Search results for the GEO ID: GSE33135  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM820619 | GPL570 |
|
HZ-CLL27-UNT
|
peripheral blood mononuclear cells, untreated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Unmutated IGHV gene / high ZAP-70 expresssion
|
High ZAP-70 chronic lymphocytic leukemia sample 27_untreated cells
|
| Sample_geo_accession | GSM820619
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820619/suppl/GSM820619_HZ-CLL27-UNT.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
GSM820620 | GPL570 |
|
HZ-CLL34-UNT
|
peripheral blood mononuclear cells, untreated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Unmutated IGHV gene / high ZAP-70 expresssion
|
High ZAP-70 chronic lymphocytic leukemia sample 34_untreated cells
|
| Sample_geo_accession | GSM820620
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820620/suppl/GSM820620_HZ-CLL34-UNT.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
GSM820621 | GPL570 |
|
HZ-CLL30-UNT
|
peripheral blood mononuclear cells, untreated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Unmutated IGHV gene / high ZAP-70 expresssion
|
High ZAP-70 chronic lymphocytic leukemia sample 30_untreated cells
|
| Sample_geo_accession | GSM820621
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820621/suppl/GSM820621_HZ-CLL30-UNT.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
GSM820622 | GPL570 |
|
HZ-CLL31-UNT
|
peripheral blood mononuclear cells, untreated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Unmutated IGHV gene / high ZAP-70 expresssion
|
High ZAP-70 chronic lymphocytic leukemia sample 31_untreated cells
|
| Sample_geo_accession | GSM820622
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820622/suppl/GSM820622_HZ-CLL31-UNT.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
GSM820623 | GPL570 |
|
HZ-CLL43-UNT
|
peripheral blood mononuclear cells, untreated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Unmutated IGHV gene / high ZAP-70 expresssion
|
High ZAP-70 chronic lymphocytic leukemia sample 43_untreated cells
|
| Sample_geo_accession | GSM820623
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820623/suppl/GSM820623_HZ-CLL43-UNT.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
GSM820624 | GPL570 |
|
HZ-CLL26-UNT
|
peripheral blood mononuclear cells, untreated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Unmutated IGHV gene / high ZAP-70 expresssion
|
High ZAP-70 chronic lymphocytic leukemia sample 26_untreated cells
|
| Sample_geo_accession | GSM820624
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820624/suppl/GSM820624_HZ-CLL26-UNT.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
GSM820625 | GPL570 |
|
HZ-CLL35-UNT
|
peripheral blood mononuclear cells, untreated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Unmutated IGHV gene / high ZAP-70 expresssion
|
High ZAP-70 chronic lymphocytic leukemia sample 35_untreated cells
|
| Sample_geo_accession | GSM820625
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820625/suppl/GSM820625_HZ-CLL35-UNT.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
GSM820626 | GPL570 |
|
HZ-CLL27-DXM
|
peripheral blood mononuclear cells, 6 hours dexamethasone treated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Unmutated IGHV gene / high ZAP-70 expresssion
|
High ZAP-70 chronic lymphocytic leukemia sample 27_treated cells
|
| Sample_geo_accession | GSM820626
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820626/suppl/GSM820626_HZ-CLL27-DXM.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
GSM820627 | GPL570 |
|
HZ-CLL34-DXM
|
peripheral blood mononuclear cells, 6 hours dexamethasone treated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Unmutated IGHV gene / high ZAP-70 expresssion
|
High ZAP-70 chronic lymphocytic leukemia sample 34_treated cells
|
| Sample_geo_accession | GSM820627
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820627/suppl/GSM820627_HZ-CLL34-DXM.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
GSM820628 | GPL570 |
|
HZ-CLL30-DXM
|
peripheral blood mononuclear cells, 6 hours dexamethasone treated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Unmutated IGHV gene / high ZAP-70 expresssion
|
High ZAP-70 chronic lymphocytic leukemia sample 30_treated cells
|
| Sample_geo_accession | GSM820628
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820628/suppl/GSM820628_HZ-CLL30-DXM.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
GSM820629 | GPL570 |
|
HZ-CLL31-DXM
|
peripheral blood mononuclear cells, 6 hours dexamethasone treated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Unmutated IGHV gene / high ZAP-70 expresssion
|
High ZAP-70 chronic lymphocytic leukemia sample 31_treated cells
|
| Sample_geo_accession | GSM820629
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820629/suppl/GSM820629_HZ-CLL31-DXM.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
GSM820630 | GPL570 |
|
HZ-CLL43-DXM
|
peripheral blood mononuclear cells, 6 hours dexamethasone treated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Unmutated IGHV gene / high ZAP-70 expresssion
|
High ZAP-70 chronic lymphocytic leukemia sample 43_treated cells
|
| Sample_geo_accession | GSM820630
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820630/suppl/GSM820630_HZ-CLL43-DXM.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
GSM820631 | GPL570 |
|
HZ-CLL26-DXM
|
peripheral blood mononuclear cells, 6 hours dexamethasone treated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Unmutated IGHV gene / high ZAP-70 expresssion
|
High ZAP-70 chronic lymphocytic leukemia sample 26_treated cells
|
| Sample_geo_accession | GSM820631
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820631/suppl/GSM820631_HZ-CLL26-DXM.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
GSM820632 | GPL570 |
|
HZ-CLL35-DXM
|
peripheral blood mononuclear cells, 6 hours dexamethasone treated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Unmutated IGHV gene / high ZAP-70 expresssion
|
High ZAP-70 chronic lymphocytic leukemia sample 35_treated cells
|
| Sample_geo_accession | GSM820632
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820632/suppl/GSM820632_HZ-CLL35-DXM.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
GSM820633 | GPL570 |
|
LZ-CLL20-UNT
|
peripheral blood mononuclear cells, untreated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Mutated IGHV gene / low ZAP-70 expresssion
|
Low ZAP-70 chronic lymphocytic leukemia sample 20_untreated cells
|
| Sample_geo_accession | GSM820633
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820633/suppl/GSM820633_LZ-CLL20-UNT.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
GSM820634 | GPL570 |
|
LZ-CLL9-UNT
|
peripheral blood mononuclear cells, untreated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Mutated IGHV gene / low ZAP-70 expresssion
|
Low ZAP-70 chronic lymphocytic leukemia sample 9_untreated cells
|
| Sample_geo_accession | GSM820634
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820634/suppl/GSM820634_LZ-CLL9-UNT.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
GSM820635 | GPL570 |
|
LZ-CLL13-UNT
|
peripheral blood mononuclear cells, untreated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Mutated IGHV gene / low ZAP-70 expresssion
|
Low ZAP-70 chronic lymphocytic leukemia sample 13_untreated cells
|
| Sample_geo_accession | GSM820635
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820635/suppl/GSM820635_LZ-CLL13-UNT.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
GSM820636 | GPL570 |
|
LZ-CLL21-UNT
|
peripheral blood mononuclear cells, untreated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Mutated IGHV gene / low ZAP-70 expresssion
|
Low ZAP-70 chronic lymphocytic leukemia sample 21_untreated cells
|
| Sample_geo_accession | GSM820636
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820636/suppl/GSM820636_LZ-CLL21-UNT.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
GSM820637 | GPL570 |
|
LZ-CLL3-UNT
|
peripheral blood mononuclear cells, untreated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Mutated IGHV gene / low ZAP-70 expresssion
|
Low ZAP-70 chronic lymphocytic leukemia sample 3_untreated cells
|
| Sample_geo_accession | GSM820637
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820637/suppl/GSM820637_LZ-CLL3-UNT.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
GSM820638 | GPL570 |
|
LZ-CLL20-DXM
|
peripheral blood mononuclear cells, 6 hours dexamethasone treated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Mutated IGHV gene / low ZAP-70 expresssion
|
Low ZAP-70 chronic lymphocytic leukemia sample 20_treated cells
|
| Sample_geo_accession | GSM820638
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820638/suppl/GSM820638_LZ-CLL20-DXM.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
GSM820639 | GPL570 |
|
LZ-CLL9-DXM
|
peripheral blood mononuclear cells, 6 hours dexamethasone treated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Mutated IGHV gene / low ZAP-70 expresssion
|
Low ZAP-70 chronic lymphocytic leukemia sample 9_treated cells
|
| Sample_geo_accession | GSM820639
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820639/suppl/GSM820639_LZ-CLL9-DXM.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
GSM820640 | GPL570 |
|
LZ-CLL13-DXM
|
peripheral blood mononuclear cells, 6 hours dexamethasone treated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Mutated IGHV gene / low ZAP-70 expresssion
|
Low ZAP-70 chronic lymphocytic leukemia sample 13_treated cells
|
| Sample_geo_accession | GSM820640
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820640/suppl/GSM820640_LZ-CLL13-DXM.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
GSM820641 | GPL570 |
|
LZ-CLL21-DXM
|
peripheral blood mononuclear cells, 6 hours dexamethasone treated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Mutated IGHV gene / low ZAP-70 expresssion
|
Low ZAP-70 chronic lymphocytic leukemia sample 21_treated cells
|
| Sample_geo_accession | GSM820641
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820641/suppl/GSM820641_LZ-CLL21-DXM.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
GSM820642 | GPL570 |
|
LZ-CLL3-DXM
|
peripheral blood mononuclear cells, 6 hours dexamethasone treated
|
cell type: chronic lymphocytic leukemia
ighv/zap-70 status: Mutated IGHV gene / low ZAP-70 expresssion
|
Low ZAP-70 chronic lymphocytic leukemia sample 3_treated cells
|
| Sample_geo_accession | GSM820642
| | Sample_status | Public on Dec 04 2012
| | Sample_submission_date | Oct 21 2011
| | Sample_last_update_date | Dec 04 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were split in two for control and incubation with dexamethasone (Merck KGaA, Darmstadt, Germany) at a pharmacological active concentration of 13.25 µM.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells from CLL patients were thawed at 37ºC and resuspended in standard culture medium (RPMI-1640 medium (Gibco, Paisley, Scotland, UK) supplemented with 10% heat-inactivated FBS (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Lonza, Viviers, Belgium), 2 mM L-glutamine and 1 mM sodium pyruvate (Gibco)) and cultured at 37ºC in a 5% CO2 atmosphere at a density of 1 x 106 cells/ml. Peripheral blood mononuclear cells were allowed to recover from the thawing process for one hour before manipulation
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from 5x105 cells with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)
| | Sample_hyb_protocol | Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).
| | Sample_data_processing | Expression measures were normalized and summarized using the frozen robust multiarray analysis (fRMA) methodology
| | Sample_platform_id | GPL570
| | Sample_contact_name | Maria Joao,,Baptista
| | Sample_contact_email | mjoaobap@hotmail.com
| | Sample_contact_laboratory | Laboratory of Experimental Hematology
| | Sample_contact_department | Department of Hematology
| | Sample_contact_institute | Hospital Vall d’Hebron, Institut Recerca Vall d’Hebron
| | Sample_contact_address | Pg de la Vall d’Hebron 119-129
| | Sample_contact_city | Barcelona
| | Sample_contact_zip/postal_code | 08035
| | Sample_contact_country | Spain
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM820nnn/GSM820642/suppl/GSM820642_LZ-CLL3-DXM.CEL.gz
| | Sample_series_id | GSE33135
| | Sample_data_row_count | 54675
| | |
|
| |
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