Search results for the GEO ID: GSE37409  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM918090 | GPL570 |
|
pCDNA3empty
|
A673 cell line expressing doxycycline-inducible short hairpin RNA against EWS-FLI1 (A673sh)
|
cell line: EWS-FLI1
transfection: with the empty vector control (pCDNA3)
|
A673sh transiently transfected with the empty vector control (pCDNA3), replica 1
|
| Sample_geo_accession | GSM918090
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Apr 18 2012
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | transient transfection of A673sh cells using the Lipofectamine Plus reagent (Invitrogen) according to the manufacturer's recommendations.
| | Sample_growth_protocol_ch1 | A673sh cells were maintained in DMEM (Invitrogen) supplemented with 10% FCS (PAA), 2µg/ml Blasticidine (Invitrogen) and 50µg/ml Zeocin (Cayla, France). EWS-FLI1 knockdown was induced by addition of doxycycline (Sigma-Aldrich, St. Louis, MO, USA). Cells were placed in a Thermo-CO2 incubator with a humidified atmosphere containing 5% CO2 (Thermo Electron Corp).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared with a Qiagen RNAeasy kit (QIAGEN) following the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target labelling and hybridization. For Affymetrix GeneChip analysis, 2.0µg total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer's protocols (Gene Expression Analysis, Technical Manual, Revison #4; Eukaryotic Target Preparation, Revison #3).
| | Sample_hyb_protocol | Following RNA purification, 20µg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to U133-plus2 microarrays. The arrays were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the fRMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maximilian,,Kauer
| | Sample_contact_email | maximilian.kauer@ccri.at
| | Sample_contact_laboratory | Heinrich Kovar
| | Sample_contact_department | Molecular Biology
| | Sample_contact_institute | CCRI, St.Anna Children Cancer Research Institute
| | Sample_contact_address | Zimmermannplatz 10
| | Sample_contact_city | Vienna
| | Sample_contact_zip/postal_code | 1090
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918090/suppl/GSM918090.CEL.gz
| | Sample_series_id | GSE37409
| | Sample_data_row_count | 54675
| | |
|
GSM918091 | GPL570 |
|
FLAG_FOXO1_AAA
|
A673 cell line expressing doxycycline-inducible short hairpin RNA against EWS-FLI1 (A673sh)
|
cell line: EWS-FLI1
transfection: A673sh transiently with the pCDNA3-based FLAG-FOXO1-AAA plasmid
|
A673sh transiently transfected with the pCDNA3-based FLAG-FOXO1-AAA plasmid (AKT phosphorylation resistant Flag-tagged FOXO1, T24A S256A S319A), replica 1
|
| Sample_geo_accession | GSM918091
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Apr 18 2012
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | transient transfection of A673sh cells using the Lipofectamine Plus reagent (Invitrogen) according to the manufacturer's recommendations.
| | Sample_growth_protocol_ch1 | A673sh cells were maintained in DMEM (Invitrogen) supplemented with 10% FCS (PAA), 2µg/ml Blasticidine (Invitrogen) and 50µg/ml Zeocin (Cayla, France). EWS-FLI1 knockdown was induced by addition of doxycycline (Sigma-Aldrich, St. Louis, MO, USA). Cells were placed in a Thermo-CO2 incubator with a humidified atmosphere containing 5% CO2 (Thermo Electron Corp).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared with a Qiagen RNAeasy kit (QIAGEN) following the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target labelling and hybridization. For Affymetrix GeneChip analysis, 2.0µg total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer's protocols (Gene Expression Analysis, Technical Manual, Revison #4; Eukaryotic Target Preparation, Revison #3).
| | Sample_hyb_protocol | Following RNA purification, 20µg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to U133-plus2 microarrays. The arrays were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the fRMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maximilian,,Kauer
| | Sample_contact_email | maximilian.kauer@ccri.at
| | Sample_contact_laboratory | Heinrich Kovar
| | Sample_contact_department | Molecular Biology
| | Sample_contact_institute | CCRI, St.Anna Children Cancer Research Institute
| | Sample_contact_address | Zimmermannplatz 10
| | Sample_contact_city | Vienna
| | Sample_contact_zip/postal_code | 1090
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918091/suppl/GSM918091.CEL.gz
| | Sample_series_id | GSE37409
| | Sample_data_row_count | 54675
| | |
|
GSM918092 | GPL570 |
|
FLAG_FOXO1_double
|
A673 cell line expressing doxycycline-inducible short hairpin RNA against EWS-FLI1 (A673sh)
|
cell line: EWS-FLI1
transfection: A673sh transiently with the pCDNA3-based FLAG-FOXO1-S249A/S298A plasmid
|
A673sh transiently transfected with the pCDNA3-based FLAG-FOXO1-S249A/S298A plasmid (CDK2 phosphorylation resistant Flag-tagged FOXO1, S249A/S298A), replica 1
|
| Sample_geo_accession | GSM918092
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Apr 18 2012
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | transient transfection of A673sh cells using the Lipofectamine Plus reagent (Invitrogen) according to the manufacturer's recommendations.
| | Sample_growth_protocol_ch1 | A673sh cells were maintained in DMEM (Invitrogen) supplemented with 10% FCS (PAA), 2µg/ml Blasticidine (Invitrogen) and 50µg/ml Zeocin (Cayla, France). EWS-FLI1 knockdown was induced by addition of doxycycline (Sigma-Aldrich, St. Louis, MO, USA). Cells were placed in a Thermo-CO2 incubator with a humidified atmosphere containing 5% CO2 (Thermo Electron Corp).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared with a Qiagen RNAeasy kit (QIAGEN) following the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target labelling and hybridization. For Affymetrix GeneChip analysis, 2.0µg total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer's protocols (Gene Expression Analysis, Technical Manual, Revison #4; Eukaryotic Target Preparation, Revison #3).
| | Sample_hyb_protocol | Following RNA purification, 20µg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to U133-plus2 microarrays. The arrays were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the fRMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maximilian,,Kauer
| | Sample_contact_email | maximilian.kauer@ccri.at
| | Sample_contact_laboratory | Heinrich Kovar
| | Sample_contact_department | Molecular Biology
| | Sample_contact_institute | CCRI, St.Anna Children Cancer Research Institute
| | Sample_contact_address | Zimmermannplatz 10
| | Sample_contact_city | Vienna
| | Sample_contact_zip/postal_code | 1090
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918092/suppl/GSM918092.CEL.gz
| | Sample_series_id | GSE37409
| | Sample_data_row_count | 54675
| | |
|
GSM918093 | GPL570 |
|
sh_scrm_noDox1
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A673 cell line expressing doxycycline-inducible short hairpin RNA against EWS-FLI1 (A673sh)
|
cell line: EWS-FLI1
transfection: A673sh transiently with the pRS-sh-scrambled plasmid
|
A673sh transiently transfected with the pRS-sh-scrambled plasmid, replica 1
|
| Sample_geo_accession | GSM918093
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Apr 18 2012
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | transient transfection of A673sh cells using the Lipofectamine Plus reagent (Invitrogen) according to the manufacturer's recommendations.
| | Sample_growth_protocol_ch1 | A673sh cells were maintained in DMEM (Invitrogen) supplemented with 10% FCS (PAA), 2µg/ml Blasticidine (Invitrogen) and 50µg/ml Zeocin (Cayla, France). EWS-FLI1 knockdown was induced by addition of doxycycline (Sigma-Aldrich, St. Louis, MO, USA). Cells were placed in a Thermo-CO2 incubator with a humidified atmosphere containing 5% CO2 (Thermo Electron Corp).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared with a Qiagen RNAeasy kit (QIAGEN) following the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target labelling and hybridization. For Affymetrix GeneChip analysis, 2.0µg total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer's protocols (Gene Expression Analysis, Technical Manual, Revison #4; Eukaryotic Target Preparation, Revison #3).
| | Sample_hyb_protocol | Following RNA purification, 20µg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to U133-plus2 microarrays. The arrays were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the fRMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maximilian,,Kauer
| | Sample_contact_email | maximilian.kauer@ccri.at
| | Sample_contact_laboratory | Heinrich Kovar
| | Sample_contact_department | Molecular Biology
| | Sample_contact_institute | CCRI, St.Anna Children Cancer Research Institute
| | Sample_contact_address | Zimmermannplatz 10
| | Sample_contact_city | Vienna
| | Sample_contact_zip/postal_code | 1090
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918093/suppl/GSM918093.CEL.gz
| | Sample_series_id | GSE37409
| | Sample_data_row_count | 54675
| | |
|
GSM918094 | GPL570 |
|
sh_scrm_Dox1
|
A673 cell line expressing doxycycline-inducible short hairpin RNA against EWS-FLI1 (A673sh)
|
cell line: EWS-FLI1
transfection: A673sh transiently with the pRS-sh-scrambled plasmid + doxycycline for 48h post transfection
|
A673sh transiently transfected with the pRS-sh-scrambled plasmid + doxycycline for 48h post transfection, replica 1
|
| Sample_geo_accession | GSM918094
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Apr 18 2012
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | transient transfection of A673sh cells using the Lipofectamine Plus reagent (Invitrogen) according to the manufacturer's recommendations, EWS-FLI1 knockdown was induced by addition of 1µg/ml doxycycline for 48h
| | Sample_growth_protocol_ch1 | A673sh cells were maintained in DMEM (Invitrogen) supplemented with 10% FCS (PAA), 2µg/ml Blasticidine (Invitrogen) and 50µg/ml Zeocin (Cayla, France). EWS-FLI1 knockdown was induced by addition of doxycycline (Sigma-Aldrich, St. Louis, MO, USA). Cells were placed in a Thermo-CO2 incubator with a humidified atmosphere containing 5% CO2 (Thermo Electron Corp).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared with a Qiagen RNAeasy kit (QIAGEN) following the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target labelling and hybridization. For Affymetrix GeneChip analysis, 2.0µg total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer's protocols (Gene Expression Analysis, Technical Manual, Revison #4; Eukaryotic Target Preparation, Revison #3).
| | Sample_hyb_protocol | Following RNA purification, 20µg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to U133-plus2 microarrays. The arrays were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the fRMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maximilian,,Kauer
| | Sample_contact_email | maximilian.kauer@ccri.at
| | Sample_contact_laboratory | Heinrich Kovar
| | Sample_contact_department | Molecular Biology
| | Sample_contact_institute | CCRI, St.Anna Children Cancer Research Institute
| | Sample_contact_address | Zimmermannplatz 10
| | Sample_contact_city | Vienna
| | Sample_contact_zip/postal_code | 1090
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918094/suppl/GSM918094.CEL.gz
| | Sample_series_id | GSE37409
| | Sample_data_row_count | 54675
| | |
|
GSM918095 | GPL570 |
|
shFOXO1_noDox1
|
A673 cell line expressing doxycycline-inducible short hairpin RNA against EWS-FLI1 (A673sh)
|
cell line: EWS-FLI1
transfection: A673sh transiently with the pRS-sh-FOXO1 plasmid targeting endogenous FOXO1wt
|
A673sh transiently transfected with the pRS-sh-FOXO1 plasmid targeting endogenous FOXO1wt, replica 1
|
| Sample_geo_accession | GSM918095
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Apr 18 2012
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | transient transfection of A673sh cells using the Lipofectamine Plus reagent (Invitrogen) according to the manufacturer's recommendations.
| | Sample_growth_protocol_ch1 | A673sh cells were maintained in DMEM (Invitrogen) supplemented with 10% FCS (PAA), 2µg/ml Blasticidine (Invitrogen) and 50µg/ml Zeocin (Cayla, France). EWS-FLI1 knockdown was induced by addition of doxycycline (Sigma-Aldrich, St. Louis, MO, USA). Cells were placed in a Thermo-CO2 incubator with a humidified atmosphere containing 5% CO2 (Thermo Electron Corp).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared with a Qiagen RNAeasy kit (QIAGEN) following the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target labelling and hybridization. For Affymetrix GeneChip analysis, 2.0µg total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer's protocols (Gene Expression Analysis, Technical Manual, Revison #4; Eukaryotic Target Preparation, Revison #3).
| | Sample_hyb_protocol | Following RNA purification, 20µg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to U133-plus2 microarrays. The arrays were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the fRMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maximilian,,Kauer
| | Sample_contact_email | maximilian.kauer@ccri.at
| | Sample_contact_laboratory | Heinrich Kovar
| | Sample_contact_department | Molecular Biology
| | Sample_contact_institute | CCRI, St.Anna Children Cancer Research Institute
| | Sample_contact_address | Zimmermannplatz 10
| | Sample_contact_city | Vienna
| | Sample_contact_zip/postal_code | 1090
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918095/suppl/GSM918095.CEL.gz
| | Sample_series_id | GSE37409
| | Sample_data_row_count | 54675
| | |
|
GSM918096 | GPL570 |
|
shFOXO1_Dox1
|
A673 cell line expressing doxycycline-inducible short hairpin RNA against EWS-FLI1 (A673sh)
|
cell line: EWS-FLI1
transfection: A673sh transiently with the pRS-sh-FOXO1 plasmid targeting endogenous FOXO1wt + doxycycline for 48h post transfection
|
A673sh transiently transfected with the pRS-sh-FOXO1 plasmid targeting endogenous FOXO1wt + doxycycline for 48h post transfection, replica 1
|
| Sample_geo_accession | GSM918096
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Apr 18 2012
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | transient transfection of A673sh cells using the Lipofectamine Plus reagent (Invitrogen) according to the manufacturer's recommendations, EWS-FLI1 knockdown was induced by addition of 1µg/ml doxycycline for 48h
| | Sample_growth_protocol_ch1 | A673sh cells were maintained in DMEM (Invitrogen) supplemented with 10% FCS (PAA), 2µg/ml Blasticidine (Invitrogen) and 50µg/ml Zeocin (Cayla, France). EWS-FLI1 knockdown was induced by addition of doxycycline (Sigma-Aldrich, St. Louis, MO, USA). Cells were placed in a Thermo-CO2 incubator with a humidified atmosphere containing 5% CO2 (Thermo Electron Corp).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared with a Qiagen RNAeasy kit (QIAGEN) following the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target labelling and hybridization. For Affymetrix GeneChip analysis, 2.0µg total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer's protocols (Gene Expression Analysis, Technical Manual, Revison #4; Eukaryotic Target Preparation, Revison #3).
| | Sample_hyb_protocol | Following RNA purification, 20µg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to U133-plus2 microarrays. The arrays were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the fRMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maximilian,,Kauer
| | Sample_contact_email | maximilian.kauer@ccri.at
| | Sample_contact_laboratory | Heinrich Kovar
| | Sample_contact_department | Molecular Biology
| | Sample_contact_institute | CCRI, St.Anna Children Cancer Research Institute
| | Sample_contact_address | Zimmermannplatz 10
| | Sample_contact_city | Vienna
| | Sample_contact_zip/postal_code | 1090
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918096/suppl/GSM918096.CEL.gz
| | Sample_series_id | GSE37409
| | Sample_data_row_count | 54675
| | |
|
GSM918097 | GPL570 |
|
sh_scrm_noDox2
|
A673 cell line expressing doxycycline-inducible short hairpin RNA against EWS-FLI1 (A673sh)
|
cell line: EWS-FLI1
transfection: A673sh transiently with the pRS-sh-scrambled plasmid
|
A673sh transiently transfected with the pRS-sh-scrambled plasmid, replica 2
|
| Sample_geo_accession | GSM918097
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Apr 18 2012
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | transient transfection of A673sh cells using the Lipofectamine Plus reagent (Invitrogen) according to the manufacturer's recommendations.
| | Sample_growth_protocol_ch1 | A673sh cells were maintained in DMEM (Invitrogen) supplemented with 10% FCS (PAA), 2µg/ml Blasticidine (Invitrogen) and 50µg/ml Zeocin (Cayla, France). EWS-FLI1 knockdown was induced by addition of doxycycline (Sigma-Aldrich, St. Louis, MO, USA). Cells were placed in a Thermo-CO2 incubator with a humidified atmosphere containing 5% CO2 (Thermo Electron Corp).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared with a Qiagen RNAeasy kit (QIAGEN) following the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target labelling and hybridization. For Affymetrix GeneChip analysis, 2.0µg total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer's protocols (Gene Expression Analysis, Technical Manual, Revison #4; Eukaryotic Target Preparation, Revison #3).
| | Sample_hyb_protocol | Following RNA purification, 20µg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to U133-plus2 microarrays. The arrays were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the fRMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maximilian,,Kauer
| | Sample_contact_email | maximilian.kauer@ccri.at
| | Sample_contact_laboratory | Heinrich Kovar
| | Sample_contact_department | Molecular Biology
| | Sample_contact_institute | CCRI, St.Anna Children Cancer Research Institute
| | Sample_contact_address | Zimmermannplatz 10
| | Sample_contact_city | Vienna
| | Sample_contact_zip/postal_code | 1090
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918097/suppl/GSM918097.CEL.gz
| | Sample_series_id | GSE37409
| | Sample_data_row_count | 54675
| | |
|
GSM918098 | GPL570 |
|
sh_scrm_Dox2
|
A673 cell line expressing doxycycline-inducible short hairpin RNA against EWS-FLI1 (A673sh)
|
cell line: EWS-FLI1
transfection: A673sh transiently with the pRS-sh-scrambled plasmid + doxycycline for 48h post transfection
|
A673sh transiently transfected with the pRS-sh-scrambled plasmid + doxycycline for 48h post transfection, replica 2
|
| Sample_geo_accession | GSM918098
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Apr 18 2012
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | transient transfection of A673sh cells using the Lipofectamine Plus reagent (Invitrogen) according to the manufacturer's recommendations, EWS-FLI1 knockdown was induced by addition of 1µg/ml doxycycline for 48h
| | Sample_growth_protocol_ch1 | A673sh cells were maintained in DMEM (Invitrogen) supplemented with 10% FCS (PAA), 2µg/ml Blasticidine (Invitrogen) and 50µg/ml Zeocin (Cayla, France). EWS-FLI1 knockdown was induced by addition of doxycycline (Sigma-Aldrich, St. Louis, MO, USA). Cells were placed in a Thermo-CO2 incubator with a humidified atmosphere containing 5% CO2 (Thermo Electron Corp).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared with a Qiagen RNAeasy kit (QIAGEN) following the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target labelling and hybridization. For Affymetrix GeneChip analysis, 2.0µg total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer's protocols (Gene Expression Analysis, Technical Manual, Revison #4; Eukaryotic Target Preparation, Revison #3).
| | Sample_hyb_protocol | Following RNA purification, 20µg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to U133-plus2 microarrays. The arrays were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the fRMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maximilian,,Kauer
| | Sample_contact_email | maximilian.kauer@ccri.at
| | Sample_contact_laboratory | Heinrich Kovar
| | Sample_contact_department | Molecular Biology
| | Sample_contact_institute | CCRI, St.Anna Children Cancer Research Institute
| | Sample_contact_address | Zimmermannplatz 10
| | Sample_contact_city | Vienna
| | Sample_contact_zip/postal_code | 1090
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918098/suppl/GSM918098.CEL.gz
| | Sample_series_id | GSE37409
| | Sample_data_row_count | 54675
| | |
|
GSM918099 | GPL570 |
|
shFOXO1_noDox2
|
A673 cell line expressing doxycycline-inducible short hairpin RNA against EWS-FLI1 (A673sh)
|
cell line: EWS-FLI1
transfection: A673sh transiently with the pRS-sh-FOXO1 plasmid targeting endogenous FOXO1wt
|
A673sh transiently transfected with the pRS-sh-FOXO1 plasmid targeting endogenous FOXO1wt, replica 2
|
| Sample_geo_accession | GSM918099
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Apr 18 2012
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | transient transfection of A673sh cells using the Lipofectamine Plus reagent (Invitrogen) according to the manufacturer's recommendations.
| | Sample_growth_protocol_ch1 | A673sh cells were maintained in DMEM (Invitrogen) supplemented with 10% FCS (PAA), 2µg/ml Blasticidine (Invitrogen) and 50µg/ml Zeocin (Cayla, France). EWS-FLI1 knockdown was induced by addition of doxycycline (Sigma-Aldrich, St. Louis, MO, USA). Cells were placed in a Thermo-CO2 incubator with a humidified atmosphere containing 5% CO2 (Thermo Electron Corp).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared with a Qiagen RNAeasy kit (QIAGEN) following the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target labelling and hybridization. For Affymetrix GeneChip analysis, 2.0µg total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer's protocols (Gene Expression Analysis, Technical Manual, Revison #4; Eukaryotic Target Preparation, Revison #3).
| | Sample_hyb_protocol | Following RNA purification, 20µg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to U133-plus2 microarrays. The arrays were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the fRMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maximilian,,Kauer
| | Sample_contact_email | maximilian.kauer@ccri.at
| | Sample_contact_laboratory | Heinrich Kovar
| | Sample_contact_department | Molecular Biology
| | Sample_contact_institute | CCRI, St.Anna Children Cancer Research Institute
| | Sample_contact_address | Zimmermannplatz 10
| | Sample_contact_city | Vienna
| | Sample_contact_zip/postal_code | 1090
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918099/suppl/GSM918099.CEL.gz
| | Sample_series_id | GSE37409
| | Sample_data_row_count | 54675
| | |
|
GSM918100 | GPL570 |
|
shFOXO1_Dox2
|
A673 cell line expressing doxycycline-inducible short hairpin RNA against EWS-FLI1 (A673sh)
|
cell line: EWS-FLI1
transfection: A673sh transiently with the pRS-sh-FOXO1 plasmid targeting endogenous FOXO1wt + doxycycline for 48h post transfection
|
A673sh transiently transfected with the pRS-sh-FOXO1 plasmid targeting endogenous FOXO1wt + doxycycline for 48h post transfection, replica 2
|
| Sample_geo_accession | GSM918100
| | Sample_status | Public on Jul 01 2013
| | Sample_submission_date | Apr 18 2012
| | Sample_last_update_date | Jul 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | transient transfection of A673sh cells using the Lipofectamine Plus reagent (Invitrogen) according to the manufacturer's recommendations, EWS-FLI1 knockdown was induced by addition of 1µg/ml doxycycline for 48h
| | Sample_growth_protocol_ch1 | A673sh cells were maintained in DMEM (Invitrogen) supplemented with 10% FCS (PAA), 2µg/ml Blasticidine (Invitrogen) and 50µg/ml Zeocin (Cayla, France). EWS-FLI1 knockdown was induced by addition of doxycycline (Sigma-Aldrich, St. Louis, MO, USA). Cells were placed in a Thermo-CO2 incubator with a humidified atmosphere containing 5% CO2 (Thermo Electron Corp).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared with a Qiagen RNAeasy kit (QIAGEN) following the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target labelling and hybridization. For Affymetrix GeneChip analysis, 2.0µg total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer's protocols (Gene Expression Analysis, Technical Manual, Revison #4; Eukaryotic Target Preparation, Revison #3).
| | Sample_hyb_protocol | Following RNA purification, 20µg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to U133-plus2 microarrays. The arrays were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the fRMA algorithm
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maximilian,,Kauer
| | Sample_contact_email | maximilian.kauer@ccri.at
| | Sample_contact_laboratory | Heinrich Kovar
| | Sample_contact_department | Molecular Biology
| | Sample_contact_institute | CCRI, St.Anna Children Cancer Research Institute
| | Sample_contact_address | Zimmermannplatz 10
| | Sample_contact_city | Vienna
| | Sample_contact_zip/postal_code | 1090
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918100/suppl/GSM918100.CEL.gz
| | Sample_series_id | GSE37409
| | Sample_data_row_count | 54675
| | |
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