Search results for the GEO ID: GSE12453  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM312811 | GPL570 |
|
cHL1
|
classical Hodgkin lymphoma case 1
|
primary lymphoma cells laser-microdissected from a patient diagnosed with classical Hodgkin lymphoma (cHL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312811
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Lymphoma cells were microdissected as single cells according to their characteristic morphological criteria concerning nuclear shape and diameter, chromatin distribution, nucleoli, and amount and density of cytoplasm. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312811/suppl/GSM312811.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312812 | GPL570 |
|
cHL2
|
classical Hodgkin lymphoma case 2
|
primary lymphoma cells laser-microdissected from a patient diagnosed with classical Hodgkin lymphoma (cHL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312812
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Lymphoma cells were microdissected as single cells according to their characteristic morphological criteria concerning nuclear shape and diameter, chromatin distribution, nucleoli, and amount and density of cytoplasm. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312812/suppl/GSM312812.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312813 | GPL570 |
|
cHL3
|
classical Hodgkin lymphoma case 3
|
primary lymphoma cells laser-microdissected from a patient diagnosed with classical Hodgkin lymphoma (cHL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312813
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Lymphoma cells were microdissected as single cells according to their characteristic morphological criteria concerning nuclear shape and diameter, chromatin distribution, nucleoli, and amount and density of cytoplasm. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312813/suppl/GSM312813.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312814 | GPL570 |
|
cHL4
|
classical Hodgkin lymphoma case 4
|
primary lymphoma cells laser-microdissected from a patient diagnosed with classical Hodgkin lymphoma (cHL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312814
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Lymphoma cells were microdissected as single cells according to their characteristic morphological criteria concerning nuclear shape and diameter, chromatin distribution, nucleoli, and amount and density of cytoplasm. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312814/suppl/GSM312814.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312815 | GPL570 |
|
cHL5
|
classical Hodgkin lymphoma case 5
|
primary lymphoma cells laser-microdissected from a patient diagnosed with classical Hodgkin lymphoma (cHL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312815
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Lymphoma cells were microdissected as single cells according to their characteristic morphological criteria concerning nuclear shape and diameter, chromatin distribution, nucleoli, and amount and density of cytoplasm. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312815/suppl/GSM312815.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312816 | GPL570 |
|
cHL6
|
classical Hodgkin lymphoma case 6
|
primary lymphoma cells laser-microdissected from a patient diagnosed with classical Hodgkin lymphoma (cHL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312816
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Lymphoma cells were microdissected as single cells according to their characteristic morphological criteria concerning nuclear shape and diameter, chromatin distribution, nucleoli, and amount and density of cytoplasm. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312816/suppl/GSM312816.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312817 | GPL570 |
|
cHL7
|
classical Hodgkin lymphoma case 7
|
primary lymphoma cells laser-microdissected from a patient diagnosed with classical Hodgkin lymphoma (cHL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312817
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Lymphoma cells were microdissected as single cells according to their characteristic morphological criteria concerning nuclear shape and diameter, chromatin distribution, nucleoli, and amount and density of cytoplasm. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312817/suppl/GSM312817.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312818 | GPL570 |
|
cHL8
|
classical Hodgkin lymphoma case 8
|
primary lymphoma cells laser-microdissected from a patient diagnosed with classical Hodgkin lymphoma (cHL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312818
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Lymphoma cells were microdissected as single cells according to their characteristic morphological criteria concerning nuclear shape and diameter, chromatin distribution, nucleoli, and amount and density of cytoplasm. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312818/suppl/GSM312818.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312819 | GPL570 |
|
cHL9
|
classical Hodgkin lymphoma case 9
|
primary lymphoma cells laser-microdissected from a patient diagnosed with classical Hodgkin lymphoma (cHL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312819
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Lymphoma cells were microdissected as single cells according to their characteristic morphological criteria concerning nuclear shape and diameter, chromatin distribution, nucleoli, and amount and density of cytoplasm. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312819/suppl/GSM312819.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312820 | GPL570 |
|
cHL10
|
classical Hodgkin lymphoma case 10
|
primary lymphoma cells laser-microdissected from a patient diagnosed with classical Hodgkin lymphoma (cHL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312820
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Lymphoma cells were microdissected as single cells according to their characteristic morphological criteria concerning nuclear shape and diameter, chromatin distribution, nucleoli, and amount and density of cytoplasm. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312820/suppl/GSM312820.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312821 | GPL570 |
|
cHL11
|
classical Hodgkin lymphoma case 11
|
primary lymphoma cells laser-microdissected from a patient diagnosed with classical Hodgkin lymphoma (cHL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312821
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Lymphoma cells were microdissected as single cells according to their characteristic morphological criteria concerning nuclear shape and diameter, chromatin distribution, nucleoli, and amount and density of cytoplasm. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312821/suppl/GSM312821.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312822 | GPL570 |
|
cHL12
|
classical Hodgkin lymphoma case 12
|
primary lymphoma cells laser-microdissected from a patient diagnosed with classical Hodgkin lymphoma (cHL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312822
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Lymphoma cells were microdissected as single cells according to their characteristic morphological criteria concerning nuclear shape and diameter, chromatin distribution, nucleoli, and amount and density of cytoplasm. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312822/suppl/GSM312822.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312823 | GPL570 |
|
NLPHL1
|
nodular lymphocte-predominant Hodgkin lymphoma case 1
|
primary lymphoma cells laser-microdissected from a patient diagnosed with nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312823
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Lymphoma cells were microdissected as single cells according to their characteristic morphological criteria concerning nuclear shape and diameter, chromatin distribution, nucleoli, and amount and density of cytoplasm. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312823/suppl/GSM312823.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312824 | GPL570 |
|
NLPHL2
|
nodular lymphocte-predominant Hodgkin lymphoma case 2
|
primary lymphoma cells laser-microdissected from a patient diagnosed with nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312824
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Lymphoma cells were microdissected as single cells according to their characteristic morphological criteria concerning nuclear shape and diameter, chromatin distribution, nucleoli, and amount and density of cytoplasm. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312824/suppl/GSM312824.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312825 | GPL570 |
|
NLPHL3
|
nodular lymphocte-predominant Hodgkin lymphoma case 3
|
primary lymphoma cells laser-microdissected from a patient diagnosed with nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312825
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Lymphoma cells were microdissected as single cells according to their characteristic morphological criteria concerning nuclear shape and diameter, chromatin distribution, nucleoli, and amount and density of cytoplasm. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312825/suppl/GSM312825.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312826 | GPL570 |
|
NLPHL4
|
nodular lymphocte-predominant Hodgkin lymphoma case 4
|
primary lymphoma cells laser-microdissected from a patient diagnosed with nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312826
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Lymphoma cells were microdissected as single cells according to their characteristic morphological criteria concerning nuclear shape and diameter, chromatin distribution, nucleoli, and amount and density of cytoplasm. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312826/suppl/GSM312826.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312839 | GPL570 |
|
NLPHL5
|
nodular lymphocte-predominant Hodgkin lymphoma case 5
|
primary lymphoma cells laser-microdissected from a patient diagnosed with nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312839
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Lymphoma cells were microdissected as single cells according to their characteristic morphological criteria concerning nuclear shape and diameter, chromatin distribution, nucleoli, and amount and density of cytoplasm. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312839/suppl/GSM312839.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312840 | GPL570 |
|
TCRBL1
|
T-cell rich B-cell lymphoma case 1
|
primary lymphoma cells laser-microdissected from a patient diagnosed with T-cell rich B-cell lymphoma (TCRBL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312840
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Lymphoma cells were microdissected as single cells according to their characteristic morphological criteria concerning nuclear shape and diameter, chromatin distribution, nucleoli, and amount and density of cytoplasm. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312840/suppl/GSM312840.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312841 | GPL570 |
|
TCRBL2
|
T-cell rich B-cell lymphoma case 2
|
primary lymphoma cells laser-microdissected from a patient diagnosed with T-cell rich B-cell lymphoma (TCRBL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312841
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Lymphoma cells were microdissected as single cells according to their characteristic morphological criteria concerning nuclear shape and diameter, chromatin distribution, nucleoli, and amount and density of cytoplasm. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312841/suppl/GSM312841.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312843 | GPL570 |
|
TCRBL3
|
T-cell rich B-cell lymphoma case 3
|
primary lymphoma cells laser-microdissected from a patient diagnosed with T-cell rich B-cell lymphoma (TCRBL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312843
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Lymphoma cells were microdissected as single cells according to their characteristic morphological criteria concerning nuclear shape and diameter, chromatin distribution, nucleoli, and amount and density of cytoplasm. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312843/suppl/GSM312843.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312844 | GPL570 |
|
TCRBL4
|
T-cell rich B-cell lymphoma case 4
|
primary lymphoma cells laser-microdissected from a patient diagnosed with T-cell rich B-cell lymphoma (TCRBL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312844
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Lymphoma cells were microdissected as single cells according to their characteristic morphological criteria concerning nuclear shape and diameter, chromatin distribution, nucleoli, and amount and density of cytoplasm. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312844/suppl/GSM312844.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312845 | GPL570 |
|
FL1
|
follicular lymphoma case 1
|
primary lymphoma cells laser-microdissected from a patient diagnosed with follicular lymphoma (FL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312845
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312845/suppl/GSM312845.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312846 | GPL570 |
|
FL2
|
follicular lymphoma case 2
|
primary lymphoma cells laser-microdissected from a patient diagnosed with follicular lymphoma (FL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312846
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312846/suppl/GSM312846.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312847 | GPL570 |
|
FL3
|
follicular lymphoma case 3
|
primary lymphoma cells laser-microdissected from a patient diagnosed with follicular lymphoma (FL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312847
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312847/suppl/GSM312847.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312848 | GPL570 |
|
FL4
|
follicular lymphoma case 4
|
primary lymphoma cells laser-microdissected from a patient diagnosed with follicular lymphoma (FL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312848
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312848/suppl/GSM312848.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312849 | GPL570 |
|
FL5
|
follicular lymphoma case 5
|
primary lymphoma cells laser-microdissected from a patient diagnosed with follicular lymphoma (FL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312849
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312849/suppl/GSM312849.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312851 | GPL570 |
|
BL1
|
Burkitt lymphoma case 1
|
primary lymphoma cells laser-microdissected from a patient diagnosed with Burkitt lymphoma (BL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312851
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312851/suppl/GSM312851.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312853 | GPL570 |
|
BL2
|
Burkitt lymphoma case 2
|
primary lymphoma cells laser-microdissected from a patient diagnosed with Burkitt lymphoma (BL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312853
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312853/suppl/GSM312853.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312854 | GPL570 |
|
BL3
|
Burkitt lymphoma case 3
|
primary lymphoma cells laser-microdissected from a patient diagnosed with Burkitt lymphoma (BL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312854
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312854/suppl/GSM312854.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312856 | GPL570 |
|
BL4
|
Burkitt lymphoma case 4
|
primary lymphoma cells laser-microdissected from a patient diagnosed with Burkitt lymphoma (BL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312856
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312856/suppl/GSM312856.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312857 | GPL570 |
|
BL5
|
Burkitt lymphoma case 5
|
primary lymphoma cells laser-microdissected from a patient diagnosed with Burkitt lymphoma (BL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312857
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312857/suppl/GSM312857.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312858 | GPL570 |
|
DLBCL1
|
diffuse large B-cell lymphoma case 1
|
primary lymphoma cells laser-microdissected from a patient diagnosed with diffuse large B-cell lymphoma (DLBCL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312858
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312858/suppl/GSM312858.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312859 | GPL570 |
|
DLBCL2
|
diffuse large B-cell lymphoma case 2
|
primary lymphoma cells laser-microdissected from a patient diagnosed with diffuse large B-cell lymphoma (DLBCL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312859
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312859/suppl/GSM312859.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312860 | GPL570 |
|
DLBCL3
|
diffuse large B-cell lymphoma case 3
|
primary lymphoma cells laser-microdissected from a patient diagnosed with diffuse large B-cell lymphoma (DLBCL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312860
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312860/suppl/GSM312860.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312861 | GPL570 |
|
DLBCL4
|
diffuse large B-cell lymphoma case 4
|
primary lymphoma cells laser-microdissected from a patient diagnosed with diffuse large B-cell lymphoma (DLBCL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312861
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312861/suppl/GSM312861.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312862 | GPL570 |
|
DLBCL5
|
diffuse large B-cell lymphoma case 5
|
primary lymphoma cells laser-microdissected from a patient diagnosed with diffuse large B-cell lymphoma (DLBCL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312862
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312862/suppl/GSM312862.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312863 | GPL570 |
|
DLBCL6
|
diffuse large B-cell lymphoma case 6
|
primary lymphoma cells laser-microdissected from a patient diagnosed with diffuse large B-cell lymphoma (DLBCL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312863
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312863/suppl/GSM312863.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312864 | GPL570 |
|
DLBCL7
|
diffuse large B-cell lymphoma case 7
|
primary lymphoma cells laser-microdissected from a patient diagnosed with diffuse large B-cell lymphoma (DLBCL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312864
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312864/suppl/GSM312864.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312865 | GPL570 |
|
DLBCL8
|
diffuse large B-cell lymphoma case 8
|
primary lymphoma cells laser-microdissected from a patient diagnosed with diffuse large B-cell lymphoma (DLBCL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312865
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312865/suppl/GSM312865.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312867 | GPL570 |
|
DLBCL9
|
diffuse large B-cell lymphoma case 9
|
primary lymphoma cells laser-microdissected from a patient diagnosed with diffuse large B-cell lymphoma (DLBCL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312867
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312867/suppl/GSM312867.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312868 | GPL570 |
|
DLBCL10
|
diffuse large B-cell lymphoma case 10
|
primary lymphoma cells laser-microdissected from a patient diagnosed with diffuse large B-cell lymphoma (DLBCL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312868
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312868/suppl/GSM312868.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312869 | GPL570 |
|
DLBCL11
|
diffuse large B-cell lymphoma case 11
|
primary lymphoma cells laser-microdissected from a patient diagnosed with diffuse large B-cell lymphoma (DLBCL)
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312869
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Five μm-thick frozen sections of lymph nodes from lymphoma patients were mounted on membrane-covered slides (PALM, Bernried, Germany), incubated with hematoxylin containing 200 U/ml RNase inhibitor (Roche, Mannheim, Germany) for 4 minutes, washed in molecular biology grade water for 2 minutes, incubated in 2% eosin for 15 seconds, washed again, and dried at 37°C for 3 hours. Microdissection was performed using the Laser Microdissection and Pressure Catapulting (LMPC) technique with an UV-laser beam (PALM). Areas with at least 95% lymphoma cells were selected, so that these lymphoma cells could be microdissected in areas. Cells were directly catapulted into Purescript lysis buffer (Gentra) and pooled in groups of 1000 – 2000 lymphoma cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312869/suppl/GSM312869.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312870 | GPL570 |
|
N1
|
naive B-cells donor 1
|
naive B cell, isolated from peripheral blood of healthy donors by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312870
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | cells were isolated from peripheral blood of five healthy adult donors. blood samples were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 naïve B cells were isolated by magnetic cell separation, depleting CD27+ (memory B cells, T cell subpopulation) and CD11b+ (monocytes, macrophages, granulocytes, NK cells) cells, using the MACS system (Miltenyi Biotech, Bergisch Gladbach, Germany) followed by fluorescence-activated cell sorting (FACS) of IgD+ CD27- cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312870/suppl/GSM312870.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312872 | GPL570 |
|
N2
|
naive B-cells donor 2
|
naive B cell, isolated from peripheral blood of healthy donors by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312872
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | cells were isolated from peripheral blood of five healthy adult donors. blood samples were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 naïve B cells were isolated by magnetic cell separation, depleting CD27+ (memory B cells, T cell subpopulation) and CD11b+ (monocytes, macrophages, granulocytes, NK cells) cells, using the MACS system (Miltenyi Biotech, Bergisch Gladbach, Germany) followed by fluorescence-activated cell sorting (FACS) of IgD+ CD27- cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312872/suppl/GSM312872.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312874 | GPL570 |
|
N3
|
naive B-cells donor 3
|
naive B cell, isolated from peripheral blood of healthy donors by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312874
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | cells were isolated from peripheral blood of five healthy adult donors. blood samples were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 naïve B cells were isolated by magnetic cell separation, depleting CD27+ (memory B cells, T cell subpopulation) and CD11b+ (monocytes, macrophages, granulocytes, NK cells) cells, using the MACS system (Miltenyi Biotech, Bergisch Gladbach, Germany) followed by fluorescence-activated cell sorting (FACS) of IgD+ CD27- cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312874/suppl/GSM312874.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312875 | GPL570 |
|
N4
|
naive B-cells donor 4
|
naive B cell, isolated from peripheral blood of healthy donors by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312875
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | cells were isolated from peripheral blood of five healthy adult donors. blood samples were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 naïve B cells were isolated by magnetic cell separation, depleting CD27+ (memory B cells, T cell subpopulation) and CD11b+ (monocytes, macrophages, granulocytes, NK cells) cells, using the MACS system (Miltenyi Biotech, Bergisch Gladbach, Germany) followed by fluorescence-activated cell sorting (FACS) of IgD+ CD27- cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312875/suppl/GSM312875.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312876 | GPL570 |
|
N5
|
naive B-cells donor 5
|
naive B cell, isolated from peripheral blood of healthy donors by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312876
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | cells were isolated from peripheral blood of five healthy adult donors. blood samples were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 naïve B cells were isolated by magnetic cell separation, depleting CD27+ (memory B cells, T cell subpopulation) and CD11b+ (monocytes, macrophages, granulocytes, NK cells) cells, using the MACS system (Miltenyi Biotech, Bergisch Gladbach, Germany) followed by fluorescence-activated cell sorting (FACS) of IgD+ CD27- cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312876/suppl/GSM312876.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312877 | GPL570 |
|
M1
|
memory B cells donor 1
|
memory B cells, isolated from peripheral blood of healthy donors by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312877
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | cells were isolated from peripheral blood of five healthy adult donors. blood samples were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 memory B cells were isolated by MACS depletion of CD11b+ and CD3+ cells followed by FACS-sorting of CD20+ CD27+ cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312877/suppl/GSM312877.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312879 | GPL570 |
|
M2
|
memory B cells donor 2
|
memory B cells, isolated from peripheral blood of healthy donors by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312879
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | cells were isolated from peripheral blood of five healthy adult donors. blood samples were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 memory B cells were isolated by MACS depletion of CD11b+ and CD3+ cells followed by FACS-sorting of CD20+ CD27+ cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312879/suppl/GSM312879.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312882 | GPL570 |
|
M3
|
memory B cells donor 3
|
memory B cells, isolated from peripheral blood of healthy donors by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312882
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | cells were isolated from peripheral blood of five healthy adult donors. blood samples were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 memory B cells were isolated by MACS depletion of CD11b+ and CD3+ cells followed by FACS-sorting of CD20+ CD27+ cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312882/suppl/GSM312882.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312883 | GPL570 |
|
M4
|
memory B cells donor 4
|
memory B cells, isolated from peripheral blood of healthy donors by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312883
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | cells were isolated from peripheral blood of five healthy adult donors. blood samples were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 memory B cells were isolated by MACS depletion of CD11b+ and CD3+ cells followed by FACS-sorting of CD20+ CD27+ cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312883/suppl/GSM312883.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312886 | GPL570 |
|
M5
|
memory B cells donor 5
|
memory B cells, isolated from peripheral blood of healthy donors by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312886
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | cells were isolated from peripheral blood of five healthy adult donors. blood samples were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 memory B cells were isolated by MACS depletion of CD11b+ and CD3+ cells followed by FACS-sorting of CD20+ CD27+ cells.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312886/suppl/GSM312886.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312887 | GPL570 |
|
CC1
|
centrocytes donor 1
|
centrocytes, isolated from tonsils by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312887
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tonsils for the isolation of centrocytes (CC) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 tonsillar centrocytes were isolated by FACS-sorting according to the following marker expression: CD20high CD38+ CD77-.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312887/suppl/GSM312887.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312890 | GPL570 |
|
CC2
|
centrocytes donor 2
|
centrocytes, isolated from tonsils by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312890
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tonsils for the isolation of centrocytes (CC) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 tonsillar centrocytes were isolated by FACS-sorting according to the following marker expression: CD20high CD38+ CD77-.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312890/suppl/GSM312890.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312893 | GPL570 |
|
CC3
|
centrocytes donor 3
|
centrocytes, isolated from tonsils by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312893
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tonsils for the isolation of centrocytes (CC) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 tonsillar centrocytes were isolated by FACS-sorting according to the following marker expression: CD20high CD38+ CD77-.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312893/suppl/GSM312893.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312894 | GPL570 |
|
CC4
|
centrocytes donor 4
|
centrocytes, isolated from tonsils by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312894
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tonsils for the isolation of centrocytes (CC) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 tonsillar centrocytes were isolated by FACS-sorting according to the following marker expression: CD20high CD38+ CD77-.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312894/suppl/GSM312894.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312895 | GPL570 |
|
CC5
|
centrocytes donor 5
|
centrocytes, isolated from tonsils by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312895
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tonsils for the isolation of centrocytes (CC) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 tonsillar centrocytes were isolated by FACS-sorting according to the following marker expression: CD20high CD38+ CD77-.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312895/suppl/GSM312895.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312937 | GPL570 |
|
CB1
|
centroblasts donor 1
|
centroblasts, isolated from tonsils by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312937
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tonsils for the isolation of centroblasts (CB) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 tonsillar centroblasts were isolated by FACS-sorting according to the following marker expression: CD20high CD38+ CD77+.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312937/suppl/GSM312937.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312938 | GPL570 |
|
CB2
|
centroblasts donor 2
|
centroblasts, isolated from tonsils by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312938
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tonsils for the isolation of centroblasts (CB) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 tonsillar centroblasts were isolated by FACS-sorting according to the following marker expression: CD20high CD38+ CD77+.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312938/suppl/GSM312938.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312939 | GPL570 |
|
CB3
|
centroblasts donor 3
|
centroblasts, isolated from tonsils by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312939
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tonsils for the isolation of centroblasts (CB) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 tonsillar centroblasts were isolated by FACS-sorting according to the following marker expression: CD20high CD38+ CD77+.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312939/suppl/GSM312939.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312940 | GPL570 |
|
CB4
|
centroblasts donor 4
|
centroblasts, isolated from tonsils by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312940
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tonsils for the isolation of centroblasts (CB) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 tonsillar centroblasts were isolated by FACS-sorting according to the following marker expression: CD20high CD38+ CD77+.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312940/suppl/GSM312940.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312941 | GPL570 |
|
CB5
|
centroblasts donor 5
|
centroblasts, isolated from tonsils by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312941
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tonsils for the isolation of centroblasts (CB) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 tonsillar centroblasts were isolated by FACS-sorting according to the following marker expression: CD20high CD38+ CD77+.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312941/suppl/GSM312941.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312942 | GPL570 |
|
PC1
|
plasma cells donor 1
|
plasma cells, isolated from tonsils by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312942
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tonsils for the isolation of plasma cells (PC) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 tonsillar plasma cells were isolated by FACS-sorting according to the following marker expression: CD20low CD38high.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312942/suppl/GSM312942.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312943 | GPL570 |
|
PC2
|
plasma cells donor 2
|
plasma cells, isolated from tonsils by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312943
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tonsils for the isolation of plasma cells (PC) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 tonsillar plasma cells were isolated by FACS-sorting according to the following marker expression: CD20low CD38high.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312943/suppl/GSM312943.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312944 | GPL570 |
|
PC3
|
plasma cells donor 3
|
plasma cells, isolated from tonsils by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312944
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tonsils for the isolation of plasma cells (PC) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 tonsillar plasma cells were isolated by FACS-sorting according to the following marker expression: CD20low CD38high.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312944/suppl/GSM312944.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312945 | GPL570 |
|
PC4
|
plasma cells donor 4
|
plasma cells, isolated from tonsils by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
|
| Sample_geo_accession | GSM312945
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tonsils for the isolation of plasma cells (PC) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 tonsillar plasma cells were isolated by FACS-sorting according to the following marker expression: CD20low CD38high.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312945/suppl/GSM312945.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
| | |
|
GSM312946 | GPL570 |
|
PC5
|
plasma cells donor 5
|
plasma cells, isolated from tonsils by fluorescence-activated cell sorting
|
Analysis of differential gene expression in primary human lymphoma cells of nodular lymphocyte-predominant Hodgkin lymphoma (NLPHL) in comparison with primary lymphoma cells of classical Hodgkin lymphoma cells and other B-non-Hodgkin lymphoma (B-NHL) samples and subsets of non-neoplastic B lymphocytes isolated from blood or tonsils.
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| Sample_geo_accession | GSM312946
| | Sample_status | Public on Oct 01 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 30 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tonsils for the isolation of plasma cells (PC) were obtained from patients undergoing routine tonsillectomy. Tonsils were immediately cooled at 0-4°C and cells were further processed and immediately sorted after staining at this low temperature to avoid changes in gene expression, due to RNA turnover or signalling effects of the antibodies used for staining. 2000 tonsillar plasma cells were isolated by FACS-sorting according to the following marker expression: CD20low CD38high.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The Purescript RNA Isolation Kit (Gentra) was applied using 80 μg glycogen (Roche) as a carrier and reducing all reagents to one-tenth of the amounts given in the standard protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The T7 RNA polymerase-based RiboAmpTM RNA Amplification Kit, version C (Arcturus, Mountain View, CA, USA) was used to amplify the RNA by in vitro transcription. In the first cDNA synthesis, 1.5 μg T4 gene 32 protein (Ambion, Austin, USA) were added to the reaction to improve specificity and yield of the reaction. The first cDNA synthesis was followed by an in vitro transcription (IVT) and a second cDNA synthesis using random hexamers. 100 ng of the second cDNA synthesis product were used in the labeling reaction with the BioArray High Yield Transcription Labeling Kit (ENZO Life Science, Farmingdale, NY, USA) with the following modifications: the incubation-time was prolonged to 8 hours and the ENZO T7 RNA polymerase (150 U) was substituted by Stratagene T7 RNA polymerase (300 U) (Stratagene, La Jolla, CA, USA).
| | Sample_hyb_protocol | Fragmentation of cRNA, microarray hybridisation to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays, washing steps of the microarrays was performed according to the Affymetrix protocol.
| | Sample_scan_protocol | Scanning was performed according to the Affymetrix protocol.
| | Sample_data_processing | Probe level normalization was conducted using the variance stabilization method of Huber et al. (Huber et al., 2002, Bioinformatics 18 Suppl 1:S96-104)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ralf,,Küppers
| | Sample_contact_email | ralf.kueppers@uk-essen.de
| | Sample_contact_phone | 0049 201 723 3384
| | Sample_contact_fax | 0049 201 723 3386
| | Sample_contact_department | Institute for Cell Biology (Tumor Research)
| | Sample_contact_institute | University of Duisburg-Essen, Medical School
| | Sample_contact_address | Virchowstr. 173
| | Sample_contact_city | Essen
| | Sample_contact_zip/postal_code | 45122
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312946/suppl/GSM312946.CEL.gz
| | Sample_series_id | GSE12453
| | Sample_data_row_count | 54675
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