate biotin-labelled cRNA (10 µg) by means of GeneChip 3' IVT Express Kit (Affymetrix). Sample processing was performed exactly as described by the microarray manufacturer (Affymetrix). Quality control of cRNA was performed using a bioanalyzer (Agilent 2001 Biosizing; Agilent Technologies, Böblingen, Germany).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome-430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized with the Robust Microarray Averaging (RMA) algorithm. Following experimental normalization signals < 50 were defined as background. Expression values were calculated as the ratio of non-stimulated (control) and anti-EpCAM stimulated SP vs. non-SP signals. Gene expression that was at least 25% increased or decreased in replicate experiments was considered as differentially expressed.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas,,Krüwel
| | Sample_contact_institute | Fraunhofer Institute for Toxicology and Experimental Medicine
| | Sample_contact_address | Nikolai-Fuchs-Str. 1
| | Sample_contact_city | Hannover
| | Sample_contact_zip/postal_code | 30625
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774589/suppl/GSM774589_A2C12_nonSP_EpCAM_2_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774589/suppl/GSM774589_A2C12_nonSP_EpCAM_2_Mouse430_2_.rma.chp.gz
| | Sample_series_id | GSE31246
| | Sample_series_id | GSE31317
| | Sample_data_row_count | 45101
| | |
|
GSM774590 | GPL1261 |
|
A2C12 anti-EpCAM treated non-SP cells biological replicate 3
|
A2C12 anti-EpCAM treated non-SP cells
|
background strain: C57BL/6
cell line: A2C12
cell fraction: non-SP
treatment: anti-EpCAM
|
lung tumour cell line from a c-myc/c-raf double transgenic mouse model
|
| Sample_geo_accession | GSM774590
| | Sample_status | Public on Aug 08 2012
| | Sample_submission_date | Aug 08 2011
| | Sample_last_update_date | Aug 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were treated with a monoclonal anti-mouse EpCAM antibody at concentrations of 100 µg/ml for 48 h. Subsequently, 10^6 cells/ml were resuspended in warm DMEM containing 2% FCS and 10 mmol/l HEPES buffer (Sigma-Aldrich, Munich, Germany). Hoechst 33342 dye was added to a final concentration of 5 µg/ml in the presence or absence of reserpine (50 µmol/l; Sigma-Aldrich, Munich, Germany) and incubated at 37°C for 90 min with gentle shaking. Afterwards, the cells were centrifuged at 4°C and resuspended in ice-cold Hank's balanced salt solution (HBSS, Invitrogen, Karlsruhe, Germany) containing 2% FCS and 10 mmol/l HEPES. Viable cells were visualized by propidium iodide staining (Invitrogen, Karlsruhe, Germany) and was added to a final concentration of 2 µg/ml. The cells were filtered by a 40 µm cell strainer to obtain a single cell suspension before sorting. Analyses and sorting were carried out on a FACSAria cytometer (Becton Dickinson, Heidelberg, Germany). Emissions of Hoechst 33342 (Hoechst-red and Hoechst-blue) were detected using 695/40 nm band-pass and 450/40 nm band-pass filters, respectively.
| | Sample_growth_protocol_ch1 | Cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM; PAA, Cölbe, Germany) supplemented with 10% foetal calf serum, 2 mmol/l L-glutamine, 100 units/ml streptomycin and 100 µg/ml penicillin in a humidified atmosphere containing 5% CO2 at 37°C. Cells were plated in 96well microtiter plates at a density of 5000 cells/well 24 h prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA-extraction was done with the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA (200 ng) was used to generate biotin-labelled cRNA (10 µg) by means of GeneChip 3' IVT Express Kit (Affymetrix). Sample processing was performed exactly as described by the microarray manufacturer (Affymetrix). Quality control of cRNA was performed using a bioanalyzer (Agilent 2001 Biosizing; Agilent Technologies, Böblingen, Germany).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome-430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized with the Robust Microarray Averaging (RMA) algorithm. Following experimental normalization signals < 50 were defined as background. Expression values were calculated as the ratio of non-stimulated (control) and anti-EpCAM stimulated SP vs. non-SP signals. Gene expression that was at least 25% increased or decreased in replicate experiments was considered as differentially expressed.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas,,Krüwel
| | Sample_contact_institute | Fraunhofer Institute for Toxicology and Experimental Medicine
| | Sample_contact_address | Nikolai-Fuchs-Str. 1
| | Sample_contact_city | Hannover
| | Sample_contact_zip/postal_code | 30625
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774590/suppl/GSM774590_A2C12_nonSP_EpCAM_4_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774590/suppl/GSM774590_A2C12_nonSP_EpCAM_4_Mouse430_2_.rma.chp.gz
| | Sample_series_id | GSE31246
| | Sample_series_id | GSE31317
| | Sample_data_row_count | 45101
| | |
|
GSM774591 | GPL1261 |
|
A2C12 SP cells biological replicate 1
|
A2C12 SP cells
|
background strain: C57BL/6
cell line: A2C12
cell fraction: SP
treatment: none
|
lung tumour cell line from a c-myc/c-raf double transgenic mouse model
|
| Sample_geo_accession | GSM774591
| | Sample_status | Public on Aug 08 2012
| | Sample_submission_date | Aug 08 2011
| | Sample_last_update_date | Aug 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were treated with a monoclonal anti-mouse EpCAM antibody at concentrations of 100 µg/ml for 48 h. Subsequently, 10^6 cells/ml were resuspended in warm DMEM containing 2% FCS and 10 mmol/l HEPES buffer (Sigma-Aldrich, Munich, Germany). Hoechst 33342 dye was added to a final concentration of 5 µg/ml in the presence or absence of reserpine (50 µmol/l; Sigma-Aldrich, Munich, Germany) and incubated at 37°C for 90 min with gentle shaking. Afterwards, the cells were centrifuged at 4°C and resuspended in ice-cold Hank's balanced salt solution (HBSS, Invitrogen, Karlsruhe, Germany) containing 2% FCS and 10 mmol/l HEPES. Viable cells were visualized by propidium iodide staining (Invitrogen, Karlsruhe, Germany) and was added to a final concentration of 2 µg/ml. The cells were filtered by a 40 µm cell strainer to obtain a single cell suspension before sorting. Analyses and sorting were carried out on a FACSAria cytometer (Becton Dickinson, Heidelberg, Germany). Emissions of Hoechst 33342 (Hoechst-red and Hoechst-blue) were detected using 695/40 nm band-pass and 450/40 nm band-pass filters, respectively.
| | Sample_growth_protocol_ch1 | Cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM; PAA, Cölbe, Germany) supplemented with 10% foetal calf serum, 2 mmol/l L-glutamine, 100 units/ml streptomycin and 100 µg/ml penicillin in a humidified atmosphere containing 5% CO2 at 37°C. Cells were plated in 96well microtiter plates at a density of 5000 cells/well 24 h prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA-extraction was done with the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA (200 ng) was used to generate biotin-labelled cRNA (10 µg) by means of GeneChip 3' IVT Express Kit (Affymetrix). Sample processing was performed exactly as described by the microarray manufacturer (Affymetrix). Quality control of cRNA was performed using a bioanalyzer (Agilent 2001 Biosizing; Agilent Technologies, Böblingen, Germany).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome-430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized with the Robust Microarray Averaging (RMA) algorithm. Following experimental normalization signals < 50 were defined as background. Expression values were calculated as the ratio of non-stimulated (control) and anti-EpCAM stimulated SP vs. non-SP signals. Gene expression that was at least 25% increased or decreased in replicate experiments was considered as differentially expressed.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas,,Krüwel
| | Sample_contact_institute | Fraunhofer Institute for Toxicology and Experimental Medicine
| | Sample_contact_address | Nikolai-Fuchs-Str. 1
| | Sample_contact_city | Hannover
| | Sample_contact_zip/postal_code | 30625
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774591/suppl/GSM774591_A2C12_SP_2_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774591/suppl/GSM774591_A2C12_SP_2_Mouse430_2_.rma.chp.gz
| | Sample_series_id | GSE31246
| | Sample_series_id | GSE31317
| | Sample_data_row_count | 45101
| | |
|
GSM774592 | GPL1261 |
|
A2C12 SP cells biological replicate 2
|
A2C12 SP cells
|
background strain: C57BL/6
cell line: A2C12
cell fraction: SP
treatment: none
|
lung tumour cell line from a c-myc/c-raf double transgenic mouse model
|
| Sample_geo_accession | GSM774592
| | Sample_status | Public on Aug 08 2012
| | Sample_submission_date | Aug 08 2011
| | Sample_last_update_date | Aug 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were treated with a monoclonal anti-mouse EpCAM antibody at concentrations of 100 µg/ml for 48 h. Subsequently, 10^6 cells/ml were resuspended in warm DMEM containing 2% FCS and 10 mmol/l HEPES buffer (Sigma-Aldrich, Munich, Germany). Hoechst 33342 dye was added to a final concentration of 5 µg/ml in the presence or absence of reserpine (50 µmol/l; Sigma-Aldrich, Munich, Germany) and incubated at 37°C for 90 min with gentle shaking. Afterwards, the cells were centrifuged at 4°C and resuspended in ice-cold Hank's balanced salt solution (HBSS, Invitrogen, Karlsruhe, Germany) containing 2% FCS and 10 mmol/l HEPES. Viable cells were visualized by propidium iodide staining (Invitrogen, Karlsruhe, Germany) and was added to a final concentration of 2 µg/ml. The cells were filtered by a 40 µm cell strainer to obtain a single cell suspension before sorting. Analyses and sorting were carried out on a FACSAria cytometer (Becton Dickinson, Heidelberg, Germany). Emissions of Hoechst 33342 (Hoechst-red and Hoechst-blue) were detected using 695/40 nm band-pass and 450/40 nm band-pass filters, respectively.
| | Sample_growth_protocol_ch1 | Cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM; PAA, Cölbe, Germany) supplemented with 10% foetal calf serum, 2 mmol/l L-glutamine, 100 units/ml streptomycin and 100 µg/ml penicillin in a humidified atmosphere containing 5% CO2 at 37°C. Cells were plated in 96well microtiter plates at a density of 5000 cells/well 24 h prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA-extraction was done with the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA (200 ng) was used to generate biotin-labelled cRNA (10 µg) by means of GeneChip 3' IVT Express Kit (Affymetrix). Sample processing was performed exactly as described by the microarray manufacturer (Affymetrix). Quality control of cRNA was performed using a bioanalyzer (Agilent 2001 Biosizing; Agilent Technologies, Böblingen, Germany).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome-430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized with the Robust Microarray Averaging (RMA) algorithm. Following experimental normalization signals < 50 were defined as background. Expression values were calculated as the ratio of non-stimulated (control) and anti-EpCAM stimulated SP vs. non-SP signals. Gene expression that was at least 25% increased or decreased in replicate experiments was considered as differentially expressed.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas,,Krüwel
| | Sample_contact_institute | Fraunhofer Institute for Toxicology and Experimental Medicine
| | Sample_contact_address | Nikolai-Fuchs-Str. 1
| | Sample_contact_city | Hannover
| | Sample_contact_zip/postal_code | 30625
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774592/suppl/GSM774592_A2C12_SP_3_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774592/suppl/GSM774592_A2C12_SP_3_Mouse430_2_.rma.chp.gz
| | Sample_series_id | GSE31246
| | Sample_series_id | GSE31317
| | Sample_data_row_count | 45101
| | |
|
GSM774593 | GPL1261 |
|
A2C12 SP cells biological replicate 3
|
A2C12 SP cells
|
background strain: C57BL/6
cell line: A2C12
cell fraction: SP
treatment: none
|
lung tumour cell line from a c-myc/c-raf double transgenic mouse model
|
| Sample_geo_accession | GSM774593
| | Sample_status | Public on Aug 08 2012
| | Sample_submission_date | Aug 08 2011
| | Sample_last_update_date | Aug 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were treated with a monoclonal anti-mouse EpCAM antibody at concentrations of 100 µg/ml for 48 h. Subsequently, 10^6 cells/ml were resuspended in warm DMEM containing 2% FCS and 10 mmol/l HEPES buffer (Sigma-Aldrich, Munich, Germany). Hoechst 33342 dye was added to a final concentration of 5 µg/ml in the presence or absence of reserpine (50 µmol/l; Sigma-Aldrich, Munich, Germany) and incubated at 37°C for 90 min with gentle shaking. Afterwards, the cells were centrifuged at 4°C and resuspended in ice-cold Hank's balanced salt solution (HBSS, Invitrogen, Karlsruhe, Germany) containing 2% FCS and 10 mmol/l HEPES. Viable cells were visualized by propidium iodide staining (Invitrogen, Karlsruhe, Germany) and was added to a final concentration of 2 µg/ml. The cells were filtered by a 40 µm cell strainer to obtain a single cell suspension before sorting. Analyses and sorting were carried out on a FACSAria cytometer (Becton Dickinson, Heidelberg, Germany). Emissions of Hoechst 33342 (Hoechst-red and Hoechst-blue) were detected using 695/40 nm band-pass and 450/40 nm band-pass filters, respectively.
| | Sample_growth_protocol_ch1 | Cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM; PAA, Cölbe, Germany) supplemented with 10% foetal calf serum, 2 mmol/l L-glutamine, 100 units/ml streptomycin and 100 µg/ml penicillin in a humidified atmosphere containing 5% CO2 at 37°C. Cells were plated in 96well microtiter plates at a density of 5000 cells/well 24 h prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA-extraction was done with the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA (200 ng) was used to generate biotin-labelled cRNA (10 µg) by means of GeneChip 3' IVT Express Kit (Affymetrix). Sample processing was performed exactly as described by the microarray manufacturer (Affymetrix). Quality control of cRNA was performed using a bioanalyzer (Agilent 2001 Biosizing; Agilent Technologies, Böblingen, Germany).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome-430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized with the Robust Microarray Averaging (RMA) algorithm. Following experimental normalization signals < 50 were defined as background. Expression values were calculated as the ratio of non-stimulated (control) and anti-EpCAM stimulated SP vs. non-SP signals. Gene expression that was at least 25% increased or decreased in replicate experiments was considered as differentially expressed.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas,,Krüwel
| | Sample_contact_institute | Fraunhofer Institute for Toxicology and Experimental Medicine
| | Sample_contact_address | Nikolai-Fuchs-Str. 1
| | Sample_contact_city | Hannover
| | Sample_contact_zip/postal_code | 30625
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774593/suppl/GSM774593_A2C12_SP_4_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774593/suppl/GSM774593_A2C12_SP_4_Mouse430_2_.rma.chp.gz
| | Sample_series_id | GSE31246
| | Sample_series_id | GSE31317
| | Sample_data_row_count | 45101
| | |
|
GSM774594 | GPL1261 |
|
A2C12 anti-EpCAM treated SP cells biological replicate 1
|
A2C12 anti-EpCAM treated SP cells
|
background strain: C57BL/6
cell line: A2C12
cell fraction: SP
treatment: anti-EpCAM
|
lung tumour cell line from a c-myc/c-raf double transgenic mouse model
|
| Sample_geo_accession | GSM774594
| | Sample_status | Public on Aug 08 2012
| | Sample_submission_date | Aug 08 2011
| | Sample_last_update_date | Aug 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were treated with a monoclonal anti-mouse EpCAM antibody at concentrations of 100 µg/ml for 48 h. Subsequently, 10^6 cells/ml were resuspended in warm DMEM containing 2% FCS and 10 mmol/l HEPES buffer (Sigma-Aldrich, Munich, Germany). Hoechst 33342 dye was added to a final concentration of 5 µg/ml in the presence or absence of reserpine (50 µmol/l; Sigma-Aldrich, Munich, Germany) and incubated at 37°C for 90 min with gentle shaking. Afterwards, the cells were centrifuged at 4°C and resuspended in ice-cold Hank's balanced salt solution (HBSS, Invitrogen, Karlsruhe, Germany) containing 2% FCS and 10 mmol/l HEPES. Viable cells were visualized by propidium iodide staining (Invitrogen, Karlsruhe, Germany) and was added to a final concentration of 2 µg/ml. The cells were filtered by a 40 µm cell strainer to obtain a single cell suspension before sorting. Analyses and sorting were carried out on a FACSAria cytometer (Becton Dickinson, Heidelberg, Germany). Emissions of Hoechst 33342 (Hoechst-red and Hoechst-blue) were detected using 695/40 nm band-pass and 450/40 nm band-pass filters, respectively.
| | Sample_growth_protocol_ch1 | Cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM; PAA, Cölbe, Germany) supplemented with 10% foetal calf serum, 2 mmol/l L-glutamine, 100 units/ml streptomycin and 100 µg/ml penicillin in a humidified atmosphere containing 5% CO2 at 37°C. Cells were plated in 96well microtiter plates at a density of 5000 cells/well 24 h prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA-extraction was done with the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA (200 ng) was used to generate biotin-labelled cRNA (10 µg) by means of GeneChip 3' IVT Express Kit (Affymetrix). Sample processing was performed exactly as described by the microarray manufacturer (Affymetrix). Quality control of cRNA was performed using a bioanalyzer (Agilent 2001 Biosizing; Agilent Technologies, Böblingen, Germany).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome-430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized with the Robust Microarray Averaging (RMA) algorithm. Following experimental normalization signals < 50 were defined as background. Expression values were calculated as the ratio of non-stimulated (control) and anti-EpCAM stimulated SP vs. non-SP signals. Gene expression that was at least 25% increased or decreased in replicate experiments was considered as differentially expressed.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas,,Krüwel
| | Sample_contact_institute | Fraunhofer Institute for Toxicology and Experimental Medicine
| | Sample_contact_address | Nikolai-Fuchs-Str. 1
| | Sample_contact_city | Hannover
| | Sample_contact_zip/postal_code | 30625
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774594/suppl/GSM774594_A2C12_SP_EpCAM_1_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774594/suppl/GSM774594_A2C12_SP_EpCAM_1_Mouse430_2_.rma.chp.gz
| | Sample_series_id | GSE31246
| | Sample_series_id | GSE31317
| | Sample_data_row_count | 45101
| | |
|
GSM774595 | GPL1261 |
|
A2C12 anti-EpCAM treated SP cells biological replicate 2
|
A2C12 anti-EpCAM treated SP cells
|
background strain: C57BL/6
cell line: A2C12
cell fraction: SP
treatment: anti-EpCAM
|
lung tumour cell line from a c-myc/c-raf double transgenic mouse model
|
| Sample_geo_accession | GSM774595
| | Sample_status | Public on Aug 08 2012
| | Sample_submission_date | Aug 08 2011
| | Sample_last_update_date | Aug 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were treated with a monoclonal anti-mouse EpCAM antibody at concentrations of 100 µg/ml for 48 h. Subsequently, 10^6 cells/ml were resuspended in warm DMEM containing 2% FCS and 10 mmol/l HEPES buffer (Sigma-Aldrich, Munich, Germany). Hoechst 33342 dye was added to a final concentration of 5 µg/ml in the presence or absence of reserpine (50 µmol/l; Sigma-Aldrich, Munich, Germany) and incubated at 37°C for 90 min with gentle shaking. Afterwards, the cells were centrifuged at 4°C and resuspended in ice-cold Hank's balanced salt solution (HBSS, Invitrogen, Karlsruhe, Germany) containing 2% FCS and 10 mmol/l HEPES. Viable cells were visualized by propidium iodide staining (Invitrogen, Karlsruhe, Germany) and was added to a final concentration of 2 µg/ml. The cells were filtered by a 40 µm cell strainer to obtain a single cell suspension before sorting. Analyses and sorting were carried out on a FACSAria cytometer (Becton Dickinson, Heidelberg, Germany). Emissions of Hoechst 33342 (Hoechst-red and Hoechst-blue) were detected using 695/40 nm band-pass and 450/40 nm band-pass filters, respectively.
| | Sample_growth_protocol_ch1 | Cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM; PAA, Cölbe, Germany) supplemented with 10% foetal calf serum, 2 mmol/l L-glutamine, 100 units/ml streptomycin and 100 µg/ml penicillin in a humidified atmosphere containing 5% CO2 at 37°C. Cells were plated in 96well microtiter plates at a density of 5000 cells/well 24 h prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA-extraction was done with the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA (200 ng) was used to generate biotin-labelled cRNA (10 µg) by means of GeneChip 3' IVT Express Kit (Affymetrix). Sample processing was performed exactly as described by the microarray manufacturer (Affymetrix). Quality control of cRNA was performed using a bioanalyzer (Agilent 2001 Biosizing; Agilent Technologies, Böblingen, Germany).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome-430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized with the Robust Microarray Averaging (RMA) algorithm. Following experimental normalization signals < 50 were defined as background. Expression values were calculated as the ratio of non-stimulated (control) and anti-EpCAM stimulated SP vs. non-SP signals. Gene expression that was at least 25% increased or decreased in replicate experiments was considered as differentially expressed.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas,,Krüwel
| | Sample_contact_institute | Fraunhofer Institute for Toxicology and Experimental Medicine
| | Sample_contact_address | Nikolai-Fuchs-Str. 1
| | Sample_contact_city | Hannover
| | Sample_contact_zip/postal_code | 30625
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774595/suppl/GSM774595_A2C12_SP_EpCAM_2_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774595/suppl/GSM774595_A2C12_SP_EpCAM_2_Mouse430_2_.rma.chp.gz
| | Sample_series_id | GSE31246
| | Sample_series_id | GSE31317
| | Sample_data_row_count | 45101
| | |
|
GSM774596 | GPL1261 |
|
A2C12 anti-EpCAM treated SP cells biological replicate 3
|
A2C12 anti-EpCAM treated SP cells
|
background strain: C57BL/6
cell line: A2C12
cell fraction: SP
treatment: anti-EpCAM
|
lung tumour cell line from a c-myc/c-raf double transgenic mouse model
|
| Sample_geo_accession | GSM774596
| | Sample_status | Public on Aug 08 2012
| | Sample_submission_date | Aug 08 2011
| | Sample_last_update_date | Aug 08 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were treated with a monoclonal anti-mouse EpCAM antibody at concentrations of 100 µg/ml for 48 h. Subsequently, 10^6 cells/ml were resuspended in warm DMEM containing 2% FCS and 10 mmol/l HEPES buffer (Sigma-Aldrich, Munich, Germany). Hoechst 33342 dye was added to a final concentration of 5 µg/ml in the presence or absence of reserpine (50 µmol/l; Sigma-Aldrich, Munich, Germany) and incubated at 37°C for 90 min with gentle shaking. Afterwards, the cells were centrifuged at 4°C and resuspended in ice-cold Hank's balanced salt solution (HBSS, Invitrogen, Karlsruhe, Germany) containing 2% FCS and 10 mmol/l HEPES. Viable cells were visualized by propidium iodide staining (Invitrogen, Karlsruhe, Germany) and was added to a final concentration of 2 µg/ml. The cells were filtered by a 40 µm cell strainer to obtain a single cell suspension before sorting. Analyses and sorting were carried out on a FACSAria cytometer (Becton Dickinson, Heidelberg, Germany). Emissions of Hoechst 33342 (Hoechst-red and Hoechst-blue) were detected using 695/40 nm band-pass and 450/40 nm band-pass filters, respectively.
| | Sample_growth_protocol_ch1 | Cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM; PAA, Cölbe, Germany) supplemented with 10% foetal calf serum, 2 mmol/l L-glutamine, 100 units/ml streptomycin and 100 µg/ml penicillin in a humidified atmosphere containing 5% CO2 at 37°C. Cells were plated in 96well microtiter plates at a density of 5000 cells/well 24 h prior treatment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA-extraction was done with the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA (200 ng) was used to generate biotin-labelled cRNA (10 µg) by means of GeneChip 3' IVT Express Kit (Affymetrix). Sample processing was performed exactly as described by the microarray manufacturer (Affymetrix). Quality control of cRNA was performed using a bioanalyzer (Agilent 2001 Biosizing; Agilent Technologies, Böblingen, Germany).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome-430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized with the Robust Microarray Averaging (RMA) algorithm. Following experimental normalization signals < 50 were defined as background. Expression values were calculated as the ratio of non-stimulated (control) and anti-EpCAM stimulated SP vs. non-SP signals. Gene expression that was at least 25% increased or decreased in replicate experiments was considered as differentially expressed.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Thomas,,Krüwel
| | Sample_contact_institute | Fraunhofer Institute for Toxicology and Experimental Medicine
| | Sample_contact_address | Nikolai-Fuchs-Str. 1
| | Sample_contact_city | Hannover
| | Sample_contact_zip/postal_code | 30625
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774596/suppl/GSM774596_A2C12_SP_EpCAM_4_Mouse430_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774596/suppl/GSM774596_A2C12_SP_EpCAM_4_Mouse430_2_.rma.chp.gz
| | Sample_series_id | GSE31246
| | Sample_series_id | GSE31317
| | Sample_data_row_count | 45101
| | |
|
| |
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