Search results for the GEO ID: GSE18946  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM469242 | GPL570 |
|
DG75_GFP_rep1
|
DG75 cells transduced with the GFP construct
|
cell line: DG75
construct: GFP
|
none
|
| Sample_geo_accession | GSM469242
| | Sample_status | Public on Oct 28 2011
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Oct 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stable expressing cell line for the microarray analysis were generated using the “Virapower” lentiviral transduction system with the vector pLENTI6/V5 (Invitrogen) in which was cloned using Gateway technology (Invitrogen), the ten intronic KSHV miRNAs. The control lentiviral vector pLENTI6/V5-EGFP was a kind gift from Oliver Rossmann. In order to generate lentivirus for transduction of cells with KSHV miRNAs, the ViraPower Lentiviral Gateway Expression System (Invitrogen) was employed according to the manufacturer’s instructions. Two days after transduction, when the EGFP signal in the control cells became visible, Blasticidin (1 μg/ml) was added to the medium to select for the transgene and gradually raised to a final concentration of 7.5 μg/ml for DG75 cells and 3 μg/ml for EA.hy926 cells after six days. Cell lines were used for experiments when 100% of control cells expressed EGFP.
| | Sample_growth_protocol_ch1 | DG-75 were grown in RPMI 1640 medium containing 10 % fetal calf serum (FCS), 100 IU/ml Penicillin, 100 μg/ml Streptomycin and 2 mM L-Glutamine. EA.hy926 were grown in DMEM supplemented with 10% FCS and penicillin/streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Expression 3' Amplification One-Cycle Target Labeling Kit and Control Reagents (Affymetrix) were used for the biotin-labelling of the probes according to the manufacturer’s instructions.
| | Sample_hyb_protocol | GeneChip Hybridization, Wash and Stain Kit (Affymetrix) and a Hybridization Oven 640 (Affymetrix) were used for the pre-hybridization step and for hybridizing the target mix to a eukaryotic GeneChip probe array (Affymetrix) according to the manufacturer’s instructions. The washing and staining steps were realised using a Fluidics Station 450 (Affymetrix) operated by the GeneChip Operating Software GCOS (Affymetrix) according to the manufacturer’s instructions.
| | Sample_scan_protocol | The array's scan was realised using a GeneChip Scanner 3000 7G (Affymetrix) operated by the GeneChip Operating Software GCOS(Affymetrix) according to the manufacturer’s instructions.
| | Sample_data_processing | We imported the CEL files into the R software using the BioConductor affy package (Gentleman et al., 2004). The probe intensities were corrected for optical noise, adjusted for non-specific binding and quantile normalized with the gcRMA algorithm (Wu et al., 2004).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean,,Hausser
| | Sample_contact_institute | Biozentrum, Universität Basel
| | Sample_contact_address | Klingelbergstrasse 50/70
| | Sample_contact_city | Basel
| | Sample_contact_zip/postal_code | 4056
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469242/suppl/GSM469242.CEL.gz
| | Sample_series_id | GSE18946
| | Sample_data_row_count | 54675
| | |
|
GSM469243 | GPL570 |
|
DG75_GFP_rep2
|
DG75 cells transduced with the GFP construct
|
cell line: DG75
construct: GFP
|
none
|
| Sample_geo_accession | GSM469243
| | Sample_status | Public on Oct 28 2011
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Oct 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stable expressing cell line for the microarray analysis were generated using the “Virapower” lentiviral transduction system with the vector pLENTI6/V5 (Invitrogen) in which was cloned using Gateway technology (Invitrogen), the ten intronic KSHV miRNAs. The control lentiviral vector pLENTI6/V5-EGFP was a kind gift from Oliver Rossmann. In order to generate lentivirus for transduction of cells with KSHV miRNAs, the ViraPower Lentiviral Gateway Expression System (Invitrogen) was employed according to the manufacturer’s instructions. Two days after transduction, when the EGFP signal in the control cells became visible, Blasticidin (1 μg/ml) was added to the medium to select for the transgene and gradually raised to a final concentration of 7.5 μg/ml for DG75 cells and 3 μg/ml for EA.hy926 cells after six days. Cell lines were used for experiments when 100% of control cells expressed EGFP.
| | Sample_growth_protocol_ch1 | DG-75 were grown in RPMI 1640 medium containing 10 % fetal calf serum (FCS), 100 IU/ml Penicillin, 100 μg/ml Streptomycin and 2 mM L-Glutamine. EA.hy926 were grown in DMEM supplemented with 10% FCS and penicillin/streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Expression 3' Amplification One-Cycle Target Labeling Kit and Control Reagents (Affymetrix) were used for the biotin-labelling of the probes according to the manufacturer’s instructions.
| | Sample_hyb_protocol | GeneChip Hybridization, Wash and Stain Kit (Affymetrix) and a Hybridization Oven 640 (Affymetrix) were used for the pre-hybridization step and for hybridizing the target mix to a eukaryotic GeneChip probe array (Affymetrix) according to the manufacturer’s instructions. The washing and staining steps were realised using a Fluidics Station 450 (Affymetrix) operated by the GeneChip Operating Software GCOS (Affymetrix) according to the manufacturer’s instructions.
| | Sample_scan_protocol | The array's scan was realised using a GeneChip Scanner 3000 7G (Affymetrix) operated by the GeneChip Operating Software GCOS(Affymetrix) according to the manufacturer’s instructions.
| | Sample_data_processing | We imported the CEL files into the R software using the BioConductor affy package (Gentleman et al., 2004). The probe intensities were corrected for optical noise, adjusted for non-specific binding and quantile normalized with the gcRMA algorithm (Wu et al., 2004).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean,,Hausser
| | Sample_contact_institute | Biozentrum, Universität Basel
| | Sample_contact_address | Klingelbergstrasse 50/70
| | Sample_contact_city | Basel
| | Sample_contact_zip/postal_code | 4056
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469243/suppl/GSM469243.CEL.gz
| | Sample_series_id | GSE18946
| | Sample_data_row_count | 54675
| | |
|
GSM469244 | GPL570 |
|
DG75_GFP_rep3
|
DG75 cells transduced with the GFP construct
|
cell line: DG75
construct: GFP
|
none
|
| Sample_geo_accession | GSM469244
| | Sample_status | Public on Oct 28 2011
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Oct 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stable expressing cell line for the microarray analysis were generated using the “Virapower” lentiviral transduction system with the vector pLENTI6/V5 (Invitrogen) in which was cloned using Gateway technology (Invitrogen), the ten intronic KSHV miRNAs. The control lentiviral vector pLENTI6/V5-EGFP was a kind gift from Oliver Rossmann. In order to generate lentivirus for transduction of cells with KSHV miRNAs, the ViraPower Lentiviral Gateway Expression System (Invitrogen) was employed according to the manufacturer’s instructions. Two days after transduction, when the EGFP signal in the control cells became visible, Blasticidin (1 μg/ml) was added to the medium to select for the transgene and gradually raised to a final concentration of 7.5 μg/ml for DG75 cells and 3 μg/ml for EA.hy926 cells after six days. Cell lines were used for experiments when 100% of control cells expressed EGFP.
| | Sample_growth_protocol_ch1 | DG-75 were grown in RPMI 1640 medium containing 10 % fetal calf serum (FCS), 100 IU/ml Penicillin, 100 μg/ml Streptomycin and 2 mM L-Glutamine. EA.hy926 were grown in DMEM supplemented with 10% FCS and penicillin/streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Expression 3' Amplification One-Cycle Target Labeling Kit and Control Reagents (Affymetrix) were used for the biotin-labelling of the probes according to the manufacturer’s instructions.
| | Sample_hyb_protocol | GeneChip Hybridization, Wash and Stain Kit (Affymetrix) and a Hybridization Oven 640 (Affymetrix) were used for the pre-hybridization step and for hybridizing the target mix to a eukaryotic GeneChip probe array (Affymetrix) according to the manufacturer’s instructions. The washing and staining steps were realised using a Fluidics Station 450 (Affymetrix) operated by the GeneChip Operating Software GCOS (Affymetrix) according to the manufacturer’s instructions.
| | Sample_scan_protocol | The array's scan was realised using a GeneChip Scanner 3000 7G (Affymetrix) operated by the GeneChip Operating Software GCOS(Affymetrix) according to the manufacturer’s instructions.
| | Sample_data_processing | We imported the CEL files into the R software using the BioConductor affy package (Gentleman et al., 2004). The probe intensities were corrected for optical noise, adjusted for non-specific binding and quantile normalized with the gcRMA algorithm (Wu et al., 2004).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean,,Hausser
| | Sample_contact_institute | Biozentrum, Universität Basel
| | Sample_contact_address | Klingelbergstrasse 50/70
| | Sample_contact_city | Basel
| | Sample_contact_zip/postal_code | 4056
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469244/suppl/GSM469244.CEL.gz
| | Sample_series_id | GSE18946
| | Sample_data_row_count | 54675
| | |
|
GSM469245 | GPL570 |
|
DG75_K10_rep1
|
DG75 cells transduced with the K10/12 construct
|
cell line: DG75
construct: K10/12
|
none
|
| Sample_geo_accession | GSM469245
| | Sample_status | Public on Oct 28 2011
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Oct 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stable expressing cell line for the microarray analysis were generated using the “Virapower” lentiviral transduction system with the vector pLENTI6/V5 (Invitrogen) in which was cloned using Gateway technology (Invitrogen), the ten intronic KSHV miRNAs. The control lentiviral vector pLENTI6/V5-EGFP was a kind gift from Oliver Rossmann. In order to generate lentivirus for transduction of cells with KSHV miRNAs, the ViraPower Lentiviral Gateway Expression System (Invitrogen) was employed according to the manufacturer’s instructions. Two days after transduction, when the EGFP signal in the control cells became visible, Blasticidin (1 μg/ml) was added to the medium to select for the transgene and gradually raised to a final concentration of 7.5 μg/ml for DG75 cells and 3 μg/ml for EA.hy926 cells after six days. Cell lines were used for experiments when 100% of control cells expressed EGFP.
| | Sample_growth_protocol_ch1 | DG-75 were grown in RPMI 1640 medium containing 10 % fetal calf serum (FCS), 100 IU/ml Penicillin, 100 μg/ml Streptomycin and 2 mM L-Glutamine. EA.hy926 were grown in DMEM supplemented with 10% FCS and penicillin/streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Expression 3' Amplification One-Cycle Target Labeling Kit and Control Reagents (Affymetrix) were used for the biotin-labelling of the probes according to the manufacturer’s instructions.
| | Sample_hyb_protocol | GeneChip Hybridization, Wash and Stain Kit (Affymetrix) and a Hybridization Oven 640 (Affymetrix) were used for the pre-hybridization step and for hybridizing the target mix to a eukaryotic GeneChip probe array (Affymetrix) according to the manufacturer’s instructions. The washing and staining steps were realised using a Fluidics Station 450 (Affymetrix) operated by the GeneChip Operating Software GCOS (Affymetrix) according to the manufacturer’s instructions.
| | Sample_scan_protocol | The array's scan was realised using a GeneChip Scanner 3000 7G (Affymetrix) operated by the GeneChip Operating Software GCOS(Affymetrix) according to the manufacturer’s instructions.
| | Sample_data_processing | We imported the CEL files into the R software using the BioConductor affy package (Gentleman et al., 2004). The probe intensities were corrected for optical noise, adjusted for non-specific binding and quantile normalized with the gcRMA algorithm (Wu et al., 2004).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean,,Hausser
| | Sample_contact_institute | Biozentrum, Universität Basel
| | Sample_contact_address | Klingelbergstrasse 50/70
| | Sample_contact_city | Basel
| | Sample_contact_zip/postal_code | 4056
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469245/suppl/GSM469245.CEL.gz
| | Sample_series_id | GSE18946
| | Sample_data_row_count | 54675
| | |
|
GSM469246 | GPL570 |
|
DG75_K10_rep2
|
DG75 cells transduced with the K10/12 construct
|
cell line: DG75
construct: K10/12
|
none
|
| Sample_geo_accession | GSM469246
| | Sample_status | Public on Oct 28 2011
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Oct 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stable expressing cell line for the microarray analysis were generated using the “Virapower” lentiviral transduction system with the vector pLENTI6/V5 (Invitrogen) in which was cloned using Gateway technology (Invitrogen), the ten intronic KSHV miRNAs. The control lentiviral vector pLENTI6/V5-EGFP was a kind gift from Oliver Rossmann. In order to generate lentivirus for transduction of cells with KSHV miRNAs, the ViraPower Lentiviral Gateway Expression System (Invitrogen) was employed according to the manufacturer’s instructions. Two days after transduction, when the EGFP signal in the control cells became visible, Blasticidin (1 μg/ml) was added to the medium to select for the transgene and gradually raised to a final concentration of 7.5 μg/ml for DG75 cells and 3 μg/ml for EA.hy926 cells after six days. Cell lines were used for experiments when 100% of control cells expressed EGFP.
| | Sample_growth_protocol_ch1 | DG-75 were grown in RPMI 1640 medium containing 10 % fetal calf serum (FCS), 100 IU/ml Penicillin, 100 μg/ml Streptomycin and 2 mM L-Glutamine. EA.hy926 were grown in DMEM supplemented with 10% FCS and penicillin/streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Expression 3' Amplification One-Cycle Target Labeling Kit and Control Reagents (Affymetrix) were used for the biotin-labelling of the probes according to the manufacturer’s instructions.
| | Sample_hyb_protocol | GeneChip Hybridization, Wash and Stain Kit (Affymetrix) and a Hybridization Oven 640 (Affymetrix) were used for the pre-hybridization step and for hybridizing the target mix to a eukaryotic GeneChip probe array (Affymetrix) according to the manufacturer’s instructions. The washing and staining steps were realised using a Fluidics Station 450 (Affymetrix) operated by the GeneChip Operating Software GCOS (Affymetrix) according to the manufacturer’s instructions.
| | Sample_scan_protocol | The array's scan was realised using a GeneChip Scanner 3000 7G (Affymetrix) operated by the GeneChip Operating Software GCOS(Affymetrix) according to the manufacturer’s instructions.
| | Sample_data_processing | We imported the CEL files into the R software using the BioConductor affy package (Gentleman et al., 2004). The probe intensities were corrected for optical noise, adjusted for non-specific binding and quantile normalized with the gcRMA algorithm (Wu et al., 2004).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean,,Hausser
| | Sample_contact_institute | Biozentrum, Universität Basel
| | Sample_contact_address | Klingelbergstrasse 50/70
| | Sample_contact_city | Basel
| | Sample_contact_zip/postal_code | 4056
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469246/suppl/GSM469246.CEL.gz
| | Sample_series_id | GSE18946
| | Sample_data_row_count | 54675
| | |
|
GSM469247 | GPL570 |
|
DG75_K10_rep3
|
DG75 cells transduced with the K10/12 construct
|
cell line: DG75
construct: K10/12
|
none
|
| Sample_geo_accession | GSM469247
| | Sample_status | Public on Oct 28 2011
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Oct 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stable expressing cell line for the microarray analysis were generated using the “Virapower” lentiviral transduction system with the vector pLENTI6/V5 (Invitrogen) in which was cloned using Gateway technology (Invitrogen), the ten intronic KSHV miRNAs. The control lentiviral vector pLENTI6/V5-EGFP was a kind gift from Oliver Rossmann. In order to generate lentivirus for transduction of cells with KSHV miRNAs, the ViraPower Lentiviral Gateway Expression System (Invitrogen) was employed according to the manufacturer’s instructions. Two days after transduction, when the EGFP signal in the control cells became visible, Blasticidin (1 μg/ml) was added to the medium to select for the transgene and gradually raised to a final concentration of 7.5 μg/ml for DG75 cells and 3 μg/ml for EA.hy926 cells after six days. Cell lines were used for experiments when 100% of control cells expressed EGFP.
| | Sample_growth_protocol_ch1 | DG-75 were grown in RPMI 1640 medium containing 10 % fetal calf serum (FCS), 100 IU/ml Penicillin, 100 μg/ml Streptomycin and 2 mM L-Glutamine. EA.hy926 were grown in DMEM supplemented with 10% FCS and penicillin/streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Expression 3' Amplification One-Cycle Target Labeling Kit and Control Reagents (Affymetrix) were used for the biotin-labelling of the probes according to the manufacturer’s instructions.
| | Sample_hyb_protocol | GeneChip Hybridization, Wash and Stain Kit (Affymetrix) and a Hybridization Oven 640 (Affymetrix) were used for the pre-hybridization step and for hybridizing the target mix to a eukaryotic GeneChip probe array (Affymetrix) according to the manufacturer’s instructions. The washing and staining steps were realised using a Fluidics Station 450 (Affymetrix) operated by the GeneChip Operating Software GCOS (Affymetrix) according to the manufacturer’s instructions.
| | Sample_scan_protocol | The array's scan was realised using a GeneChip Scanner 3000 7G (Affymetrix) operated by the GeneChip Operating Software GCOS(Affymetrix) according to the manufacturer’s instructions.
| | Sample_data_processing | We imported the CEL files into the R software using the BioConductor affy package (Gentleman et al., 2004). The probe intensities were corrected for optical noise, adjusted for non-specific binding and quantile normalized with the gcRMA algorithm (Wu et al., 2004).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean,,Hausser
| | Sample_contact_institute | Biozentrum, Universität Basel
| | Sample_contact_address | Klingelbergstrasse 50/70
| | Sample_contact_city | Basel
| | Sample_contact_zip/postal_code | 4056
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469247/suppl/GSM469247.CEL.gz
| | Sample_series_id | GSE18946
| | Sample_data_row_count | 54675
| | |
|
GSM469248 | GPL570 |
|
DG75_K12_rep1
|
DG75 cells transduced with the K12/12 construct
|
cell line: DG75
construct: K12/12
|
none
|
| Sample_geo_accession | GSM469248
| | Sample_status | Public on Oct 28 2011
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Oct 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stable expressing cell line for the microarray analysis were generated using the “Virapower” lentiviral transduction system with the vector pLENTI6/V5 (Invitrogen) in which was cloned using Gateway technology (Invitrogen), the ten intronic KSHV miRNAs. The control lentiviral vector pLENTI6/V5-EGFP was a kind gift from Oliver Rossmann. In order to generate lentivirus for transduction of cells with KSHV miRNAs, the ViraPower Lentiviral Gateway Expression System (Invitrogen) was employed according to the manufacturer’s instructions. Two days after transduction, when the EGFP signal in the control cells became visible, Blasticidin (1 μg/ml) was added to the medium to select for the transgene and gradually raised to a final concentration of 7.5 μg/ml for DG75 cells and 3 μg/ml for EA.hy926 cells after six days. Cell lines were used for experiments when 100% of control cells expressed EGFP.
| | Sample_growth_protocol_ch1 | DG-75 were grown in RPMI 1640 medium containing 10 % fetal calf serum (FCS), 100 IU/ml Penicillin, 100 μg/ml Streptomycin and 2 mM L-Glutamine. EA.hy926 were grown in DMEM supplemented with 10% FCS and penicillin/streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Expression 3' Amplification One-Cycle Target Labeling Kit and Control Reagents (Affymetrix) were used for the biotin-labelling of the probes according to the manufacturer’s instructions.
| | Sample_hyb_protocol | GeneChip Hybridization, Wash and Stain Kit (Affymetrix) and a Hybridization Oven 640 (Affymetrix) were used for the pre-hybridization step and for hybridizing the target mix to a eukaryotic GeneChip probe array (Affymetrix) according to the manufacturer’s instructions. The washing and staining steps were realised using a Fluidics Station 450 (Affymetrix) operated by the GeneChip Operating Software GCOS (Affymetrix) according to the manufacturer’s instructions.
| | Sample_scan_protocol | The array's scan was realised using a GeneChip Scanner 3000 7G (Affymetrix) operated by the GeneChip Operating Software GCOS(Affymetrix) according to the manufacturer’s instructions.
| | Sample_data_processing | We imported the CEL files into the R software using the BioConductor affy package (Gentleman et al., 2004). The probe intensities were corrected for optical noise, adjusted for non-specific binding and quantile normalized with the gcRMA algorithm (Wu et al., 2004).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean,,Hausser
| | Sample_contact_institute | Biozentrum, Universität Basel
| | Sample_contact_address | Klingelbergstrasse 50/70
| | Sample_contact_city | Basel
| | Sample_contact_zip/postal_code | 4056
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469248/suppl/GSM469248.CEL.gz
| | Sample_series_id | GSE18946
| | Sample_data_row_count | 54675
| | |
|
GSM469249 | GPL570 |
|
DG75_K12_rep2
|
DG75 cells transduced with the K12/12 construct
|
cell line: DG75
construct: K12/12
|
none
|
| Sample_geo_accession | GSM469249
| | Sample_status | Public on Oct 28 2011
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Oct 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stable expressing cell line for the microarray analysis were generated using the “Virapower” lentiviral transduction system with the vector pLENTI6/V5 (Invitrogen) in which was cloned using Gateway technology (Invitrogen), the ten intronic KSHV miRNAs. The control lentiviral vector pLENTI6/V5-EGFP was a kind gift from Oliver Rossmann. In order to generate lentivirus for transduction of cells with KSHV miRNAs, the ViraPower Lentiviral Gateway Expression System (Invitrogen) was employed according to the manufacturer’s instructions. Two days after transduction, when the EGFP signal in the control cells became visible, Blasticidin (1 μg/ml) was added to the medium to select for the transgene and gradually raised to a final concentration of 7.5 μg/ml for DG75 cells and 3 μg/ml for EA.hy926 cells after six days. Cell lines were used for experiments when 100% of control cells expressed EGFP.
| | Sample_growth_protocol_ch1 | DG-75 were grown in RPMI 1640 medium containing 10 % fetal calf serum (FCS), 100 IU/ml Penicillin, 100 μg/ml Streptomycin and 2 mM L-Glutamine. EA.hy926 were grown in DMEM supplemented with 10% FCS and penicillin/streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Expression 3' Amplification One-Cycle Target Labeling Kit and Control Reagents (Affymetrix) were used for the biotin-labelling of the probes according to the manufacturer’s instructions.
| | Sample_hyb_protocol | GeneChip Hybridization, Wash and Stain Kit (Affymetrix) and a Hybridization Oven 640 (Affymetrix) were used for the pre-hybridization step and for hybridizing the target mix to a eukaryotic GeneChip probe array (Affymetrix) according to the manufacturer’s instructions. The washing and staining steps were realised using a Fluidics Station 450 (Affymetrix) operated by the GeneChip Operating Software GCOS (Affymetrix) according to the manufacturer’s instructions.
| | Sample_scan_protocol | The array's scan was realised using a GeneChip Scanner 3000 7G (Affymetrix) operated by the GeneChip Operating Software GCOS(Affymetrix) according to the manufacturer’s instructions.
| | Sample_data_processing | We imported the CEL files into the R software using the BioConductor affy package (Gentleman et al., 2004). The probe intensities were corrected for optical noise, adjusted for non-specific binding and quantile normalized with the gcRMA algorithm (Wu et al., 2004).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean,,Hausser
| | Sample_contact_institute | Biozentrum, Universität Basel
| | Sample_contact_address | Klingelbergstrasse 50/70
| | Sample_contact_city | Basel
| | Sample_contact_zip/postal_code | 4056
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469249/suppl/GSM469249.CEL.gz
| | Sample_series_id | GSE18946
| | Sample_data_row_count | 54675
| | |
|
GSM469250 | GPL570 |
|
DG75_K12_rep3
|
DG75 cells transduced with the K12/12 construct
|
cell line: DG75
construct: K12/12
|
none
|
| Sample_geo_accession | GSM469250
| | Sample_status | Public on Oct 28 2011
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Oct 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stable expressing cell line for the microarray analysis were generated using the “Virapower” lentiviral transduction system with the vector pLENTI6/V5 (Invitrogen) in which was cloned using Gateway technology (Invitrogen), the ten intronic KSHV miRNAs. The control lentiviral vector pLENTI6/V5-EGFP was a kind gift from Oliver Rossmann. In order to generate lentivirus for transduction of cells with KSHV miRNAs, the ViraPower Lentiviral Gateway Expression System (Invitrogen) was employed according to the manufacturer’s instructions. Two days after transduction, when the EGFP signal in the control cells became visible, Blasticidin (1 μg/ml) was added to the medium to select for the transgene and gradually raised to a final concentration of 7.5 μg/ml for DG75 cells and 3 μg/ml for EA.hy926 cells after six days. Cell lines were used for experiments when 100% of control cells expressed EGFP.
| | Sample_growth_protocol_ch1 | DG-75 were grown in RPMI 1640 medium containing 10 % fetal calf serum (FCS), 100 IU/ml Penicillin, 100 μg/ml Streptomycin and 2 mM L-Glutamine. EA.hy926 were grown in DMEM supplemented with 10% FCS and penicillin/streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Expression 3' Amplification One-Cycle Target Labeling Kit and Control Reagents (Affymetrix) were used for the biotin-labelling of the probes according to the manufacturer’s instructions.
| | Sample_hyb_protocol | GeneChip Hybridization, Wash and Stain Kit (Affymetrix) and a Hybridization Oven 640 (Affymetrix) were used for the pre-hybridization step and for hybridizing the target mix to a eukaryotic GeneChip probe array (Affymetrix) according to the manufacturer’s instructions. The washing and staining steps were realised using a Fluidics Station 450 (Affymetrix) operated by the GeneChip Operating Software GCOS (Affymetrix) according to the manufacturer’s instructions.
| | Sample_scan_protocol | The array's scan was realised using a GeneChip Scanner 3000 7G (Affymetrix) operated by the GeneChip Operating Software GCOS(Affymetrix) according to the manufacturer’s instructions.
| | Sample_data_processing | We imported the CEL files into the R software using the BioConductor affy package (Gentleman et al., 2004). The probe intensities were corrected for optical noise, adjusted for non-specific binding and quantile normalized with the gcRMA algorithm (Wu et al., 2004).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean,,Hausser
| | Sample_contact_institute | Biozentrum, Universität Basel
| | Sample_contact_address | Klingelbergstrasse 50/70
| | Sample_contact_city | Basel
| | Sample_contact_zip/postal_code | 4056
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469250/suppl/GSM469250.CEL.gz
| | Sample_series_id | GSE18946
| | Sample_data_row_count | 54675
| | |
|
GSM469251 | GPL570 |
|
EA.hy296_GFP_rep1
|
EA.hy296 cells transduced with the GFP construct
|
cell line: EA.hy296
construct: GFP
|
none
|
| Sample_geo_accession | GSM469251
| | Sample_status | Public on Oct 28 2011
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Oct 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stable expressing cell line for the microarray analysis were generated using the “Virapower” lentiviral transduction system with the vector pLENTI6/V5 (Invitrogen) in which was cloned using Gateway technology (Invitrogen), the ten intronic KSHV miRNAs. The control lentiviral vector pLENTI6/V5-EGFP was a kind gift from Oliver Rossmann. In order to generate lentivirus for transduction of cells with KSHV miRNAs, the ViraPower Lentiviral Gateway Expression System (Invitrogen) was employed according to the manufacturer’s instructions. Two days after transduction, when the EGFP signal in the control cells became visible, Blasticidin (1 μg/ml) was added to the medium to select for the transgene and gradually raised to a final concentration of 7.5 μg/ml for DG75 cells and 3 μg/ml for EA.hy926 cells after six days. Cell lines were used for experiments when 100% of control cells expressed EGFP.
| | Sample_growth_protocol_ch1 | DG-75 were grown in RPMI 1640 medium containing 10 % fetal calf serum (FCS), 100 IU/ml Penicillin, 100 μg/ml Streptomycin and 2 mM L-Glutamine. EA.hy926 were grown in DMEM supplemented with 10% FCS and penicillin/streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Expression 3' Amplification One-Cycle Target Labeling Kit and Control Reagents (Affymetrix) were used for the biotin-labelling of the probes according to the manufacturer’s instructions.
| | Sample_hyb_protocol | GeneChip Hybridization, Wash and Stain Kit (Affymetrix) and a Hybridization Oven 640 (Affymetrix) were used for the pre-hybridization step and for hybridizing the target mix to a eukaryotic GeneChip probe array (Affymetrix) according to the manufacturer’s instructions. The washing and staining steps were realised using a Fluidics Station 450 (Affymetrix) operated by the GeneChip Operating Software GCOS (Affymetrix) according to the manufacturer’s instructions.
| | Sample_scan_protocol | The array's scan was realised using a GeneChip Scanner 3000 7G (Affymetrix) operated by the GeneChip Operating Software GCOS(Affymetrix) according to the manufacturer’s instructions.
| | Sample_data_processing | We imported the CEL files into the R software using the BioConductor affy package (Gentleman et al., 2004). The probe intensities were corrected for optical noise, adjusted for non-specific binding and quantile normalized with the gcRMA algorithm (Wu et al., 2004).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean,,Hausser
| | Sample_contact_institute | Biozentrum, Universität Basel
| | Sample_contact_address | Klingelbergstrasse 50/70
| | Sample_contact_city | Basel
| | Sample_contact_zip/postal_code | 4056
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469251/suppl/GSM469251.CEL.gz
| | Sample_series_id | GSE18946
| | Sample_data_row_count | 54675
| | |
|
GSM469252 | GPL570 |
|
EA.hy296_GFP_rep2
|
EA.hy296 cells transduced with the GFP construct
|
cell line: EA.hy296
construct: GFP
|
none
|
| Sample_geo_accession | GSM469252
| | Sample_status | Public on Oct 28 2011
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Oct 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stable expressing cell line for the microarray analysis were generated using the “Virapower” lentiviral transduction system with the vector pLENTI6/V5 (Invitrogen) in which was cloned using Gateway technology (Invitrogen), the ten intronic KSHV miRNAs. The control lentiviral vector pLENTI6/V5-EGFP was a kind gift from Oliver Rossmann. In order to generate lentivirus for transduction of cells with KSHV miRNAs, the ViraPower Lentiviral Gateway Expression System (Invitrogen) was employed according to the manufacturer’s instructions. Two days after transduction, when the EGFP signal in the control cells became visible, Blasticidin (1 μg/ml) was added to the medium to select for the transgene and gradually raised to a final concentration of 7.5 μg/ml for DG75 cells and 3 μg/ml for EA.hy926 cells after six days. Cell lines were used for experiments when 100% of control cells expressed EGFP.
| | Sample_growth_protocol_ch1 | DG-75 were grown in RPMI 1640 medium containing 10 % fetal calf serum (FCS), 100 IU/ml Penicillin, 100 μg/ml Streptomycin and 2 mM L-Glutamine. EA.hy926 were grown in DMEM supplemented with 10% FCS and penicillin/streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Expression 3' Amplification One-Cycle Target Labeling Kit and Control Reagents (Affymetrix) were used for the biotin-labelling of the probes according to the manufacturer’s instructions.
| | Sample_hyb_protocol | GeneChip Hybridization, Wash and Stain Kit (Affymetrix) and a Hybridization Oven 640 (Affymetrix) were used for the pre-hybridization step and for hybridizing the target mix to a eukaryotic GeneChip probe array (Affymetrix) according to the manufacturer’s instructions. The washing and staining steps were realised using a Fluidics Station 450 (Affymetrix) operated by the GeneChip Operating Software GCOS (Affymetrix) according to the manufacturer’s instructions.
| | Sample_scan_protocol | The array's scan was realised using a GeneChip Scanner 3000 7G (Affymetrix) operated by the GeneChip Operating Software GCOS(Affymetrix) according to the manufacturer’s instructions.
| | Sample_data_processing | We imported the CEL files into the R software using the BioConductor affy package (Gentleman et al., 2004). The probe intensities were corrected for optical noise, adjusted for non-specific binding and quantile normalized with the gcRMA algorithm (Wu et al., 2004).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean,,Hausser
| | Sample_contact_institute | Biozentrum, Universität Basel
| | Sample_contact_address | Klingelbergstrasse 50/70
| | Sample_contact_city | Basel
| | Sample_contact_zip/postal_code | 4056
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469252/suppl/GSM469252.CEL.gz
| | Sample_series_id | GSE18946
| | Sample_data_row_count | 54675
| | |
|
GSM469253 | GPL570 |
|
EA.hy296_GFP_rep3
|
EA.hy296 cells transduced with the GFP construct
|
cell line: EA.hy296
construct: GFP
|
none
|
| Sample_geo_accession | GSM469253
| | Sample_status | Public on Oct 28 2011
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Oct 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stable expressing cell line for the microarray analysis were generated using the “Virapower” lentiviral transduction system with the vector pLENTI6/V5 (Invitrogen) in which was cloned using Gateway technology (Invitrogen), the ten intronic KSHV miRNAs. The control lentiviral vector pLENTI6/V5-EGFP was a kind gift from Oliver Rossmann. In order to generate lentivirus for transduction of cells with KSHV miRNAs, the ViraPower Lentiviral Gateway Expression System (Invitrogen) was employed according to the manufacturer’s instructions. Two days after transduction, when the EGFP signal in the control cells became visible, Blasticidin (1 μg/ml) was added to the medium to select for the transgene and gradually raised to a final concentration of 7.5 μg/ml for DG75 cells and 3 μg/ml for EA.hy926 cells after six days. Cell lines were used for experiments when 100% of control cells expressed EGFP.
| | Sample_growth_protocol_ch1 | DG-75 were grown in RPMI 1640 medium containing 10 % fetal calf serum (FCS), 100 IU/ml Penicillin, 100 μg/ml Streptomycin and 2 mM L-Glutamine. EA.hy926 were grown in DMEM supplemented with 10% FCS and penicillin/streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Expression 3' Amplification One-Cycle Target Labeling Kit and Control Reagents (Affymetrix) were used for the biotin-labelling of the probes according to the manufacturer’s instructions.
| | Sample_hyb_protocol | GeneChip Hybridization, Wash and Stain Kit (Affymetrix) and a Hybridization Oven 640 (Affymetrix) were used for the pre-hybridization step and for hybridizing the target mix to a eukaryotic GeneChip probe array (Affymetrix) according to the manufacturer’s instructions. The washing and staining steps were realised using a Fluidics Station 450 (Affymetrix) operated by the GeneChip Operating Software GCOS (Affymetrix) according to the manufacturer’s instructions.
| | Sample_scan_protocol | The array's scan was realised using a GeneChip Scanner 3000 7G (Affymetrix) operated by the GeneChip Operating Software GCOS(Affymetrix) according to the manufacturer’s instructions.
| | Sample_data_processing | We imported the CEL files into the R software using the BioConductor affy package (Gentleman et al., 2004). The probe intensities were corrected for optical noise, adjusted for non-specific binding and quantile normalized with the gcRMA algorithm (Wu et al., 2004).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean,,Hausser
| | Sample_contact_institute | Biozentrum, Universität Basel
| | Sample_contact_address | Klingelbergstrasse 50/70
| | Sample_contact_city | Basel
| | Sample_contact_zip/postal_code | 4056
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469253/suppl/GSM469253.CEL.gz
| | Sample_series_id | GSE18946
| | Sample_data_row_count | 54675
| | |
|
GSM469254 | GPL570 |
|
EA.hy296_K10_rep1
|
EA.hy296 cells transduced with the K10/12 construct
|
cell line: EA.hy296
construct: K10/12
|
none
|
| Sample_geo_accession | GSM469254
| | Sample_status | Public on Oct 28 2011
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Oct 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stable expressing cell line for the microarray analysis were generated using the “Virapower” lentiviral transduction system with the vector pLENTI6/V5 (Invitrogen) in which was cloned using Gateway technology (Invitrogen), the ten intronic KSHV miRNAs. The control lentiviral vector pLENTI6/V5-EGFP was a kind gift from Oliver Rossmann. In order to generate lentivirus for transduction of cells with KSHV miRNAs, the ViraPower Lentiviral Gateway Expression System (Invitrogen) was employed according to the manufacturer’s instructions. Two days after transduction, when the EGFP signal in the control cells became visible, Blasticidin (1 μg/ml) was added to the medium to select for the transgene and gradually raised to a final concentration of 7.5 μg/ml for DG75 cells and 3 μg/ml for EA.hy926 cells after six days. Cell lines were used for experiments when 100% of control cells expressed EGFP.
| | Sample_growth_protocol_ch1 | DG-75 were grown in RPMI 1640 medium containing 10 % fetal calf serum (FCS), 100 IU/ml Penicillin, 100 μg/ml Streptomycin and 2 mM L-Glutamine. EA.hy926 were grown in DMEM supplemented with 10% FCS and penicillin/streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Expression 3' Amplification One-Cycle Target Labeling Kit and Control Reagents (Affymetrix) were used for the biotin-labelling of the probes according to the manufacturer’s instructions.
| | Sample_hyb_protocol | GeneChip Hybridization, Wash and Stain Kit (Affymetrix) and a Hybridization Oven 640 (Affymetrix) were used for the pre-hybridization step and for hybridizing the target mix to a eukaryotic GeneChip probe array (Affymetrix) according to the manufacturer’s instructions. The washing and staining steps were realised using a Fluidics Station 450 (Affymetrix) operated by the GeneChip Operating Software GCOS (Affymetrix) according to the manufacturer’s instructions.
| | Sample_scan_protocol | The array's scan was realised using a GeneChip Scanner 3000 7G (Affymetrix) operated by the GeneChip Operating Software GCOS(Affymetrix) according to the manufacturer’s instructions.
| | Sample_data_processing | We imported the CEL files into the R software using the BioConductor affy package (Gentleman et al., 2004). The probe intensities were corrected for optical noise, adjusted for non-specific binding and quantile normalized with the gcRMA algorithm (Wu et al., 2004).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean,,Hausser
| | Sample_contact_institute | Biozentrum, Universität Basel
| | Sample_contact_address | Klingelbergstrasse 50/70
| | Sample_contact_city | Basel
| | Sample_contact_zip/postal_code | 4056
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469254/suppl/GSM469254.CEL.gz
| | Sample_series_id | GSE18946
| | Sample_data_row_count | 54675
| | |
|
GSM469255 | GPL570 |
|
EA.hy296_K10_rep2
|
EA.hy296 cells transduced with the K10/12 construct
|
cell line: EA.hy296
construct: K10/12
|
none
|
| Sample_geo_accession | GSM469255
| | Sample_status | Public on Oct 28 2011
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Oct 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stable expressing cell line for the microarray analysis were generated using the “Virapower” lentiviral transduction system with the vector pLENTI6/V5 (Invitrogen) in which was cloned using Gateway technology (Invitrogen), the ten intronic KSHV miRNAs. The control lentiviral vector pLENTI6/V5-EGFP was a kind gift from Oliver Rossmann. In order to generate lentivirus for transduction of cells with KSHV miRNAs, the ViraPower Lentiviral Gateway Expression System (Invitrogen) was employed according to the manufacturer’s instructions. Two days after transduction, when the EGFP signal in the control cells became visible, Blasticidin (1 μg/ml) was added to the medium to select for the transgene and gradually raised to a final concentration of 7.5 μg/ml for DG75 cells and 3 μg/ml for EA.hy926 cells after six days. Cell lines were used for experiments when 100% of control cells expressed EGFP.
| | Sample_growth_protocol_ch1 | DG-75 were grown in RPMI 1640 medium containing 10 % fetal calf serum (FCS), 100 IU/ml Penicillin, 100 μg/ml Streptomycin and 2 mM L-Glutamine. EA.hy926 were grown in DMEM supplemented with 10% FCS and penicillin/streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Expression 3' Amplification One-Cycle Target Labeling Kit and Control Reagents (Affymetrix) were used for the biotin-labelling of the probes according to the manufacturer’s instructions.
| | Sample_hyb_protocol | GeneChip Hybridization, Wash and Stain Kit (Affymetrix) and a Hybridization Oven 640 (Affymetrix) were used for the pre-hybridization step and for hybridizing the target mix to a eukaryotic GeneChip probe array (Affymetrix) according to the manufacturer’s instructions. The washing and staining steps were realised using a Fluidics Station 450 (Affymetrix) operated by the GeneChip Operating Software GCOS (Affymetrix) according to the manufacturer’s instructions.
| | Sample_scan_protocol | The array's scan was realised using a GeneChip Scanner 3000 7G (Affymetrix) operated by the GeneChip Operating Software GCOS(Affymetrix) according to the manufacturer’s instructions.
| | Sample_data_processing | We imported the CEL files into the R software using the BioConductor affy package (Gentleman et al., 2004). The probe intensities were corrected for optical noise, adjusted for non-specific binding and quantile normalized with the gcRMA algorithm (Wu et al., 2004).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean,,Hausser
| | Sample_contact_institute | Biozentrum, Universität Basel
| | Sample_contact_address | Klingelbergstrasse 50/70
| | Sample_contact_city | Basel
| | Sample_contact_zip/postal_code | 4056
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469255/suppl/GSM469255.CEL.gz
| | Sample_series_id | GSE18946
| | Sample_data_row_count | 54675
| | |
|
GSM469256 | GPL570 |
|
EA.hy296_K10_rep3
|
EA.hy296 cells transduced with the K10/12 construct
|
cell line: EA.hy296
construct: K10/12
|
none
|
| Sample_geo_accession | GSM469256
| | Sample_status | Public on Oct 28 2011
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Oct 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stable expressing cell line for the microarray analysis were generated using the “Virapower” lentiviral transduction system with the vector pLENTI6/V5 (Invitrogen) in which was cloned using Gateway technology (Invitrogen), the ten intronic KSHV miRNAs. The control lentiviral vector pLENTI6/V5-EGFP was a kind gift from Oliver Rossmann. In order to generate lentivirus for transduction of cells with KSHV miRNAs, the ViraPower Lentiviral Gateway Expression System (Invitrogen) was employed according to the manufacturer’s instructions. Two days after transduction, when the EGFP signal in the control cells became visible, Blasticidin (1 μg/ml) was added to the medium to select for the transgene and gradually raised to a final concentration of 7.5 μg/ml for DG75 cells and 3 μg/ml for EA.hy926 cells after six days. Cell lines were used for experiments when 100% of control cells expressed EGFP.
| | Sample_growth_protocol_ch1 | DG-75 were grown in RPMI 1640 medium containing 10 % fetal calf serum (FCS), 100 IU/ml Penicillin, 100 μg/ml Streptomycin and 2 mM L-Glutamine. EA.hy926 were grown in DMEM supplemented with 10% FCS and penicillin/streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Expression 3' Amplification One-Cycle Target Labeling Kit and Control Reagents (Affymetrix) were used for the biotin-labelling of the probes according to the manufacturer’s instructions.
| | Sample_hyb_protocol | GeneChip Hybridization, Wash and Stain Kit (Affymetrix) and a Hybridization Oven 640 (Affymetrix) were used for the pre-hybridization step and for hybridizing the target mix to a eukaryotic GeneChip probe array (Affymetrix) according to the manufacturer’s instructions. The washing and staining steps were realised using a Fluidics Station 450 (Affymetrix) operated by the GeneChip Operating Software GCOS (Affymetrix) according to the manufacturer’s instructions.
| | Sample_scan_protocol | The array's scan was realised using a GeneChip Scanner 3000 7G (Affymetrix) operated by the GeneChip Operating Software GCOS(Affymetrix) according to the manufacturer’s instructions.
| | Sample_data_processing | We imported the CEL files into the R software using the BioConductor affy package (Gentleman et al., 2004). The probe intensities were corrected for optical noise, adjusted for non-specific binding and quantile normalized with the gcRMA algorithm (Wu et al., 2004).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean,,Hausser
| | Sample_contact_institute | Biozentrum, Universität Basel
| | Sample_contact_address | Klingelbergstrasse 50/70
| | Sample_contact_city | Basel
| | Sample_contact_zip/postal_code | 4056
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469256/suppl/GSM469256.CEL.gz
| | Sample_series_id | GSE18946
| | Sample_data_row_count | 54675
| | |
|
GSM469257 | GPL570 |
|
EA.hy296_K12_rep1
|
EA.hy296 cells transduced with the K12/12 construct
|
cell line: EA.hy296
construct: K12/12
|
none
|
| Sample_geo_accession | GSM469257
| | Sample_status | Public on Oct 28 2011
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Oct 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stable expressing cell line for the microarray analysis were generated using the “Virapower” lentiviral transduction system with the vector pLENTI6/V5 (Invitrogen) in which was cloned using Gateway technology (Invitrogen), the ten intronic KSHV miRNAs. The control lentiviral vector pLENTI6/V5-EGFP was a kind gift from Oliver Rossmann. In order to generate lentivirus for transduction of cells with KSHV miRNAs, the ViraPower Lentiviral Gateway Expression System (Invitrogen) was employed according to the manufacturer’s instructions. Two days after transduction, when the EGFP signal in the control cells became visible, Blasticidin (1 μg/ml) was added to the medium to select for the transgene and gradually raised to a final concentration of 7.5 μg/ml for DG75 cells and 3 μg/ml for EA.hy926 cells after six days. Cell lines were used for experiments when 100% of control cells expressed EGFP.
| | Sample_growth_protocol_ch1 | DG-75 were grown in RPMI 1640 medium containing 10 % fetal calf serum (FCS), 100 IU/ml Penicillin, 100 μg/ml Streptomycin and 2 mM L-Glutamine. EA.hy926 were grown in DMEM supplemented with 10% FCS and penicillin/streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Expression 3' Amplification One-Cycle Target Labeling Kit and Control Reagents (Affymetrix) were used for the biotin-labelling of the probes according to the manufacturer’s instructions.
| | Sample_hyb_protocol | GeneChip Hybridization, Wash and Stain Kit (Affymetrix) and a Hybridization Oven 640 (Affymetrix) were used for the pre-hybridization step and for hybridizing the target mix to a eukaryotic GeneChip probe array (Affymetrix) according to the manufacturer’s instructions. The washing and staining steps were realised using a Fluidics Station 450 (Affymetrix) operated by the GeneChip Operating Software GCOS (Affymetrix) according to the manufacturer’s instructions.
| | Sample_scan_protocol | The array's scan was realised using a GeneChip Scanner 3000 7G (Affymetrix) operated by the GeneChip Operating Software GCOS(Affymetrix) according to the manufacturer’s instructions.
| | Sample_data_processing | We imported the CEL files into the R software using the BioConductor affy package (Gentleman et al., 2004). The probe intensities were corrected for optical noise, adjusted for non-specific binding and quantile normalized with the gcRMA algorithm (Wu et al., 2004).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean,,Hausser
| | Sample_contact_institute | Biozentrum, Universität Basel
| | Sample_contact_address | Klingelbergstrasse 50/70
| | Sample_contact_city | Basel
| | Sample_contact_zip/postal_code | 4056
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469257/suppl/GSM469257.CEL.gz
| | Sample_series_id | GSE18946
| | Sample_data_row_count | 54675
| | |
|
GSM469258 | GPL570 |
|
EA.hy296_K12_rep2
|
EA.hy296 cells transduced with the K12/12 construct
|
cell line: EA.hy296
construct: K12/12
|
none
|
| Sample_geo_accession | GSM469258
| | Sample_status | Public on Oct 28 2011
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Oct 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stable expressing cell line for the microarray analysis were generated using the “Virapower” lentiviral transduction system with the vector pLENTI6/V5 (Invitrogen) in which was cloned using Gateway technology (Invitrogen), the ten intronic KSHV miRNAs. The control lentiviral vector pLENTI6/V5-EGFP was a kind gift from Oliver Rossmann. In order to generate lentivirus for transduction of cells with KSHV miRNAs, the ViraPower Lentiviral Gateway Expression System (Invitrogen) was employed according to the manufacturer’s instructions. Two days after transduction, when the EGFP signal in the control cells became visible, Blasticidin (1 μg/ml) was added to the medium to select for the transgene and gradually raised to a final concentration of 7.5 μg/ml for DG75 cells and 3 μg/ml for EA.hy926 cells after six days. Cell lines were used for experiments when 100% of control cells expressed EGFP.
| | Sample_growth_protocol_ch1 | DG-75 were grown in RPMI 1640 medium containing 10 % fetal calf serum (FCS), 100 IU/ml Penicillin, 100 μg/ml Streptomycin and 2 mM L-Glutamine. EA.hy926 were grown in DMEM supplemented with 10% FCS and penicillin/streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Expression 3' Amplification One-Cycle Target Labeling Kit and Control Reagents (Affymetrix) were used for the biotin-labelling of the probes according to the manufacturer’s instructions.
| | Sample_hyb_protocol | GeneChip Hybridization, Wash and Stain Kit (Affymetrix) and a Hybridization Oven 640 (Affymetrix) were used for the pre-hybridization step and for hybridizing the target mix to a eukaryotic GeneChip probe array (Affymetrix) according to the manufacturer’s instructions. The washing and staining steps were realised using a Fluidics Station 450 (Affymetrix) operated by the GeneChip Operating Software GCOS (Affymetrix) according to the manufacturer’s instructions.
| | Sample_scan_protocol | The array's scan was realised using a GeneChip Scanner 3000 7G (Affymetrix) operated by the GeneChip Operating Software GCOS(Affymetrix) according to the manufacturer’s instructions.
| | Sample_data_processing | We imported the CEL files into the R software using the BioConductor affy package (Gentleman et al., 2004). The probe intensities were corrected for optical noise, adjusted for non-specific binding and quantile normalized with the gcRMA algorithm (Wu et al., 2004).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean,,Hausser
| | Sample_contact_institute | Biozentrum, Universität Basel
| | Sample_contact_address | Klingelbergstrasse 50/70
| | Sample_contact_city | Basel
| | Sample_contact_zip/postal_code | 4056
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469258/suppl/GSM469258.CEL.gz
| | Sample_series_id | GSE18946
| | Sample_data_row_count | 54675
| | |
|
GSM469259 | GPL570 |
|
EA.hy296_K12_rep3
|
EA.hy296 cells transduced with the K12/12 construct
|
cell line: EA.hy296
construct: K12/12
|
none
|
| Sample_geo_accession | GSM469259
| | Sample_status | Public on Oct 28 2011
| | Sample_submission_date | Nov 09 2009
| | Sample_last_update_date | Oct 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Stable expressing cell line for the microarray analysis were generated using the “Virapower” lentiviral transduction system with the vector pLENTI6/V5 (Invitrogen) in which was cloned using Gateway technology (Invitrogen), the ten intronic KSHV miRNAs. The control lentiviral vector pLENTI6/V5-EGFP was a kind gift from Oliver Rossmann. In order to generate lentivirus for transduction of cells with KSHV miRNAs, the ViraPower Lentiviral Gateway Expression System (Invitrogen) was employed according to the manufacturer’s instructions. Two days after transduction, when the EGFP signal in the control cells became visible, Blasticidin (1 μg/ml) was added to the medium to select for the transgene and gradually raised to a final concentration of 7.5 μg/ml for DG75 cells and 3 μg/ml for EA.hy926 cells after six days. Cell lines were used for experiments when 100% of control cells expressed EGFP.
| | Sample_growth_protocol_ch1 | DG-75 were grown in RPMI 1640 medium containing 10 % fetal calf serum (FCS), 100 IU/ml Penicillin, 100 μg/ml Streptomycin and 2 mM L-Glutamine. EA.hy926 were grown in DMEM supplemented with 10% FCS and penicillin/streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Expression 3' Amplification One-Cycle Target Labeling Kit and Control Reagents (Affymetrix) were used for the biotin-labelling of the probes according to the manufacturer’s instructions.
| | Sample_hyb_protocol | GeneChip Hybridization, Wash and Stain Kit (Affymetrix) and a Hybridization Oven 640 (Affymetrix) were used for the pre-hybridization step and for hybridizing the target mix to a eukaryotic GeneChip probe array (Affymetrix) according to the manufacturer’s instructions. The washing and staining steps were realised using a Fluidics Station 450 (Affymetrix) operated by the GeneChip Operating Software GCOS (Affymetrix) according to the manufacturer’s instructions.
| | Sample_scan_protocol | The array's scan was realised using a GeneChip Scanner 3000 7G (Affymetrix) operated by the GeneChip Operating Software GCOS(Affymetrix) according to the manufacturer’s instructions.
| | Sample_data_processing | We imported the CEL files into the R software using the BioConductor affy package (Gentleman et al., 2004). The probe intensities were corrected for optical noise, adjusted for non-specific binding and quantile normalized with the gcRMA algorithm (Wu et al., 2004).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jean,,Hausser
| | Sample_contact_institute | Biozentrum, Universität Basel
| | Sample_contact_address | Klingelbergstrasse 50/70
| | Sample_contact_city | Basel
| | Sample_contact_zip/postal_code | 4056
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM469nnn/GSM469259/suppl/GSM469259.CEL.gz
| | Sample_series_id | GSE18946
| | Sample_data_row_count | 54675
| | |
|
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