Search results for the GEO ID: GSE42174  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1034123 | GPL570 |
|
RL control REP1
|
DLBCL cell line RL stably transfected with a tetracycline-inducible LITAF expression vector, absence of doxycycline
|
cell line: RL
cell type: diffuse large B-cell lymphoma (DLBCL) cells stably transfected with a tetracycline-inducible LITAF expression vector
treatment: none
|
RL_LITAF_CTRL_R1
Gene expression data from a DLBCL cell line.
|
| Sample_geo_accession | GSM1034123
| | Sample_status | Public on Nov 10 2012
| | Sample_submission_date | Nov 08 2012
| | Sample_last_update_date | Nov 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Absence or presence of 4 mg/ml doxycycline for LITAF over-expression. Nucleofection (AMAXA) with Silencer Select Negative Control No. 1 (AM4611, Invitrogen) or a LITAF-specific siRNA (s18252, Invitrogen) for silencing. RNA was extracted 48h after the treatment.
| | Sample_growth_protocol_ch1 | Cell lines were grown at 37ºC and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The cDNA was prepared from 2 microg total RNA using the One-Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2.0 chip according to the protocols provided by the manufacturer.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
| | Sample_data_processing | Data were normalized with Bioconductor software using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raquel,,Malumbres
| | Sample_contact_email | rmalumbres@yahoo.com
| | Sample_contact_phone | +34 948194700
| | Sample_contact_laboratory | Molecular Oncology
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Navarra/ Center for Applied Medical Research
| | Sample_contact_address | Avenida Pio XII 55
| | Sample_contact_city | Pamplona
| | Sample_contact_state | Navarra
| | Sample_contact_zip/postal_code | 31008
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1034nnn/GSM1034123/suppl/GSM1034123_RL_LITAF_CTRL_R1.CEL.gz
| | Sample_series_id | GSE42174
| | Sample_series_id | GSE42204
| | Sample_data_row_count | 54675
| | |
|
GSM1034124 | GPL570 |
|
RL control REP2
|
DLBCL cell line RL stably transfected with a tetracycline-inducible LITAF expression vector, absence of doxycycline
|
cell line: RL
cell type: diffuse large B-cell lymphoma (DLBCL) cells stably transfected with a tetracycline-inducible LITAF expression vector
treatment: none
|
RL_LITAF_CTRL_R2
Gene expression data from a DLBCL cell line.
|
| Sample_geo_accession | GSM1034124
| | Sample_status | Public on Nov 10 2012
| | Sample_submission_date | Nov 08 2012
| | Sample_last_update_date | Nov 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Absence or presence of 4 mg/ml doxycycline for LITAF over-expression. Nucleofection (AMAXA) with Silencer Select Negative Control No. 1 (AM4611, Invitrogen) or a LITAF-specific siRNA (s18252, Invitrogen) for silencing. RNA was extracted 48h after the treatment.
| | Sample_growth_protocol_ch1 | Cell lines were grown at 37ºC and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The cDNA was prepared from 2 microg total RNA using the One-Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2.0 chip according to the protocols provided by the manufacturer.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
| | Sample_data_processing | Data were normalized with Bioconductor software using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raquel,,Malumbres
| | Sample_contact_email | rmalumbres@yahoo.com
| | Sample_contact_phone | +34 948194700
| | Sample_contact_laboratory | Molecular Oncology
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Navarra/ Center for Applied Medical Research
| | Sample_contact_address | Avenida Pio XII 55
| | Sample_contact_city | Pamplona
| | Sample_contact_state | Navarra
| | Sample_contact_zip/postal_code | 31008
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1034nnn/GSM1034124/suppl/GSM1034124_RL_LITAF_CTRL_R2.CEL.gz
| | Sample_series_id | GSE42174
| | Sample_series_id | GSE42204
| | Sample_data_row_count | 54675
| | |
|
GSM1034125 | GPL570 |
|
RL with doxycycline-induced LITAF expression REP1
|
DLBCL cell line RL stably transfected with a tetracycline-inducible LITAF expression vector, presence of doxycycline
|
cell line: RL
cell type: diffuse large B-cell lymphoma (DLBCL) cells stably transfected with a tetracycline-inducible LITAF expression vector
treatment: doxycycline
|
RL_LITAF_DOX_R1
Gene expression data from a DLBCL cell line.
|
| Sample_geo_accession | GSM1034125
| | Sample_status | Public on Nov 10 2012
| | Sample_submission_date | Nov 08 2012
| | Sample_last_update_date | Nov 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Absence or presence of 4 mg/ml doxycycline for LITAF over-expression. Nucleofection (AMAXA) with Silencer Select Negative Control No. 1 (AM4611, Invitrogen) or a LITAF-specific siRNA (s18252, Invitrogen) for silencing. RNA was extracted 48h after the treatment.
| | Sample_growth_protocol_ch1 | Cell lines were grown at 37ºC and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The cDNA was prepared from 2 microg total RNA using the One-Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2.0 chip according to the protocols provided by the manufacturer.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
| | Sample_data_processing | Data were normalized with Bioconductor software using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raquel,,Malumbres
| | Sample_contact_email | rmalumbres@yahoo.com
| | Sample_contact_phone | +34 948194700
| | Sample_contact_laboratory | Molecular Oncology
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Navarra/ Center for Applied Medical Research
| | Sample_contact_address | Avenida Pio XII 55
| | Sample_contact_city | Pamplona
| | Sample_contact_state | Navarra
| | Sample_contact_zip/postal_code | 31008
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1034nnn/GSM1034125/suppl/GSM1034125_RL_LITAF_DOX_R1.CEL.gz
| | Sample_series_id | GSE42174
| | Sample_series_id | GSE42204
| | Sample_data_row_count | 54675
| | |
|
GSM1034126 | GPL570 |
|
RL with doxycycline-induced LITAF expression REP2
|
DLBCL cell line RL stably transfected with a tetracycline-inducible LITAF expression vector, presence of doxycycline
|
cell line: RL
cell type: diffuse large B-cell lymphoma (DLBCL) cells stably transfected with a tetracycline-inducible LITAF expression vector
treatment: doxycycline
|
RL_LITAF_DOX_R2
Gene expression data from a DLBCL cell line.
|
| Sample_geo_accession | GSM1034126
| | Sample_status | Public on Nov 10 2012
| | Sample_submission_date | Nov 08 2012
| | Sample_last_update_date | Nov 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Absence or presence of 4 mg/ml doxycycline for LITAF over-expression. Nucleofection (AMAXA) with Silencer Select Negative Control No. 1 (AM4611, Invitrogen) or a LITAF-specific siRNA (s18252, Invitrogen) for silencing. RNA was extracted 48h after the treatment.
| | Sample_growth_protocol_ch1 | Cell lines were grown at 37ºC and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The cDNA was prepared from 2 microg total RNA using the One-Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2.0 chip according to the protocols provided by the manufacturer.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
| | Sample_data_processing | Data were normalized with Bioconductor software using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raquel,,Malumbres
| | Sample_contact_email | rmalumbres@yahoo.com
| | Sample_contact_phone | +34 948194700
| | Sample_contact_laboratory | Molecular Oncology
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Navarra/ Center for Applied Medical Research
| | Sample_contact_address | Avenida Pio XII 55
| | Sample_contact_city | Pamplona
| | Sample_contact_state | Navarra
| | Sample_contact_zip/postal_code | 31008
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1034nnn/GSM1034126/suppl/GSM1034126_RL_LITAF_DOX_R2.CEL.gz
| | Sample_series_id | GSE42174
| | Sample_series_id | GSE42204
| | Sample_data_row_count | 54675
| | |
|
GSM1034127 | GPL570 |
|
SC-1 control REP1
|
DLBCL cell line SC-1 stably transfected with a tetracycline-inducible LITAF expression vector, absence of doxycycline
|
cell line: SC-1
cell type: diffuse large B-cell lymphoma (DLBCL) cells stably transfected with a tetracycline-inducible LITAF expression vector
treatment: none
|
SC1_LITAF_CTRL_R1
Gene expression data from a DLBCL cell line.
|
| Sample_geo_accession | GSM1034127
| | Sample_status | Public on Nov 10 2012
| | Sample_submission_date | Nov 08 2012
| | Sample_last_update_date | Nov 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Absence or presence of 4 mg/ml doxycycline for LITAF over-expression. Nucleofection (AMAXA) with Silencer Select Negative Control No. 1 (AM4611, Invitrogen) or a LITAF-specific siRNA (s18252, Invitrogen) for silencing. RNA was extracted 48h after the treatment.
| | Sample_growth_protocol_ch1 | Cell lines were grown at 37ºC and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The cDNA was prepared from 2 microg total RNA using the One-Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2.0 chip according to the protocols provided by the manufacturer.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
| | Sample_data_processing | Data were normalized with Bioconductor software using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raquel,,Malumbres
| | Sample_contact_email | rmalumbres@yahoo.com
| | Sample_contact_phone | +34 948194700
| | Sample_contact_laboratory | Molecular Oncology
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Navarra/ Center for Applied Medical Research
| | Sample_contact_address | Avenida Pio XII 55
| | Sample_contact_city | Pamplona
| | Sample_contact_state | Navarra
| | Sample_contact_zip/postal_code | 31008
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1034nnn/GSM1034127/suppl/GSM1034127_SC_1_LITAF_CTRL_R1.CEL.gz
| | Sample_series_id | GSE42174
| | Sample_series_id | GSE42204
| | Sample_data_row_count | 54675
| | |
|
GSM1034128 | GPL570 |
|
SC-1 control REP2
|
DLBCL cell line SC-1 stably transfected with a tetracycline-inducible LITAF expression vector, absence of doxycycline
|
cell line: SC-1
cell type: diffuse large B-cell lymphoma (DLBCL) cells stably transfected with a tetracycline-inducible LITAF expression vector
treatment: none
|
SC1_LITAF_CTRL_R2
Gene expression data from a DLBCL cell line.
|
| Sample_geo_accession | GSM1034128
| | Sample_status | Public on Nov 10 2012
| | Sample_submission_date | Nov 08 2012
| | Sample_last_update_date | Nov 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Absence or presence of 4 mg/ml doxycycline for LITAF over-expression. Nucleofection (AMAXA) with Silencer Select Negative Control No. 1 (AM4611, Invitrogen) or a LITAF-specific siRNA (s18252, Invitrogen) for silencing. RNA was extracted 48h after the treatment.
| | Sample_growth_protocol_ch1 | Cell lines were grown at 37ºC and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The cDNA was prepared from 2 microg total RNA using the One-Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2.0 chip according to the protocols provided by the manufacturer.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
| | Sample_data_processing | Data were normalized with Bioconductor software using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raquel,,Malumbres
| | Sample_contact_email | rmalumbres@yahoo.com
| | Sample_contact_phone | +34 948194700
| | Sample_contact_laboratory | Molecular Oncology
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Navarra/ Center for Applied Medical Research
| | Sample_contact_address | Avenida Pio XII 55
| | Sample_contact_city | Pamplona
| | Sample_contact_state | Navarra
| | Sample_contact_zip/postal_code | 31008
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1034nnn/GSM1034128/suppl/GSM1034128_SC_1_LITAF_CTRL_R2.CEL.gz
| | Sample_series_id | GSE42174
| | Sample_series_id | GSE42204
| | Sample_data_row_count | 54675
| | |
|
GSM1034129 | GPL570 |
|
SC-1 with doxycycline-induced LITAF expression REP1
|
DLBCL cell line SC-1 stably transfected with a tetracycline-inducible LITAF expression vector, presence of doxycycline
|
cell line: SC-1
cell type: diffuse large B-cell lymphoma (DLBCL) cells stably transfected with a tetracycline-inducible LITAF expression vector
treatment: doxycycline
|
SC1_LITAF_DOX_R1
Gene expression data from a DLBCL cell line.
|
| Sample_geo_accession | GSM1034129
| | Sample_status | Public on Nov 10 2012
| | Sample_submission_date | Nov 08 2012
| | Sample_last_update_date | Nov 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Absence or presence of 4 mg/ml doxycycline for LITAF over-expression. Nucleofection (AMAXA) with Silencer Select Negative Control No. 1 (AM4611, Invitrogen) or a LITAF-specific siRNA (s18252, Invitrogen) for silencing. RNA was extracted 48h after the treatment.
| | Sample_growth_protocol_ch1 | Cell lines were grown at 37ºC and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The cDNA was prepared from 2 microg total RNA using the One-Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2.0 chip according to the protocols provided by the manufacturer.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
| | Sample_data_processing | Data were normalized with Bioconductor software using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raquel,,Malumbres
| | Sample_contact_email | rmalumbres@yahoo.com
| | Sample_contact_phone | +34 948194700
| | Sample_contact_laboratory | Molecular Oncology
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Navarra/ Center for Applied Medical Research
| | Sample_contact_address | Avenida Pio XII 55
| | Sample_contact_city | Pamplona
| | Sample_contact_state | Navarra
| | Sample_contact_zip/postal_code | 31008
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1034nnn/GSM1034129/suppl/GSM1034129_SC_1_LITAF_DOX_R1.CEL.gz
| | Sample_series_id | GSE42174
| | Sample_series_id | GSE42204
| | Sample_data_row_count | 54675
| | |
|
GSM1034130 | GPL570 |
|
SC-1 with doxycycline-induced LITAF expression REP2
|
DLBCL cell line SC-1 stably transfected with a tetracycline-inducible LITAF expression vector, presence of doxycycline
|
cell line: SC-1
cell type: diffuse large B-cell lymphoma (DLBCL) cells stably transfected with a tetracycline-inducible LITAF expression vector
treatment: doxycycline
|
SC1_LITAF_DOX_R2
Gene expression data from a DLBCL cell line.
|
| Sample_geo_accession | GSM1034130
| | Sample_status | Public on Nov 10 2012
| | Sample_submission_date | Nov 08 2012
| | Sample_last_update_date | Nov 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Absence or presence of 4 mg/ml doxycycline for LITAF over-expression. Nucleofection (AMAXA) with Silencer Select Negative Control No. 1 (AM4611, Invitrogen) or a LITAF-specific siRNA (s18252, Invitrogen) for silencing. RNA was extracted 48h after the treatment.
| | Sample_growth_protocol_ch1 | Cell lines were grown at 37ºC and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The cDNA was prepared from 2 microg total RNA using the One-Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2.0 chip according to the protocols provided by the manufacturer.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
| | Sample_data_processing | Data were normalized with Bioconductor software using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raquel,,Malumbres
| | Sample_contact_email | rmalumbres@yahoo.com
| | Sample_contact_phone | +34 948194700
| | Sample_contact_laboratory | Molecular Oncology
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Navarra/ Center for Applied Medical Research
| | Sample_contact_address | Avenida Pio XII 55
| | Sample_contact_city | Pamplona
| | Sample_contact_state | Navarra
| | Sample_contact_zip/postal_code | 31008
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1034nnn/GSM1034130/suppl/GSM1034130_SC_1_LITAF_DOX_R2.CEL.gz
| | Sample_series_id | GSE42174
| | Sample_series_id | GSE42204
| | Sample_data_row_count | 54675
| | |
|
GSM1034131 | GPL570 |
|
KARPAS-231, non-targeting siRNA, REP1
|
DLBCL cell line KARPAS-231 transfected with a non-targeting siRNA
|
cell line: KARPAS-231
cell type: diffuse large B-cell lymphoma (DLBCL) cells
treatment: non-targeting siRNA
|
KARPAS-231_SC_R1
Gene expression data from a DLBCL cell line.
|
| Sample_geo_accession | GSM1034131
| | Sample_status | Public on Nov 10 2012
| | Sample_submission_date | Nov 08 2012
| | Sample_last_update_date | Nov 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Absence or presence of 4 mg/ml doxycycline for LITAF over-expression. Nucleofection (AMAXA) with Silencer Select Negative Control No. 1 (AM4611, Invitrogen) or a LITAF-specific siRNA (s18252, Invitrogen) for silencing. RNA was extracted 48h after the treatment.
| | Sample_growth_protocol_ch1 | Cell lines were grown at 37ºC and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The cDNA was prepared from 2 microg total RNA using the One-Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2.0 chip according to the protocols provided by the manufacturer.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
| | Sample_data_processing | Data were normalized with Bioconductor software using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raquel,,Malumbres
| | Sample_contact_email | rmalumbres@yahoo.com
| | Sample_contact_phone | +34 948194700
| | Sample_contact_laboratory | Molecular Oncology
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Navarra/ Center for Applied Medical Research
| | Sample_contact_address | Avenida Pio XII 55
| | Sample_contact_city | Pamplona
| | Sample_contact_state | Navarra
| | Sample_contact_zip/postal_code | 31008
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1034nnn/GSM1034131/suppl/GSM1034131_K231_SC_R1.CEL.gz
| | Sample_series_id | GSE42174
| | Sample_series_id | GSE42204
| | Sample_data_row_count | 54675
| | |
|
GSM1034132 | GPL570 |
|
KARPAS-231, non-targeting siRNA, REP2
|
DLBCL cell line KARPAS-231 transfected with a non-targeting siRNA
|
cell line: KARPAS-231
cell type: diffuse large B-cell lymphoma (DLBCL) cells
treatment: non-targeting siRNA
|
KARPAS-231_SC_R2
Gene expression data from a DLBCL cell line.
|
| Sample_geo_accession | GSM1034132
| | Sample_status | Public on Nov 10 2012
| | Sample_submission_date | Nov 08 2012
| | Sample_last_update_date | Nov 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Absence or presence of 4 mg/ml doxycycline for LITAF over-expression. Nucleofection (AMAXA) with Silencer Select Negative Control No. 1 (AM4611, Invitrogen) or a LITAF-specific siRNA (s18252, Invitrogen) for silencing. RNA was extracted 48h after the treatment.
| | Sample_growth_protocol_ch1 | Cell lines were grown at 37ºC and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The cDNA was prepared from 2 microg total RNA using the One-Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2.0 chip according to the protocols provided by the manufacturer.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
| | Sample_data_processing | Data were normalized with Bioconductor software using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raquel,,Malumbres
| | Sample_contact_email | rmalumbres@yahoo.com
| | Sample_contact_phone | +34 948194700
| | Sample_contact_laboratory | Molecular Oncology
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Navarra/ Center for Applied Medical Research
| | Sample_contact_address | Avenida Pio XII 55
| | Sample_contact_city | Pamplona
| | Sample_contact_state | Navarra
| | Sample_contact_zip/postal_code | 31008
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1034nnn/GSM1034132/suppl/GSM1034132_K231_SC_R2.CEL.gz
| | Sample_series_id | GSE42174
| | Sample_series_id | GSE42204
| | Sample_data_row_count | 54675
| | |
|
GSM1034133 | GPL570 |
|
KARPAS-231, non-targeting siRNA, REP3
|
DLBCL cell line KARPAS-231 transfected with a non-targeting siRNA
|
cell line: KARPAS-231
cell type: diffuse large B-cell lymphoma (DLBCL) cells
treatment: non-targeting siRNA
|
KARPAS-231_SC_R3
Gene expression data from a DLBCL cell line.
|
| Sample_geo_accession | GSM1034133
| | Sample_status | Public on Nov 10 2012
| | Sample_submission_date | Nov 08 2012
| | Sample_last_update_date | Nov 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Absence or presence of 4 mg/ml doxycycline for LITAF over-expression. Nucleofection (AMAXA) with Silencer Select Negative Control No. 1 (AM4611, Invitrogen) or a LITAF-specific siRNA (s18252, Invitrogen) for silencing. RNA was extracted 48h after the treatment.
| | Sample_growth_protocol_ch1 | Cell lines were grown at 37ºC and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The cDNA was prepared from 2 microg total RNA using the One-Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2.0 chip according to the protocols provided by the manufacturer.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
| | Sample_data_processing | Data were normalized with Bioconductor software using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raquel,,Malumbres
| | Sample_contact_email | rmalumbres@yahoo.com
| | Sample_contact_phone | +34 948194700
| | Sample_contact_laboratory | Molecular Oncology
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Navarra/ Center for Applied Medical Research
| | Sample_contact_address | Avenida Pio XII 55
| | Sample_contact_city | Pamplona
| | Sample_contact_state | Navarra
| | Sample_contact_zip/postal_code | 31008
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1034nnn/GSM1034133/suppl/GSM1034133_K231_SC_R3.CEL.gz
| | Sample_series_id | GSE42174
| | Sample_series_id | GSE42204
| | Sample_data_row_count | 54675
| | |
|
GSM1034134 | GPL570 |
|
KARPAS-231, LITAF-specific siRNA, REP1
|
DLBCL cell line KARPAS-231 transfected with a LITAF-specific siRNA
|
cell line: KARPAS-231
cell type: diffuse large B-cell lymphoma (DLBCL) cells
treatment: LITAF-specific siRNA
|
KARPAS-231_siRNA_R1
Gene expression data from a DLBCL cell line.
|
| Sample_geo_accession | GSM1034134
| | Sample_status | Public on Nov 10 2012
| | Sample_submission_date | Nov 08 2012
| | Sample_last_update_date | Nov 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Absence or presence of 4 mg/ml doxycycline for LITAF over-expression. Nucleofection (AMAXA) with Silencer Select Negative Control No. 1 (AM4611, Invitrogen) or a LITAF-specific siRNA (s18252, Invitrogen) for silencing. RNA was extracted 48h after the treatment.
| | Sample_growth_protocol_ch1 | Cell lines were grown at 37ºC and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The cDNA was prepared from 2 microg total RNA using the One-Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2.0 chip according to the protocols provided by the manufacturer.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
| | Sample_data_processing | Data were normalized with Bioconductor software using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raquel,,Malumbres
| | Sample_contact_email | rmalumbres@yahoo.com
| | Sample_contact_phone | +34 948194700
| | Sample_contact_laboratory | Molecular Oncology
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Navarra/ Center for Applied Medical Research
| | Sample_contact_address | Avenida Pio XII 55
| | Sample_contact_city | Pamplona
| | Sample_contact_state | Navarra
| | Sample_contact_zip/postal_code | 31008
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1034nnn/GSM1034134/suppl/GSM1034134_K231_siRNA_R1.CEL.gz
| | Sample_series_id | GSE42174
| | Sample_series_id | GSE42204
| | Sample_data_row_count | 54675
| | |
|
GSM1034135 | GPL570 |
|
KARPAS-231, LITAF-specific siRNA, REP2
|
DLBCL cell line KARPAS-231 transfected with a LITAF-specific siRNA
|
cell line: KARPAS-231
cell type: diffuse large B-cell lymphoma (DLBCL) cells
treatment: LITAF-specific siRNA
|
KARPAS-231_siRNA_R2
Gene expression data from a DLBCL cell line.
|
| Sample_geo_accession | GSM1034135
| | Sample_status | Public on Nov 10 2012
| | Sample_submission_date | Nov 08 2012
| | Sample_last_update_date | Nov 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Absence or presence of 4 mg/ml doxycycline for LITAF over-expression. Nucleofection (AMAXA) with Silencer Select Negative Control No. 1 (AM4611, Invitrogen) or a LITAF-specific siRNA (s18252, Invitrogen) for silencing. RNA was extracted 48h after the treatment.
| | Sample_growth_protocol_ch1 | Cell lines were grown at 37ºC and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The cDNA was prepared from 2 microg total RNA using the One-Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2.0 chip according to the protocols provided by the manufacturer.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
| | Sample_data_processing | Data were normalized with Bioconductor software using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raquel,,Malumbres
| | Sample_contact_email | rmalumbres@yahoo.com
| | Sample_contact_phone | +34 948194700
| | Sample_contact_laboratory | Molecular Oncology
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Navarra/ Center for Applied Medical Research
| | Sample_contact_address | Avenida Pio XII 55
| | Sample_contact_city | Pamplona
| | Sample_contact_state | Navarra
| | Sample_contact_zip/postal_code | 31008
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1034nnn/GSM1034135/suppl/GSM1034135_K231_siRNA_R2.CEL.gz
| | Sample_series_id | GSE42174
| | Sample_series_id | GSE42204
| | Sample_data_row_count | 54675
| | |
|
GSM1034136 | GPL570 |
|
KARPAS-231, LITAF-specific siRNA, REP3
|
DLBCL cell line KARPAS-231 transfected with a LITAF-specific siRNA
|
cell line: KARPAS-231
cell type: diffuse large B-cell lymphoma (DLBCL) cells
treatment: LITAF-specific siRNA
|
KARPAS-231_siRNA_R3
Gene expression data from a DLBCL cell line.
|
| Sample_geo_accession | GSM1034136
| | Sample_status | Public on Nov 10 2012
| | Sample_submission_date | Nov 08 2012
| | Sample_last_update_date | Nov 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Absence or presence of 4 mg/ml doxycycline for LITAF over-expression. Nucleofection (AMAXA) with Silencer Select Negative Control No. 1 (AM4611, Invitrogen) or a LITAF-specific siRNA (s18252, Invitrogen) for silencing. RNA was extracted 48h after the treatment.
| | Sample_growth_protocol_ch1 | Cell lines were grown at 37ºC and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The cDNA was prepared from 2 microg total RNA using the One-Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2.0 chip according to the protocols provided by the manufacturer.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
| | Sample_data_processing | Data were normalized with Bioconductor software using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raquel,,Malumbres
| | Sample_contact_email | rmalumbres@yahoo.com
| | Sample_contact_phone | +34 948194700
| | Sample_contact_laboratory | Molecular Oncology
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Navarra/ Center for Applied Medical Research
| | Sample_contact_address | Avenida Pio XII 55
| | Sample_contact_city | Pamplona
| | Sample_contact_state | Navarra
| | Sample_contact_zip/postal_code | 31008
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1034nnn/GSM1034136/suppl/GSM1034136_K231_siRNA_R3.CEL.gz
| | Sample_series_id | GSE42174
| | Sample_series_id | GSE42204
| | Sample_data_row_count | 54675
| | |
|
GSM1034137 | GPL570 |
|
VAL, non-targeting siRNA, REP1
|
DLBCL cell line VAL transfected with a non-targeting siRNA
|
cell line: VAL
cell type: diffuse large B-cell lymphoma (DLBCL) cells
treatment: non-targeting siRNA
|
VAL_SC_R1
Gene expression data from a DLBCL cell line.
|
| Sample_geo_accession | GSM1034137
| | Sample_status | Public on Nov 10 2012
| | Sample_submission_date | Nov 08 2012
| | Sample_last_update_date | Nov 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Absence or presence of 4 mg/ml doxycycline for LITAF over-expression. Nucleofection (AMAXA) with Silencer Select Negative Control No. 1 (AM4611, Invitrogen) or a LITAF-specific siRNA (s18252, Invitrogen) for silencing. RNA was extracted 48h after the treatment.
| | Sample_growth_protocol_ch1 | Cell lines were grown at 37ºC and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The cDNA was prepared from 2 microg total RNA using the One-Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2.0 chip according to the protocols provided by the manufacturer.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
| | Sample_data_processing | Data were normalized with Bioconductor software using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raquel,,Malumbres
| | Sample_contact_email | rmalumbres@yahoo.com
| | Sample_contact_phone | +34 948194700
| | Sample_contact_laboratory | Molecular Oncology
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Navarra/ Center for Applied Medical Research
| | Sample_contact_address | Avenida Pio XII 55
| | Sample_contact_city | Pamplona
| | Sample_contact_state | Navarra
| | Sample_contact_zip/postal_code | 31008
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1034nnn/GSM1034137/suppl/GSM1034137_VAL_SC_R1.CEL.gz
| | Sample_series_id | GSE42174
| | Sample_series_id | GSE42204
| | Sample_data_row_count | 54675
| | |
|
GSM1034138 | GPL570 |
|
VAL, non-targeting siRNA, REP2
|
DLBCL cell line VAL transfected with a non-targeting siRNA
|
cell line: VAL
cell type: diffuse large B-cell lymphoma (DLBCL) cells
treatment: non-targeting siRNA
|
VAL_SC_R2
Gene expression data from a DLBCL cell line.
|
| Sample_geo_accession | GSM1034138
| | Sample_status | Public on Nov 10 2012
| | Sample_submission_date | Nov 08 2012
| | Sample_last_update_date | Nov 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Absence or presence of 4 mg/ml doxycycline for LITAF over-expression. Nucleofection (AMAXA) with Silencer Select Negative Control No. 1 (AM4611, Invitrogen) or a LITAF-specific siRNA (s18252, Invitrogen) for silencing. RNA was extracted 48h after the treatment.
| | Sample_growth_protocol_ch1 | Cell lines were grown at 37ºC and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The cDNA was prepared from 2 microg total RNA using the One-Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2.0 chip according to the protocols provided by the manufacturer.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
| | Sample_data_processing | Data were normalized with Bioconductor software using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raquel,,Malumbres
| | Sample_contact_email | rmalumbres@yahoo.com
| | Sample_contact_phone | +34 948194700
| | Sample_contact_laboratory | Molecular Oncology
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Navarra/ Center for Applied Medical Research
| | Sample_contact_address | Avenida Pio XII 55
| | Sample_contact_city | Pamplona
| | Sample_contact_state | Navarra
| | Sample_contact_zip/postal_code | 31008
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1034nnn/GSM1034138/suppl/GSM1034138_VAL_SC_R2.CEL.gz
| | Sample_series_id | GSE42174
| | Sample_series_id | GSE42204
| | Sample_data_row_count | 54675
| | |
|
GSM1034139 | GPL570 |
|
VAL, non-targeting siRNA, REP3
|
DLBCL cell line VAL transfected with a non-targeting siRNA
|
cell line: VAL
cell type: diffuse large B-cell lymphoma (DLBCL) cells
treatment: non-targeting siRNA
|
VAL_SC_R3
Gene expression data from a DLBCL cell line.
|
| Sample_geo_accession | GSM1034139
| | Sample_status | Public on Nov 10 2012
| | Sample_submission_date | Nov 08 2012
| | Sample_last_update_date | Nov 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Absence or presence of 4 mg/ml doxycycline for LITAF over-expression. Nucleofection (AMAXA) with Silencer Select Negative Control No. 1 (AM4611, Invitrogen) or a LITAF-specific siRNA (s18252, Invitrogen) for silencing. RNA was extracted 48h after the treatment.
| | Sample_growth_protocol_ch1 | Cell lines were grown at 37ºC and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The cDNA was prepared from 2 microg total RNA using the One-Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2.0 chip according to the protocols provided by the manufacturer.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
| | Sample_data_processing | Data were normalized with Bioconductor software using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raquel,,Malumbres
| | Sample_contact_email | rmalumbres@yahoo.com
| | Sample_contact_phone | +34 948194700
| | Sample_contact_laboratory | Molecular Oncology
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Navarra/ Center for Applied Medical Research
| | Sample_contact_address | Avenida Pio XII 55
| | Sample_contact_city | Pamplona
| | Sample_contact_state | Navarra
| | Sample_contact_zip/postal_code | 31008
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1034nnn/GSM1034139/suppl/GSM1034139_VAL_SC_R3.CEL.gz
| | Sample_series_id | GSE42174
| | Sample_series_id | GSE42204
| | Sample_data_row_count | 54675
| | |
|
GSM1034140 | GPL570 |
|
VAL, LITAF-specific siRNA, REP1
|
DLBCL cell line VAL transfected with a LITAF-specific siRNA
|
cell line: VAL
cell type: diffuse large B-cell lymphoma (DLBCL) cells
treatment: LITAF-specific siRNA
|
VAL_siRNA_R1
Gene expression data from a DLBCL cell line.
|
| Sample_geo_accession | GSM1034140
| | Sample_status | Public on Nov 10 2012
| | Sample_submission_date | Nov 08 2012
| | Sample_last_update_date | Nov 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Absence or presence of 4 mg/ml doxycycline for LITAF over-expression. Nucleofection (AMAXA) with Silencer Select Negative Control No. 1 (AM4611, Invitrogen) or a LITAF-specific siRNA (s18252, Invitrogen) for silencing. RNA was extracted 48h after the treatment.
| | Sample_growth_protocol_ch1 | Cell lines were grown at 37ºC and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The cDNA was prepared from 2 microg total RNA using the One-Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2.0 chip according to the protocols provided by the manufacturer.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
| | Sample_data_processing | Data were normalized with Bioconductor software using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raquel,,Malumbres
| | Sample_contact_email | rmalumbres@yahoo.com
| | Sample_contact_phone | +34 948194700
| | Sample_contact_laboratory | Molecular Oncology
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Navarra/ Center for Applied Medical Research
| | Sample_contact_address | Avenida Pio XII 55
| | Sample_contact_city | Pamplona
| | Sample_contact_state | Navarra
| | Sample_contact_zip/postal_code | 31008
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1034nnn/GSM1034140/suppl/GSM1034140_VAL_siRNA_R1.CEL.gz
| | Sample_series_id | GSE42174
| | Sample_series_id | GSE42204
| | Sample_data_row_count | 54675
| | |
|
GSM1034141 | GPL570 |
|
VAL, LITAF-specific siRNA, REP2
|
DLBCL cell line VAL transfected with a LITAF-specific siRNA
|
cell line: VAL
cell type: diffuse large B-cell lymphoma (DLBCL) cells
treatment: LITAF-specific siRNA
|
VAL_siRNA_R2
Gene expression data from a DLBCL cell line.
|
| Sample_geo_accession | GSM1034141
| | Sample_status | Public on Nov 10 2012
| | Sample_submission_date | Nov 08 2012
| | Sample_last_update_date | Nov 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Absence or presence of 4 mg/ml doxycycline for LITAF over-expression. Nucleofection (AMAXA) with Silencer Select Negative Control No. 1 (AM4611, Invitrogen) or a LITAF-specific siRNA (s18252, Invitrogen) for silencing. RNA was extracted 48h after the treatment.
| | Sample_growth_protocol_ch1 | Cell lines were grown at 37ºC and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The cDNA was prepared from 2 microg total RNA using the One-Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2.0 chip according to the protocols provided by the manufacturer.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
| | Sample_data_processing | Data were normalized with Bioconductor software using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raquel,,Malumbres
| | Sample_contact_email | rmalumbres@yahoo.com
| | Sample_contact_phone | +34 948194700
| | Sample_contact_laboratory | Molecular Oncology
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Navarra/ Center for Applied Medical Research
| | Sample_contact_address | Avenida Pio XII 55
| | Sample_contact_city | Pamplona
| | Sample_contact_state | Navarra
| | Sample_contact_zip/postal_code | 31008
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1034nnn/GSM1034141/suppl/GSM1034141_VAL_siRNA_R2.CEL.gz
| | Sample_series_id | GSE42174
| | Sample_series_id | GSE42204
| | Sample_data_row_count | 54675
| | |
|
GSM1034142 | GPL570 |
|
VAL, LITAF-specific siRNA, REP3
|
DLBCL cell line VAL transfected with a LITAF-specific siRNA
|
cell line: VAL
cell type: diffuse large B-cell lymphoma (DLBCL) cells
treatment: LITAF-specific siRNA
|
VAL_siRNA_R3
Gene expression data from a DLBCL cell line.
|
| Sample_geo_accession | GSM1034142
| | Sample_status | Public on Nov 10 2012
| | Sample_submission_date | Nov 08 2012
| | Sample_last_update_date | Nov 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Absence or presence of 4 mg/ml doxycycline for LITAF over-expression. Nucleofection (AMAXA) with Silencer Select Negative Control No. 1 (AM4611, Invitrogen) or a LITAF-specific siRNA (s18252, Invitrogen) for silencing. RNA was extracted 48h after the treatment.
| | Sample_growth_protocol_ch1 | Cell lines were grown at 37ºC and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The cDNA was prepared from 2 microg total RNA using the One-Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2.0 chip according to the protocols provided by the manufacturer.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
| | Sample_data_processing | Data were normalized with Bioconductor software using the RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raquel,,Malumbres
| | Sample_contact_email | rmalumbres@yahoo.com
| | Sample_contact_phone | +34 948194700
| | Sample_contact_laboratory | Molecular Oncology
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Navarra/ Center for Applied Medical Research
| | Sample_contact_address | Avenida Pio XII 55
| | Sample_contact_city | Pamplona
| | Sample_contact_state | Navarra
| | Sample_contact_zip/postal_code | 31008
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1034nnn/GSM1034142/suppl/GSM1034142_VAL_siRNA_R3.CEL.gz
| | Sample_series_id | GSE42174
| | Sample_series_id | GSE42204
| | Sample_data_row_count | 54675
| | |
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