Search results for the GEO ID: GSE21252  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM531248 | GPL96 |
|
Daudi + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h), rep1
|
Daudi, A/T treatment
|
cell line: Daudi
cell type: B-cell lymphoma cells
treatment: 5-aza-dC, trichostatin A
|
Daudi_A/T-treated _1
|
| Sample_geo_accession | GSM531248
| | Sample_status | Public on May 05 2011
| | Sample_submission_date | Apr 07 2010
| | Sample_last_update_date | May 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A/T-treatment: B-cell lines were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA.
| | Sample_growth_protocol_ch1 | Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
| | Sample_data_processing | We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Volkhard,,Seitz
| | Sample_contact_email | Volkhard.Seitz@charite.de
| | Sample_contact_department | Institute of Pathology
| | Sample_contact_institute | Charité Universitätsmedizin
| | Sample_contact_address | Hindenburgdamm 30
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 12200
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531248/suppl/GSM531248_Daudi_A_T_treated_1.CEL.gz
| | Sample_relation | Reanalysis of: GSM207568
| | Sample_series_id | GSE21252
| | Sample_series_id | GSE21254
| | Sample_data_row_count | 22283
| | |
|
GSM531249 | GPL96 |
|
Daudi + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h), rep2
|
Daudi, A/T treatment
|
cell line: Daudi
cell type: B-cell lymphoma cells
treatment: 5-aza-dC, trichostatin A
|
Daudi_A/T-treated_2
|
| Sample_geo_accession | GSM531249
| | Sample_status | Public on May 05 2011
| | Sample_submission_date | Apr 07 2010
| | Sample_last_update_date | May 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A/T-treatment: B-cell lines were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA.
| | Sample_growth_protocol_ch1 | Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
| | Sample_data_processing | We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Volkhard,,Seitz
| | Sample_contact_email | Volkhard.Seitz@charite.de
| | Sample_contact_department | Institute of Pathology
| | Sample_contact_institute | Charité Universitätsmedizin
| | Sample_contact_address | Hindenburgdamm 30
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 12200
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531249/suppl/GSM531249_Daudi_A_T_treated_2.CEL.gz
| | Sample_relation | Reanalysis of: GSM207577
| | Sample_series_id | GSE21252
| | Sample_series_id | GSE21254
| | Sample_data_row_count | 22283
| | |
|
GSM531250 | GPL96 |
|
Daudi untreated, rep1
|
Daudi, untreated
|
cell line: Daudi
cell type: B-cell lymphoma cells
treatment: untreated
|
Daudi_untreated_1
|
| Sample_geo_accession | GSM531250
| | Sample_status | Public on May 05 2011
| | Sample_submission_date | Apr 07 2010
| | Sample_last_update_date | May 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A/T-treatment: B-cell lines were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA.
| | Sample_growth_protocol_ch1 | Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
| | Sample_data_processing | We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Volkhard,,Seitz
| | Sample_contact_email | Volkhard.Seitz@charite.de
| | Sample_contact_department | Institute of Pathology
| | Sample_contact_institute | Charité Universitätsmedizin
| | Sample_contact_address | Hindenburgdamm 30
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 12200
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531250/suppl/GSM531250_Daudi_1.CEL.gz
| | Sample_relation | Reanalysis of: GSM207578
| | Sample_series_id | GSE21252
| | Sample_series_id | GSE21254
| | Sample_data_row_count | 22283
| | |
|
GSM531251 | GPL96 |
|
Daudi untreated, rep2
|
Daudi, untreated
|
cell line: Daudi
cell type: B-cell lymphoma cells
treatment: untreated
|
Daudi_untreated_2
|
| Sample_geo_accession | GSM531251
| | Sample_status | Public on May 05 2011
| | Sample_submission_date | Apr 07 2010
| | Sample_last_update_date | May 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A/T-treatment: B-cell lines were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA.
| | Sample_growth_protocol_ch1 | Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
| | Sample_data_processing | We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Volkhard,,Seitz
| | Sample_contact_email | Volkhard.Seitz@charite.de
| | Sample_contact_department | Institute of Pathology
| | Sample_contact_institute | Charité Universitätsmedizin
| | Sample_contact_address | Hindenburgdamm 30
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 12200
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531251/suppl/GSM531251_Daudi_2.CEL.gz
| | Sample_relation | Reanalysis of: GSM207579
| | Sample_series_id | GSE21252
| | Sample_series_id | GSE21254
| | Sample_data_row_count | 22283
| | |
|
GSM531252 | GPL96 |
|
Namalwa + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h), rep1
|
Namalwa, A/T treatment
|
cell line: Namalwa
cell type: B-cell lymphoma cells
treatment: 5-aza-dC, trichostatin A
|
Namalwa_A/T-treated_1
|
| Sample_geo_accession | GSM531252
| | Sample_status | Public on May 05 2011
| | Sample_submission_date | Apr 07 2010
| | Sample_last_update_date | May 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A/T-treatment: B-cell lines were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA.
| | Sample_growth_protocol_ch1 | Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
| | Sample_data_processing | We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Volkhard,,Seitz
| | Sample_contact_email | Volkhard.Seitz@charite.de
| | Sample_contact_department | Institute of Pathology
| | Sample_contact_institute | Charité Universitätsmedizin
| | Sample_contact_address | Hindenburgdamm 30
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 12200
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531252/suppl/GSM531252_Namalwa_A_T_treated_1.CEL.gz
| | Sample_relation | Reanalysis of: GSM207638
| | Sample_series_id | GSE21252
| | Sample_series_id | GSE21254
| | Sample_data_row_count | 22283
| | |
|
GSM531253 | GPL96 |
|
Namalwa + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h), rep2
|
Namalwa, A/T treatment
|
cell line: Namalwa
cell type: B-cell lymphoma cells
treatment: 5-aza-dC, trichostatin A
|
Namalwa_A/T-treated_2
|
| Sample_geo_accession | GSM531253
| | Sample_status | Public on May 05 2011
| | Sample_submission_date | Apr 07 2010
| | Sample_last_update_date | May 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A/T-treatment: B-cell lines were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA.
| | Sample_growth_protocol_ch1 | Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
| | Sample_data_processing | We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Volkhard,,Seitz
| | Sample_contact_email | Volkhard.Seitz@charite.de
| | Sample_contact_department | Institute of Pathology
| | Sample_contact_institute | Charité Universitätsmedizin
| | Sample_contact_address | Hindenburgdamm 30
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 12200
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531253/suppl/GSM531253_Namalwa_A_T_treated_2.CEL.gz
| | Sample_relation | Reanalysis of: GSM207639
| | Sample_series_id | GSE21252
| | Sample_series_id | GSE21254
| | Sample_data_row_count | 22283
| | |
|
GSM531254 | GPL96 |
|
Namalwa untreated, rep1
|
Namalwa, untreated
|
cell line: Namalwa
cell type: B-cell lymphoma cells
treatment: untreated
|
Namalwa_untreated_1
|
| Sample_geo_accession | GSM531254
| | Sample_status | Public on May 05 2011
| | Sample_submission_date | Apr 07 2010
| | Sample_last_update_date | May 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A/T-treatment: B-cell lines were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA.
| | Sample_growth_protocol_ch1 | Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
| | Sample_data_processing | We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Volkhard,,Seitz
| | Sample_contact_email | Volkhard.Seitz@charite.de
| | Sample_contact_department | Institute of Pathology
| | Sample_contact_institute | Charité Universitätsmedizin
| | Sample_contact_address | Hindenburgdamm 30
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 12200
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531254/suppl/GSM531254_Namalwa_1.CEL.gz
| | Sample_relation | Reanalysis of: GSM207640
| | Sample_series_id | GSE21252
| | Sample_series_id | GSE21254
| | Sample_data_row_count | 22283
| | |
|
GSM531255 | GPL96 |
|
Namalwa untreated, rep2
|
Namalwa, untreated
|
cell line: Namalwa
cell type: B-cell lymphoma cells
treatment: untreated
|
Namalwa_untreated_2
|
| Sample_geo_accession | GSM531255
| | Sample_status | Public on May 05 2011
| | Sample_submission_date | Apr 07 2010
| | Sample_last_update_date | May 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A/T-treatment: B-cell lines were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA.
| | Sample_growth_protocol_ch1 | Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
| | Sample_data_processing | We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Volkhard,,Seitz
| | Sample_contact_email | Volkhard.Seitz@charite.de
| | Sample_contact_department | Institute of Pathology
| | Sample_contact_institute | Charité Universitätsmedizin
| | Sample_contact_address | Hindenburgdamm 30
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 12200
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531255/suppl/GSM531255_Namalwa_2.CEL.gz
| | Sample_relation | Reanalysis of: GSM207641
| | Sample_series_id | GSE21252
| | Sample_series_id | GSE21254
| | Sample_data_row_count | 22283
| | |
|
GSM531256 | GPL96 |
|
Raji + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h), rep1
|
Raji, A/T treatment
|
cell line: Raji
cell type: B-cell lymphoma cells
treatment: 5-aza-dC, trichostatin A
|
Raji_A/T-treated_1
|
| Sample_geo_accession | GSM531256
| | Sample_status | Public on May 05 2011
| | Sample_submission_date | Apr 07 2010
| | Sample_last_update_date | May 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A/T-treatment: B-cell lines were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA.
| | Sample_growth_protocol_ch1 | Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
| | Sample_data_processing | We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Volkhard,,Seitz
| | Sample_contact_email | Volkhard.Seitz@charite.de
| | Sample_contact_department | Institute of Pathology
| | Sample_contact_institute | Charité Universitätsmedizin
| | Sample_contact_address | Hindenburgdamm 30
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 12200
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531256/suppl/GSM531256_Raji_A_T_treated_1.CEL.gz
| | Sample_relation | Reanalysis of: GSM207642
| | Sample_series_id | GSE21252
| | Sample_series_id | GSE21254
| | Sample_data_row_count | 22283
| | |
|
GSM531257 | GPL96 |
|
Raji + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h), rep2
|
Raji, A/T treatment
|
cell line: Raji
cell type: B-cell lymphoma cells
treatment: 5-aza-dC, trichostatin A
|
Raji_A/T-treated_2
|
| Sample_geo_accession | GSM531257
| | Sample_status | Public on May 05 2011
| | Sample_submission_date | Apr 07 2010
| | Sample_last_update_date | May 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A/T-treatment: B-cell lines were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA.
| | Sample_growth_protocol_ch1 | Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
| | Sample_data_processing | We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Volkhard,,Seitz
| | Sample_contact_email | Volkhard.Seitz@charite.de
| | Sample_contact_department | Institute of Pathology
| | Sample_contact_institute | Charité Universitätsmedizin
| | Sample_contact_address | Hindenburgdamm 30
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 12200
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531257/suppl/GSM531257_Raji_A_T_treated_2.CEL.gz
| | Sample_relation | Reanalysis of: GSM207643
| | Sample_series_id | GSE21252
| | Sample_series_id | GSE21254
| | Sample_data_row_count | 22283
| | |
|
GSM531258 | GPL96 |
|
Raji untreated, rep1
|
Raji, untreated
|
cell line: Raji
cell type: B-cell lymphoma cells
treatment: untreated
|
Raji_untreated_1
|
| Sample_geo_accession | GSM531258
| | Sample_status | Public on May 05 2011
| | Sample_submission_date | Apr 07 2010
| | Sample_last_update_date | May 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A/T-treatment: B-cell lines were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA.
| | Sample_growth_protocol_ch1 | Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
| | Sample_data_processing | We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Volkhard,,Seitz
| | Sample_contact_email | Volkhard.Seitz@charite.de
| | Sample_contact_department | Institute of Pathology
| | Sample_contact_institute | Charité Universitätsmedizin
| | Sample_contact_address | Hindenburgdamm 30
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 12200
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531258/suppl/GSM531258_Raji_1.CEL.gz
| | Sample_relation | Reanalysis of: GSM207644
| | Sample_series_id | GSE21252
| | Sample_series_id | GSE21254
| | Sample_data_row_count | 22283
| | |
|
GSM531259 | GPL96 |
|
Raji untreated, rep2
|
Raji, untreated
|
cell line: Raji
cell type: B-cell lymphoma cells
treatment: untreated
|
Raji_untreated_2
|
| Sample_geo_accession | GSM531259
| | Sample_status | Public on May 05 2011
| | Sample_submission_date | Apr 07 2010
| | Sample_last_update_date | May 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A/T-treatment: B-cell lines were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA.
| | Sample_growth_protocol_ch1 | Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
| | Sample_data_processing | We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Volkhard,,Seitz
| | Sample_contact_email | Volkhard.Seitz@charite.de
| | Sample_contact_department | Institute of Pathology
| | Sample_contact_institute | Charité Universitätsmedizin
| | Sample_contact_address | Hindenburgdamm 30
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 12200
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531259/suppl/GSM531259_Raji_2.CEL.gz
| | Sample_relation | Reanalysis of: GSM207645
| | Sample_series_id | GSE21252
| | Sample_series_id | GSE21254
| | Sample_data_row_count | 22283
| | |
|
GSM531260 | GPL96 |
|
SU-DHL4 + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h), rep1
|
SU-DHL4, A/T treatment
|
cell line: SU-DHL4
cell type: B-cell lymphoma cells
treatment: 5-aza-dC, trichostatin A
|
SU-DHL4_A/T-treated_1
|
| Sample_geo_accession | GSM531260
| | Sample_status | Public on May 05 2011
| | Sample_submission_date | Apr 07 2010
| | Sample_last_update_date | May 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A/T-treatment: B-cell lines were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA.
| | Sample_growth_protocol_ch1 | Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
| | Sample_data_processing | We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Volkhard,,Seitz
| | Sample_contact_email | Volkhard.Seitz@charite.de
| | Sample_contact_department | Institute of Pathology
| | Sample_contact_institute | Charité Universitätsmedizin
| | Sample_contact_address | Hindenburgdamm 30
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 12200
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531260/suppl/GSM531260_SU-DHL4_A_T_treated_1.CEL.gz
| | Sample_series_id | GSE21252
| | Sample_series_id | GSE21254
| | Sample_data_row_count | 22283
| | |
|
GSM531261 | GPL96 |
|
SU-DHL4 + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h), rep2
|
SU-DHL4, A/T treatment
|
cell line: SU-DHL4
cell type: B-cell lymphoma cells
treatment: 5-aza-dC, trichostatin A
|
SU-DHL4_A/T-treated_2
|
| Sample_geo_accession | GSM531261
| | Sample_status | Public on May 05 2011
| | Sample_submission_date | Apr 07 2010
| | Sample_last_update_date | May 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A/T-treatment: B-cell lines were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA.
| | Sample_growth_protocol_ch1 | Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
| | Sample_data_processing | We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Volkhard,,Seitz
| | Sample_contact_email | Volkhard.Seitz@charite.de
| | Sample_contact_department | Institute of Pathology
| | Sample_contact_institute | Charité Universitätsmedizin
| | Sample_contact_address | Hindenburgdamm 30
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 12200
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531261/suppl/GSM531261_SU-DHL4_A_T_treated_2.CEL.gz
| | Sample_series_id | GSE21252
| | Sample_series_id | GSE21254
| | Sample_data_row_count | 22283
| | |
|
GSM531262 | GPL96 |
|
SU-DHL4 untreated, rep1
|
SU-DHL4, untreated
|
cell line: SU-DHL4
cell type: B-cell lymphoma cells
treatment: untreated
|
SU-DHL4_untreated_1
|
| Sample_geo_accession | GSM531262
| | Sample_status | Public on May 05 2011
| | Sample_submission_date | Apr 07 2010
| | Sample_last_update_date | May 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A/T-treatment: B-cell lines were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA.
| | Sample_growth_protocol_ch1 | Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
| | Sample_data_processing | We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Volkhard,,Seitz
| | Sample_contact_email | Volkhard.Seitz@charite.de
| | Sample_contact_department | Institute of Pathology
| | Sample_contact_institute | Charité Universitätsmedizin
| | Sample_contact_address | Hindenburgdamm 30
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 12200
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531262/suppl/GSM531262_SU-DHL4_1.CEL.gz
| | Sample_series_id | GSE21252
| | Sample_series_id | GSE21254
| | Sample_data_row_count | 22283
| | |
|
GSM531263 | GPL96 |
|
SU-DHL4 untreated, rep2
|
SU-DHL4, untreated
|
cell line: SU-DHL4
cell type: B-cell lymphoma cells
treatment: untreated
|
SU-DHL4_untreated_2
|
| Sample_geo_accession | GSM531263
| | Sample_status | Public on May 05 2011
| | Sample_submission_date | Apr 07 2010
| | Sample_last_update_date | May 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A/T-treatment: B-cell lines were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA.
| | Sample_growth_protocol_ch1 | Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
| | Sample_data_processing | We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Volkhard,,Seitz
| | Sample_contact_email | Volkhard.Seitz@charite.de
| | Sample_contact_department | Institute of Pathology
| | Sample_contact_institute | Charité Universitätsmedizin
| | Sample_contact_address | Hindenburgdamm 30
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 12200
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531263/suppl/GSM531263_SU-DHL4_2.CEL.gz
| | Sample_series_id | GSE21252
| | Sample_series_id | GSE21254
| | Sample_data_row_count | 22283
| | |
|
GSM531264 | GPL96 |
|
SU-DHL6 + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h), rep1
|
SU-DHL6, A/T treatment
|
cell line: SU-DHL6
cell type: B-cell lymphoma cells
treatment: 5-aza-dC, trichostatin A
|
SU-DHL6_A/T-treated_1
|
| Sample_geo_accession | GSM531264
| | Sample_status | Public on May 05 2011
| | Sample_submission_date | Apr 07 2010
| | Sample_last_update_date | May 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A/T-treatment: B-cell lines were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA.
| | Sample_growth_protocol_ch1 | Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
| | Sample_data_processing | We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Volkhard,,Seitz
| | Sample_contact_email | Volkhard.Seitz@charite.de
| | Sample_contact_department | Institute of Pathology
| | Sample_contact_institute | Charité Universitätsmedizin
| | Sample_contact_address | Hindenburgdamm 30
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 12200
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531264/suppl/GSM531264_SU-DHL6_A_T_treated_1.CEL.gz
| | Sample_series_id | GSE21252
| | Sample_series_id | GSE21254
| | Sample_data_row_count | 22283
| | |
|
GSM531265 | GPL96 |
|
SU-DHL6 + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h), rep2
|
SU-DHL6, A/T treatment
|
cell line: SU-DHL6
cell type: B-cell lymphoma cells
treatment: 5-aza-dC, trichostatin A
|
SU-DHL6_A/T-treated_2
|
| Sample_geo_accession | GSM531265
| | Sample_status | Public on May 05 2011
| | Sample_submission_date | Apr 07 2010
| | Sample_last_update_date | May 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A/T-treatment: B-cell lines were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA.
| | Sample_growth_protocol_ch1 | Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
| | Sample_data_processing | We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Volkhard,,Seitz
| | Sample_contact_email | Volkhard.Seitz@charite.de
| | Sample_contact_department | Institute of Pathology
| | Sample_contact_institute | Charité Universitätsmedizin
| | Sample_contact_address | Hindenburgdamm 30
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 12200
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531265/suppl/GSM531265_SU-DHL6_A_T_treated_2.CEL.gz
| | Sample_series_id | GSE21252
| | Sample_series_id | GSE21254
| | Sample_data_row_count | 22283
| | |
|
GSM531266 | GPL96 |
|
SU-DHL6 untreated, rep1
|
SU-DHL6, untreated
|
cell line: SU-DHL6
cell type: B-cell lymphoma cells
treatment: untreated
|
SU-DHL6_untreated_1
|
| Sample_geo_accession | GSM531266
| | Sample_status | Public on May 05 2011
| | Sample_submission_date | Apr 07 2010
| | Sample_last_update_date | May 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A/T-treatment: B-cell lines were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA.
| | Sample_growth_protocol_ch1 | Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
| | Sample_data_processing | We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Volkhard,,Seitz
| | Sample_contact_email | Volkhard.Seitz@charite.de
| | Sample_contact_department | Institute of Pathology
| | Sample_contact_institute | Charité Universitätsmedizin
| | Sample_contact_address | Hindenburgdamm 30
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 12200
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531266/suppl/GSM531266_SU-DHL6_1.CEL.gz
| | Sample_series_id | GSE21252
| | Sample_series_id | GSE21254
| | Sample_data_row_count | 22283
| | |
|
GSM531267 | GPL96 |
|
SU-DHL6 untreated, rep2
|
SU-DHL6, untreated
|
cell line: SU-DHL6
cell type: B-cell lymphoma cells
treatment: untreated
|
SU-DHL6_untreated_2
|
| Sample_geo_accession | GSM531267
| | Sample_status | Public on May 05 2011
| | Sample_submission_date | Apr 07 2010
| | Sample_last_update_date | May 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A/T-treatment: B-cell lines were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA.
| | Sample_growth_protocol_ch1 | Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
| | Sample_data_processing | We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Volkhard,,Seitz
| | Sample_contact_email | Volkhard.Seitz@charite.de
| | Sample_contact_department | Institute of Pathology
| | Sample_contact_institute | Charité Universitätsmedizin
| | Sample_contact_address | Hindenburgdamm 30
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 12200
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531267/suppl/GSM531267_SU-DHL6_2.CEL.gz
| | Sample_series_id | GSE21252
| | Sample_series_id | GSE21254
| | Sample_data_row_count | 22283
| | |
|
GSM531268 | GPL96 |
|
HT + 5 µM 5-aza-dC (6 days) + 625 nM TSA (24 h)
|
HT, A/T treatment
|
cell line: HT
cell type: B-cell lymphoma cells
treatment: 5-aza-dC, trichostatin A
|
HT_A/T_treated
|
| Sample_geo_accession | GSM531268
| | Sample_status | Public on May 05 2011
| | Sample_submission_date | Apr 07 2010
| | Sample_last_update_date | May 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A/T-treatment: B-cell lines were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA.
| | Sample_growth_protocol_ch1 | Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
| | Sample_data_processing | We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Volkhard,,Seitz
| | Sample_contact_email | Volkhard.Seitz@charite.de
| | Sample_contact_department | Institute of Pathology
| | Sample_contact_institute | Charité Universitätsmedizin
| | Sample_contact_address | Hindenburgdamm 30
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 12200
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531268/suppl/GSM531268_HT_A_T_treated.CEL.gz
| | Sample_series_id | GSE21252
| | Sample_series_id | GSE21254
| | Sample_data_row_count | 22283
| | |
|
GSM531269 | GPL96 |
|
HT
|
HT, untreated
|
cell line: HT
cell type: B-cell lymphoma cells
treatment: untreated
|
HT_untreated
|
| Sample_geo_accession | GSM531269
| | Sample_status | Public on May 05 2011
| | Sample_submission_date | Apr 07 2010
| | Sample_last_update_date | May 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A/T-treatment: B-cell lines were treated with 5-aza-dC at a concentration of 3 µM for 6 days. 5-aza-dC and medium was replaced at day 2 and 5. At the fifth day - in addition to 3 µM 5-aza-dC - cells were incubated for 24 hours with 625 nM TSA.
| | Sample_growth_protocol_ch1 | Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between Hodgkin and B-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.
| | Sample_data_processing | We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Volkhard,,Seitz
| | Sample_contact_email | Volkhard.Seitz@charite.de
| | Sample_contact_department | Institute of Pathology
| | Sample_contact_institute | Charité Universitätsmedizin
| | Sample_contact_address | Hindenburgdamm 30
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | 12200
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM531nnn/GSM531269/suppl/GSM531269_HT.CEL.gz
| | Sample_series_id | GSE21252
| | Sample_series_id | GSE21254
| | Sample_data_row_count | 22283
| | |
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