Search results for the GEO ID: GSE10580  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM266912 | GPL570 |
|
U2OS_HA-tagged PRDM5_8 hours of doxycycline induction - Replica 1
|
U2OS human osteosarcoma cell line, HA-tagged full length PRDM5 in the doxycycline-inducible vector pSG213, 8h induction
|
U2OS (human osteosarcoma cell line) transfected with HA-tagged full length PRDM5 in the doxycycline-inducible vector pSG213 treated for 8h with 2ug/ml doxycycline to induce transgene expression.
|
U2OS cells transfected with an HA-tagged PRDM5 cloned onto the pSG213 doxycycline-inducible vector, after 8 hours of doxycycline induction - Replica 1
|
| Sample_geo_accession | GSM266912
| | Sample_status | Public on Jan 26 2009
| | Sample_submission_date | Feb 20 2008
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Doxycycline treatments were performed by adding 2ug/ml oxycycline to the culture medium.
| | Sample_growth_protocol_ch1 | U2OS cell lines were maintained in DMEM supplemented with 100 ug/ml streptomycin, 100 ug/ml penicillin, 2 mM glutamine, 10% tetracyclin free serum and 1,5 ug/ml puromycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each cell line, an RNA pool was obtained by mixing equal quantities of total RNA from each of the four independent RNA extractions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA. The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were hybridized with each biotin-labeled target.
| | Sample_scan_protocol | Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.
| | Sample_data_processing | The data were analyzed with GeneChip operating system (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Myriam,,Alcalay
| | Sample_contact_email | myriam.alcalay@ifom-ieo-campus.it
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Experimental Oncology
| | Sample_contact_institute | European Institute of Oncology
| | Sample_contact_address | Via Adamello 16
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20139
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM266nnn/GSM266912/suppl/GSM266912.cel.gz
| | Sample_series_id | GSE10580
| | Sample_data_row_count | 54675
| | |
|
GSM266913 | GPL570 |
|
U2OS_HA-tagged PRDM5_8 hours of doxycycline induction - Replica 2
|
U2OS human osteosarcoma cell line, HA-tagged full length PRDM5 in the doxycycline-inducible vector pSG213, 8h induction
|
U2OS (human osteosarcoma cell line) transfected with HA-tagged full length PRDM5 in the doxycycline-inducible vector pSG213 treated for 8h with 2ug/ml doxycycline to induce transgene expression.
|
U2OS cells transfected with an HA-tagged PRDM5 cloned onto the pSG213 doxycycline-inducible vector, after 8 hours of doxycycline induction - Replica 2
|
| Sample_geo_accession | GSM266913
| | Sample_status | Public on Jan 26 2009
| | Sample_submission_date | Feb 20 2008
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Doxycycline treatments were performed by adding 2ug/ml oxycycline to the culture medium.
| | Sample_growth_protocol_ch1 | U2OS cell lines were maintained in DMEM supplemented with 100 ug/ml streptomycin, 100 ug/ml penicillin, 2 mM glutamine, 10% tetracyclin free serum and 1,5 ug/ml puromycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each cell line, an RNA pool was obtained by mixing equal quantities of total RNA from each of the four independent RNA extractions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA. The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were hybridized with each biotin-labeled target.
| | Sample_scan_protocol | Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.
| | Sample_data_processing | The data were analyzed with GeneChip operating system (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Myriam,,Alcalay
| | Sample_contact_email | myriam.alcalay@ifom-ieo-campus.it
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Experimental Oncology
| | Sample_contact_institute | European Institute of Oncology
| | Sample_contact_address | Via Adamello 16
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20139
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM266nnn/GSM266913/suppl/GSM266913.cel.gz
| | Sample_series_id | GSE10580
| | Sample_data_row_count | 54675
| | |
|
GSM266914 | GPL570 |
|
U2OS_empty pSG213 vector_8 hours of doxycycline induction - Replica 1
|
U2OS human osteosarcoma cell line, doxycycline-inducible vector pSG213, 8h induction
|
U2OS (human osteosarcoma cell line) transfected with the doxycycline-inducible vector pSG213 treated for 8h with 2ug/ml doxycycline.
|
U2OS cells transfected with an empty pSG213 vector after 8 hours of doxycycline induction - Replica 1
|
| Sample_geo_accession | GSM266914
| | Sample_status | Public on Jan 26 2009
| | Sample_submission_date | Feb 20 2008
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Doxycycline treatments were performed by adding 2ug/ml oxycycline to the culture medium.
| | Sample_growth_protocol_ch1 | U2OS cell lines were maintained in DMEM supplemented with 100 ug/ml streptomycin, 100 ug/ml penicillin, 2 mM glutamine, 10% tetracyclin free serum and 1,5 ug/ml puromycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each cell line, an RNA pool was obtained by mixing equal quantities of total RNA from each of the four independent RNA extractions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA. The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were hybridized with each biotin-labeled target.
| | Sample_scan_protocol | Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.
| | Sample_data_processing | The data were analyzed with GeneChip operating system (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Myriam,,Alcalay
| | Sample_contact_email | myriam.alcalay@ifom-ieo-campus.it
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Experimental Oncology
| | Sample_contact_institute | European Institute of Oncology
| | Sample_contact_address | Via Adamello 16
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20139
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM266nnn/GSM266914/suppl/GSM266914.cel.gz
| | Sample_series_id | GSE10580
| | Sample_data_row_count | 54675
| | |
|
GSM266915 | GPL570 |
|
U2OS_empty pSG213 vector_8 hours of doxycycline induction - Replica 2
|
U2OS human osteosarcoma cell line, doxycycline-inducible vector pSG213, 8h induction
|
U2OS (human osteosarcoma cell line) transfected with the doxycycline-inducible vector pSG213 treated for 8h with 2ug/ml doxycycline.
|
U2OS cells transfected with an empty pSG213 vector after 8 hours of doxycycline induction - Replica 2
|
| Sample_geo_accession | GSM266915
| | Sample_status | Public on Jan 26 2009
| | Sample_submission_date | Feb 20 2008
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Doxycycline treatments were performed by adding 2ug/ml oxycycline to the culture medium.
| | Sample_growth_protocol_ch1 | U2OS cell lines were maintained in DMEM supplemented with 100 ug/ml streptomycin, 100 ug/ml penicillin, 2 mM glutamine, 10% tetracyclin free serum and 1,5 ug/ml puromycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each cell line, an RNA pool was obtained by mixing equal quantities of total RNA from each of the four independent RNA extractions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA. The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were hybridized with each biotin-labeled target.
| | Sample_scan_protocol | Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.
| | Sample_data_processing | The data were analyzed with GeneChip operating system (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Myriam,,Alcalay
| | Sample_contact_email | myriam.alcalay@ifom-ieo-campus.it
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Experimental Oncology
| | Sample_contact_institute | European Institute of Oncology
| | Sample_contact_address | Via Adamello 16
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20139
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM266nnn/GSM266915/suppl/GSM266915.cel.gz
| | Sample_series_id | GSE10580
| | Sample_data_row_count | 54675
| | |
|
GSM266916 | GPL570 |
|
U2OS_HA-tagged PRDM5_24 hours of doxycycline induction - Replica 1
|
U2OS human osteosarcoma cell line, HA-tagged full length PRDM5 in the doxycycline-inducible vector pSG213, 24h induction
|
U2OS (human osteosarcoma cell line) transfected with HA-tagged full length PRDM5 in the doxycycline-inducible vector pSG213 treated for 24h with 2ug/ml doxycycline to induce transgene expression.
|
U2OS cells transfected with an HA-tagged PRDM5 cloned onto the pSG213 doxycycline-inducible vector, after 24 hours of doxycycline induction - Replica 1
|
| Sample_geo_accession | GSM266916
| | Sample_status | Public on Jan 26 2009
| | Sample_submission_date | Feb 20 2008
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Doxycycline treatments were performed by adding 2ug/ml oxycycline to the culture medium.
| | Sample_growth_protocol_ch1 | U2OS cell lines were maintained in DMEM supplemented with 100 ug/ml streptomycin, 100 ug/ml penicillin, 2 mM glutamine, 10% tetracyclin free serum and 1,5 ug/ml puromycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each cell line, an RNA pool was obtained by mixing equal quantities of total RNA from each of the four independent RNA extractions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA. The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were hybridized with each biotin-labeled target.
| | Sample_scan_protocol | Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.
| | Sample_data_processing | The data were analyzed with GeneChip operating system (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Myriam,,Alcalay
| | Sample_contact_email | myriam.alcalay@ifom-ieo-campus.it
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Experimental Oncology
| | Sample_contact_institute | European Institute of Oncology
| | Sample_contact_address | Via Adamello 16
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20139
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM266nnn/GSM266916/suppl/GSM266916.cel.gz
| | Sample_series_id | GSE10580
| | Sample_data_row_count | 54675
| | |
|
GSM266917 | GPL570 |
|
U2OS_HA-tagged PRDM5_24 hours of doxycycline induction - Replica 2
|
U2OS human osteosarcoma cell line, HA-tagged full length PRDM5 in the doxycycline-inducible vector pSG213, 24h induction
|
U2OS (human osteosarcoma cell line) transfected with HA-tagged full length PRDM5 in the doxycycline-inducible vector pSG213 treated for 24h with 2ug/ml doxycycline to induce transgene expression.
|
U2OS cells transfected with an HA-tagged PRDM5 cloned onto the pSG213 doxycycline-inducible vector, after 24 hours of doxycycline induction - Replica 2
|
| Sample_geo_accession | GSM266917
| | Sample_status | Public on Jan 26 2009
| | Sample_submission_date | Feb 20 2008
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Doxycycline treatments were performed by adding 2ug/ml oxycycline to the culture medium.
| | Sample_growth_protocol_ch1 | U2OS cell lines were maintained in DMEM supplemented with 100 ug/ml streptomycin, 100 ug/ml penicillin, 2 mM glutamine, 10% tetracyclin free serum and 1,5 ug/ml puromycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each cell line, an RNA pool was obtained by mixing equal quantities of total RNA from each of the four independent RNA extractions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA. The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were hybridized with each biotin-labeled target.
| | Sample_scan_protocol | Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.
| | Sample_data_processing | The data were analyzed with GeneChip operating system (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Myriam,,Alcalay
| | Sample_contact_email | myriam.alcalay@ifom-ieo-campus.it
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Experimental Oncology
| | Sample_contact_institute | European Institute of Oncology
| | Sample_contact_address | Via Adamello 16
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20139
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM266nnn/GSM266917/suppl/GSM266917.cel.gz
| | Sample_series_id | GSE10580
| | Sample_data_row_count | 54675
| | |
|
GSM266918 | GPL570 |
|
U2OS_empty pSG213 vector_24 hours of doxycycline induction - Replica 1
|
U2OS human osteosarcoma cell line, doxycycline-inducible vector pSG213, 24h induction
|
U2OS (human osteosarcoma cell line) transfected with the doxycycline-inducible vector pSG213 treated for 24h with 2ug/ml doxycycline.
|
U2OS cells transfected with an empty pSG213 vector after 24 hours of doxycycline induction - Replica 1
|
| Sample_geo_accession | GSM266918
| | Sample_status | Public on Jan 26 2009
| | Sample_submission_date | Feb 20 2008
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Doxycycline treatments were performed by adding 2ug/ml oxycycline to the culture medium.
| | Sample_growth_protocol_ch1 | U2OS cell lines were maintained in DMEM supplemented with 100 ug/ml streptomycin, 100 ug/ml penicillin, 2 mM glutamine, 10% tetracyclin free serum and 1,5 ug/ml puromycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each cell line, an RNA pool was obtained by mixing equal quantities of total RNA from each of the four independent RNA extractions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA. The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were hybridized with each biotin-labeled target.
| | Sample_scan_protocol | Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.
| | Sample_data_processing | The data were analyzed with GeneChip operating system (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Myriam,,Alcalay
| | Sample_contact_email | myriam.alcalay@ifom-ieo-campus.it
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Experimental Oncology
| | Sample_contact_institute | European Institute of Oncology
| | Sample_contact_address | Via Adamello 16
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20139
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM266nnn/GSM266918/suppl/GSM266918.cel.gz
| | Sample_series_id | GSE10580
| | Sample_data_row_count | 54675
| | |
|
GSM266919 | GPL570 |
|
U2OS_empty pSG213 vector_24 hours of doxycycline induction - Replica 2
|
U2OS human osteosarcoma cell line, doxycycline-inducible vector pSG213, 24h induction
|
U2OS (human osteosarcoma cell line) transfected with the doxycycline-inducible vector pSG213 treated for 24h with 2ug/ml doxycycline.
|
U2OS cells transfected with an empty pSG213 vector after 24 hours of doxycycline induction - Replica 2
|
| Sample_geo_accession | GSM266919
| | Sample_status | Public on Jan 26 2009
| | Sample_submission_date | Feb 20 2008
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Doxycycline treatments were performed by adding 2ug/ml oxycycline to the culture medium.
| | Sample_growth_protocol_ch1 | U2OS cell lines were maintained in DMEM supplemented with 100 ug/ml streptomycin, 100 ug/ml penicillin, 2 mM glutamine, 10% tetracyclin free serum and 1,5 ug/ml puromycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each cell line, an RNA pool was obtained by mixing equal quantities of total RNA from each of the four independent RNA extractions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA. The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were hybridized with each biotin-labeled target.
| | Sample_scan_protocol | Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.
| | Sample_data_processing | The data were analyzed with GeneChip operating system (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Myriam,,Alcalay
| | Sample_contact_email | myriam.alcalay@ifom-ieo-campus.it
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Experimental Oncology
| | Sample_contact_institute | European Institute of Oncology
| | Sample_contact_address | Via Adamello 16
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20139
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM266nnn/GSM266919/suppl/GSM266919.cel.gz
| | Sample_series_id | GSE10580
| | Sample_data_row_count | 54675
| | |
|
GSM266920 | GPL570 |
|
U2OS_HA-tagged PRDM5_48 hours of doxycycline induction - Replica 1
|
U2OS human osteosarcoma cell line, HA-tagged full length PRDM5 in the doxycycline-inducible vector pSG213, 48h induction
|
U2OS (human osteosarcoma cell line) transfected with HA-tagged full length PRDM5 in the doxycycline-inducible vector pSG213 treated for 48h with 2ug/ml doxycycline to induce transgene expression.
|
U2OS cells transfected with an HA-tagged PRDM5 cloned onto the pSG213 doxycycline-inducible vector, after 48 hours of doxycycline induction - Replica 1
|
| Sample_geo_accession | GSM266920
| | Sample_status | Public on Jan 26 2009
| | Sample_submission_date | Feb 20 2008
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Doxycycline treatments were performed by adding 2ug/ml oxycycline to the culture medium.
| | Sample_growth_protocol_ch1 | U2OS cell lines were maintained in DMEM supplemented with 100 ug/ml streptomycin, 100 ug/ml penicillin, 2 mM glutamine, 10% tetracyclin free serum and 1,5 ug/ml puromycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each cell line, an RNA pool was obtained by mixing equal quantities of total RNA from each of the four independent RNA extractions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA. The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were hybridized with each biotin-labeled target.
| | Sample_scan_protocol | Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.
| | Sample_data_processing | The data were analyzed with GeneChip operating system (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Myriam,,Alcalay
| | Sample_contact_email | myriam.alcalay@ifom-ieo-campus.it
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Experimental Oncology
| | Sample_contact_institute | European Institute of Oncology
| | Sample_contact_address | Via Adamello 16
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20139
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM266nnn/GSM266920/suppl/GSM266920.cel.gz
| | Sample_series_id | GSE10580
| | Sample_data_row_count | 54675
| | |
|
GSM266921 | GPL570 |
|
U2OS_HA-tagged PRDM5_48 hours of doxycycline induction - Replica 2
|
U2OS human osteosarcoma cell line, HA-tagged full length PRDM5 in the doxycycline-inducible vector pSG213, 48h induction
|
U2OS (human osteosarcoma cell line) transfected with HA-tagged full length PRDM5 in the doxycycline-inducible vector pSG213 treated for 48h with 2ug/ml doxycycline to induce transgene expression.
|
U2OS cells transfected with an HA-tagged PRDM5 cloned onto the pSG213 doxycycline-inducible vector, after 48 hours of doxycycline induction - Replica 2
|
| Sample_geo_accession | GSM266921
| | Sample_status | Public on Jan 26 2009
| | Sample_submission_date | Feb 20 2008
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Doxycycline treatments were performed by adding 2ug/ml oxycycline to the culture medium.
| | Sample_growth_protocol_ch1 | U2OS cell lines were maintained in DMEM supplemented with 100 ug/ml streptomycin, 100 ug/ml penicillin, 2 mM glutamine, 10% tetracyclin free serum and 1,5 ug/ml puromycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each cell line, an RNA pool was obtained by mixing equal quantities of total RNA from each of the four independent RNA extractions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA. The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were hybridized with each biotin-labeled target.
| | Sample_scan_protocol | Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.
| | Sample_data_processing | The data were analyzed with GeneChip operating system (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Myriam,,Alcalay
| | Sample_contact_email | myriam.alcalay@ifom-ieo-campus.it
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Experimental Oncology
| | Sample_contact_institute | European Institute of Oncology
| | Sample_contact_address | Via Adamello 16
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20139
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM266nnn/GSM266921/suppl/GSM266921.cel.gz
| | Sample_series_id | GSE10580
| | Sample_data_row_count | 54675
| | |
|
GSM266922 | GPL570 |
|
U2OS_empty pSG213 vector_48 hours of doxycycline induction - Replica 1
|
U2OS human osteosarcoma cell line, doxycycline-inducible vector pSG213, 48h induction
|
U2OS (human osteosarcoma cell line) transfected with the doxycycline-inducible vector pSG213 treated for 48h with 2ug/ml doxycycline.
|
U2OS cells transfected with an empty pSG213 vector after 48 hours of doxycycline induction - Replica 1
|
| Sample_geo_accession | GSM266922
| | Sample_status | Public on Jan 26 2009
| | Sample_submission_date | Feb 20 2008
| | Sample_last_update_date | Jan 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Doxycycline treatments were performed by adding 2ug/ml oxycycline to the culture medium.
| | Sample_growth_protocol_ch1 | U2OS cell lines were maintained in DMEM supplemented with 100 ug/ml streptomycin, 100 ug/ml penicillin, 2 mM glutamine, 10% tetracyclin free serum and 1,5 ug/ml puromycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each cell line, an RNA pool was obtained by mixing equal quantities of total RNA from each of the four independent RNA extractions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA. The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were hybridized with each biotin-labeled target.
| | Sample_scan_protocol | Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.
| | Sample_data_processing | The data were analyzed with GeneChip operating system (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Myriam,,Alcalay
| | Sample_contact_email | myriam.alcalay@ifom-ieo-campus.it
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Experimental Oncology
| | Sample_contact_institute | European Institute of Oncology
| | Sample_contact_address | Via Adamello 16
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20139
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM266nnn/GSM266922/suppl/GSM266922.cel.gz
| | Sample_series_id | GSE10580
| | Sample_data_row_count | 54675
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