Search results for the GEO ID: GSE17354  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM433804 | GPL96 |
|
CD4+ T-cells_healty control_donor1
|
CD4+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the healthy control C1
|
tissue: peripheral blood
cell type: CD4+ T-cells
treatment type: normal donor
|
Gene expression data from CD4+ T-cells isolated from healty control
|
| Sample_geo_accession | GSM433804
| | Sample_status | Public on Jul 29 2009
| | Sample_submission_date | Jul 27 2009
| | Sample_last_update_date | Jul 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Mononuclear cells from peripheral blood were isolated by density gradient centrifugation on Ficoll-Hypaque (Nycomed Pharma A/S). Thereafter, the CD4 and CD8 T-cell subsets were purified with positive selection by immunomagnetic technique using anti-CD4 and anti-CD8 antibody-coated microbeads (Miltenyi Biotec). Two steps of purification were performed to increase the purity to greater than 98%-99%. RNA was directly extracted from cell pellets.
| | Sample_growth_protocol_ch1 | Heparinized blood samples were obtained from patients with ADA-SCID and age-matched healthy controls after parents of patients gave informed consent following standard ethical procedures and with the approval of the Institutional Ethical Committee and immediately processed for mononuclear cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from 1x10^6 cells using Eurozol reagent (Euroclone S.p.A., Italy) according to the manufacturer's instructions. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration, purity, and integrity of RNA samples using Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The one-cycle target labeling assay was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 5 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration, quality and to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Affymetrix Human HG-U133A GeneChip array hybridization and staining was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). The fragmented cRNA were hybridized to an identical lot of Affymetrix Human HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 enabled for High-Resolution Scanning.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Data analysis was performed using GeneSpring® GX 7.3.1 version (Agilent Technologies).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alessandro,,Aiuti
| | Sample_contact_email | a.aiuti@hsr.it
| | Sample_contact_phone | +39-02-26434435
| | Sample_contact_fax | +39-02-26434668
| | Sample_contact_institute | San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET)
| | Sample_contact_address | via olgettina 58
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433804/suppl/GSM433804.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433804/suppl/GSM433804.CHP.gz
| | Sample_series_id | GSE17354
| | Sample_data_row_count | 22283
| | |
|
GSM433805 | GPL96 |
|
CD8+ T-cells_healty control_donor1
|
CD8+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the healthy control C1
|
tissue: peripheral blood
cell type: CD8+ T-cells
treatment type: normal donor
|
Gene expression data from CD8+ T-cells isolated from healty control
|
| Sample_geo_accession | GSM433805
| | Sample_status | Public on Jul 29 2009
| | Sample_submission_date | Jul 27 2009
| | Sample_last_update_date | Jul 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Mononuclear cells from peripheral blood were isolated by density gradient centrifugation on Ficoll-Hypaque (Nycomed Pharma A/S). Thereafter, the CD4 and CD8 T-cell subsets were purified with positive selection by immunomagnetic technique using anti-CD4 and anti-CD8 antibody-coated microbeads (Miltenyi Biotec). Two steps of purification were performed to increase the purity to greater than 98%-99%. RNA was directly extracted from cell pellets.
| | Sample_growth_protocol_ch1 | Heparinized blood samples were obtained from patients with ADA-SCID and age-matched healthy controls after parents of patients gave informed consent following standard ethical procedures and with the approval of the Institutional Ethical Committee and immediately processed for mononuclear cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from 1x10^6 cells using Eurozol reagent (Euroclone S.p.A., Italy) according to the manufacturer's instructions. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration, purity, and integrity of RNA samples using Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The one-cycle target labeling assay was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 5 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration, quality and to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Affymetrix Human HG-U133A GeneChip array hybridization and staining was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). The fragmented cRNA were hybridized to an identical lot of Affymetrix Human HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 enabled for High-Resolution Scanning.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Data analysis was performed using GeneSpring® GX 7.3.1 version (Agilent Technologies).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alessandro,,Aiuti
| | Sample_contact_email | a.aiuti@hsr.it
| | Sample_contact_phone | +39-02-26434435
| | Sample_contact_fax | +39-02-26434668
| | Sample_contact_institute | San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET)
| | Sample_contact_address | via olgettina 58
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433805/suppl/GSM433805.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433805/suppl/GSM433805.CHP.gz
| | Sample_series_id | GSE17354
| | Sample_data_row_count | 22283
| | |
|
GSM433806 | GPL96 |
|
CD4+ T-cells_healty control_donor2
|
CD4+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the healthy control C2
|
tissue: peripheral blood
cell type: CD4+ T-cells
treatment type: normal donor
|
Gene expression data from CD4+ T-cells isolated from healty control
|
| Sample_geo_accession | GSM433806
| | Sample_status | Public on Jul 29 2009
| | Sample_submission_date | Jul 27 2009
| | Sample_last_update_date | Jul 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Mononuclear cells from peripheral blood were isolated by density gradient centrifugation on Ficoll-Hypaque (Nycomed Pharma A/S). Thereafter, the CD4 and CD8 T-cell subsets were purified with positive selection by immunomagnetic technique using anti-CD4 and anti-CD8 antibody-coated microbeads (Miltenyi Biotec). Two steps of purification were performed to increase the purity to greater than 98%-99%. RNA was directly extracted from cell pellets.
| | Sample_growth_protocol_ch1 | Heparinized blood samples were obtained from patients with ADA-SCID and age-matched healthy controls after parents of patients gave informed consent following standard ethical procedures and with the approval of the Institutional Ethical Committee and immediately processed for mononuclear cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from 1x10^6 cells using Eurozol reagent (Euroclone S.p.A., Italy) according to the manufacturer's instructions. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration, purity, and integrity of RNA samples using Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The one-cycle target labeling assay was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 5 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration, quality and to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Affymetrix Human HG-U133A GeneChip array hybridization and staining was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). The fragmented cRNA were hybridized to an identical lot of Affymetrix Human HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 enabled for High-Resolution Scanning.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Data analysis was performed using GeneSpring® GX 7.3.1 version (Agilent Technologies).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alessandro,,Aiuti
| | Sample_contact_email | a.aiuti@hsr.it
| | Sample_contact_phone | +39-02-26434435
| | Sample_contact_fax | +39-02-26434668
| | Sample_contact_institute | San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET)
| | Sample_contact_address | via olgettina 58
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433806/suppl/GSM433806.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433806/suppl/GSM433806.CHP.gz
| | Sample_series_id | GSE17354
| | Sample_data_row_count | 22283
| | |
|
GSM433807 | GPL96 |
|
CD8+ T-cells_healty control_donor2
|
CD8+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the healthy control C2
|
tissue: peripheral blood
cell type: CD8+ T-cells
treatment type: normal donor
|
Gene expression data from CD8+ T-cells isolated from healty control
|
| Sample_geo_accession | GSM433807
| | Sample_status | Public on Jul 29 2009
| | Sample_submission_date | Jul 27 2009
| | Sample_last_update_date | Jul 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Mononuclear cells from peripheral blood were isolated by density gradient centrifugation on Ficoll-Hypaque (Nycomed Pharma A/S). Thereafter, the CD4 and CD8 T-cell subsets were purified with positive selection by immunomagnetic technique using anti-CD4 and anti-CD8 antibody-coated microbeads (Miltenyi Biotec). Two steps of purification were performed to increase the purity to greater than 98%-99%. RNA was directly extracted from cell pellets.
| | Sample_growth_protocol_ch1 | Heparinized blood samples were obtained from patients with ADA-SCID and age-matched healthy controls after parents of patients gave informed consent following standard ethical procedures and with the approval of the Institutional Ethical Committee and immediately processed for mononuclear cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from 1x10^6 cells using Eurozol reagent (Euroclone S.p.A., Italy) according to the manufacturer's instructions. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration, purity, and integrity of RNA samples using Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The one-cycle target labeling assay was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 5 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration, quality and to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Affymetrix Human HG-U133A GeneChip array hybridization and staining was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). The fragmented cRNA were hybridized to an identical lot of Affymetrix Human HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 enabled for High-Resolution Scanning.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Data analysis was performed using GeneSpring® GX 7.3.1 version (Agilent Technologies).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alessandro,,Aiuti
| | Sample_contact_email | a.aiuti@hsr.it
| | Sample_contact_phone | +39-02-26434435
| | Sample_contact_fax | +39-02-26434668
| | Sample_contact_institute | San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET)
| | Sample_contact_address | via olgettina 58
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433807/suppl/GSM433807.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433807/suppl/GSM433807.CHP.gz
| | Sample_series_id | GSE17354
| | Sample_data_row_count | 22283
| | |
|
GSM433808 | GPL96 |
|
CD4+ T-cells_healty control_donor3
|
CD4+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the healthy control C3
|
tissue: peripheral blood
cell type: CD4+ T-cells
treatment type: normal donor
|
Gene expression data from CD4+ T-cells isolated from healty control
|
| Sample_geo_accession | GSM433808
| | Sample_status | Public on Jul 29 2009
| | Sample_submission_date | Jul 27 2009
| | Sample_last_update_date | Jul 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Mononuclear cells from peripheral blood were isolated by density gradient centrifugation on Ficoll-Hypaque (Nycomed Pharma A/S). Thereafter, the CD4 and CD8 T-cell subsets were purified with positive selection by immunomagnetic technique using anti-CD4 and anti-CD8 antibody-coated microbeads (Miltenyi Biotec). Two steps of purification were performed to increase the purity to greater than 98%-99%. RNA was directly extracted from cell pellets.
| | Sample_growth_protocol_ch1 | Heparinized blood samples were obtained from patients with ADA-SCID and age-matched healthy controls after parents of patients gave informed consent following standard ethical procedures and with the approval of the Institutional Ethical Committee and immediately processed for mononuclear cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from 1x10^6 cells using Eurozol reagent (Euroclone S.p.A., Italy) according to the manufacturer's instructions. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration, purity, and integrity of RNA samples using Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The one-cycle target labeling assay was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 5 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration, quality and to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Affymetrix Human HG-U133A GeneChip array hybridization and staining was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). The fragmented cRNA were hybridized to an identical lot of Affymetrix Human HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 enabled for High-Resolution Scanning.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Data analysis was performed using GeneSpring® GX 7.3.1 version (Agilent Technologies).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alessandro,,Aiuti
| | Sample_contact_email | a.aiuti@hsr.it
| | Sample_contact_phone | +39-02-26434435
| | Sample_contact_fax | +39-02-26434668
| | Sample_contact_institute | San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET)
| | Sample_contact_address | via olgettina 58
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433808/suppl/GSM433808.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433808/suppl/GSM433808.CHP.gz
| | Sample_series_id | GSE17354
| | Sample_data_row_count | 22283
| | |
|
GSM433809 | GPL96 |
|
CD8+ T-cells_healty control_donor3
|
CD8+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the healthy control C3
|
tissue: peripheral blood
cell type: CD8+ T-cells
treatment type: normal donor
|
Gene expression data from CD8+ T-cells isolated from healty control
|
| Sample_geo_accession | GSM433809
| | Sample_status | Public on Jul 29 2009
| | Sample_submission_date | Jul 27 2009
| | Sample_last_update_date | Jul 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Mononuclear cells from peripheral blood were isolated by density gradient centrifugation on Ficoll-Hypaque (Nycomed Pharma A/S). Thereafter, the CD4 and CD8 T-cell subsets were purified with positive selection by immunomagnetic technique using anti-CD4 and anti-CD8 antibody-coated microbeads (Miltenyi Biotec). Two steps of purification were performed to increase the purity to greater than 98%-99%. RNA was directly extracted from cell pellets.
| | Sample_growth_protocol_ch1 | Heparinized blood samples were obtained from patients with ADA-SCID and age-matched healthy controls after parents of patients gave informed consent following standard ethical procedures and with the approval of the Institutional Ethical Committee and immediately processed for mononuclear cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from 1x10^6 cells using Eurozol reagent (Euroclone S.p.A., Italy) according to the manufacturer's instructions. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration, purity, and integrity of RNA samples using Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The one-cycle target labeling assay was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 5 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration, quality and to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Affymetrix Human HG-U133A GeneChip array hybridization and staining was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). The fragmented cRNA were hybridized to an identical lot of Affymetrix Human HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 enabled for High-Resolution Scanning.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Data analysis was performed using GeneSpring® GX 7.3.1 version (Agilent Technologies).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alessandro,,Aiuti
| | Sample_contact_email | a.aiuti@hsr.it
| | Sample_contact_phone | +39-02-26434435
| | Sample_contact_fax | +39-02-26434668
| | Sample_contact_institute | San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET)
| | Sample_contact_address | via olgettina 58
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433809/suppl/GSM433809.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433809/suppl/GSM433809.CHP.gz
| | Sample_series_id | GSE17354
| | Sample_data_row_count | 22283
| | |
|
GSM433810 | GPL96 |
|
CD4+ T-cells_healty control_donor4
|
CD4+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the healthy control C4
|
tissue: peripheral blood
cell type: CD4+ T-cells
treatment type: normal donor
|
Gene expression data from CD4+ T-cells isolated from healty control
|
| Sample_geo_accession | GSM433810
| | Sample_status | Public on Jul 29 2009
| | Sample_submission_date | Jul 27 2009
| | Sample_last_update_date | Jul 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Mononuclear cells from peripheral blood were isolated by density gradient centrifugation on Ficoll-Hypaque (Nycomed Pharma A/S). Thereafter, the CD4 and CD8 T-cell subsets were purified with positive selection by immunomagnetic technique using anti-CD4 and anti-CD8 antibody-coated microbeads (Miltenyi Biotec). Two steps of purification were performed to increase the purity to greater than 98%-99%. RNA was directly extracted from cell pellets.
| | Sample_growth_protocol_ch1 | Heparinized blood samples were obtained from patients with ADA-SCID and age-matched healthy controls after parents of patients gave informed consent following standard ethical procedures and with the approval of the Institutional Ethical Committee and immediately processed for mononuclear cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from 1x10^6 cells using Eurozol reagent (Euroclone S.p.A., Italy) according to the manufacturer's instructions. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration, purity, and integrity of RNA samples using Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The one-cycle target labeling assay was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 5 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration, quality and to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Affymetrix Human HG-U133A GeneChip array hybridization and staining was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). The fragmented cRNA were hybridized to an identical lot of Affymetrix Human HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 enabled for High-Resolution Scanning.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Data analysis was performed using GeneSpring® GX 7.3.1 version (Agilent Technologies).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alessandro,,Aiuti
| | Sample_contact_email | a.aiuti@hsr.it
| | Sample_contact_phone | +39-02-26434435
| | Sample_contact_fax | +39-02-26434668
| | Sample_contact_institute | San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET)
| | Sample_contact_address | via olgettina 58
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433810/suppl/GSM433810.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433810/suppl/GSM433810.CHP.gz
| | Sample_series_id | GSE17354
| | Sample_data_row_count | 22283
| | |
|
GSM433811 | GPL96 |
|
CD8+ T-cells_healty control_donor4
|
CD8+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the healthy control C4
|
tissue: peripheral blood
cell type: CD8+ T-cells
treatment type: normal donor
|
Gene expression data from CD8+ T-cells isolated from healty control
|
| Sample_geo_accession | GSM433811
| | Sample_status | Public on Jul 29 2009
| | Sample_submission_date | Jul 27 2009
| | Sample_last_update_date | Jul 28 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Mononuclear cells from peripheral blood were isolated by density gradient centrifugation on Ficoll-Hypaque (Nycomed Pharma A/S). Thereafter, the CD4 and CD8 T-cell subsets were purified with positive selection by immunomagnetic technique using anti-CD4 and anti-CD8 antibody-coated microbeads (Miltenyi Biotec). Two steps of purification were performed to increase the purity to greater than 98%-99%. RNA was directly extracted from cell pellets.
| | Sample_growth_protocol_ch1 | Heparinized blood samples were obtained from patients with ADA-SCID and age-matched healthy controls after parents of patients gave informed consent following standard ethical procedures and with the approval of the Institutional Ethical Committee and immediately processed for mononuclear cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from 1x10^6 cells using Eurozol reagent (Euroclone S.p.A., Italy) according to the manufacturer's instructions. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration, purity, and integrity of RNA samples using Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The one-cycle target labeling assay was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 5 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration, quality and to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Affymetrix Human HG-U133A GeneChip array hybridization and staining was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). The fragmented cRNA were hybridized to an identical lot of Affymetrix Human HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 enabled for High-Resolution Scanning.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Data analysis was performed using GeneSpring® GX 7.3.1 version (Agilent Technologies).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alessandro,,Aiuti
| | Sample_contact_email | a.aiuti@hsr.it
| | Sample_contact_phone | +39-02-26434435
| | Sample_contact_fax | +39-02-26434668
| | Sample_contact_institute | San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET)
| | Sample_contact_address | via olgettina 58
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433811/suppl/GSM433811.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433811/suppl/GSM433811.CHP.gz
| | Sample_series_id | GSE17354
| | Sample_data_row_count | 22283
| | |
|
GSM433812 | GPL96 |
|
CD4+ T-cells_gene therapy treated ADA-SCID_patient1
|
CD4+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the ADA-SCID patient Pt1
|
tissue: peripheral blood
cell type: CD4+ T-cells
treatment type: gene therapy treated patient
|
Gene expression data from CD4+ T-cells isolated from ADA-SCID patient after autologous transplantation with genetically corrected CD34+cells
|
| Sample_geo_accession | GSM433812
| | Sample_status | Public on Jul 29 2009
| | Sample_submission_date | Jul 27 2009
| | Sample_last_update_date | Oct 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Mononuclear cells from peripheral blood were isolated by density gradient centrifugation on Ficoll-Hypaque (Nycomed Pharma A/S). Thereafter, the CD4 and CD8 T-cell subsets were purified with positive selection by immunomagnetic technique using anti-CD4 and anti-CD8 antibody-coated microbeads (Miltenyi Biotec). Two steps of purification were performed to increase the purity to greater than 98%-99%. RNA was directly extracted from cell pellets.
| | Sample_growth_protocol_ch1 | Heparinized blood samples were obtained from patients with ADA-SCID and age-matched healthy controls after parents of patients gave informed consent following standard ethical procedures and with the approval of the Institutional Ethical Committee and immediately processed for mononuclear cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from 1x10^6 cells using Eurozol reagent (Euroclone S.p.A., Italy) according to the manufacturer's instructions. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration, purity, and integrity of RNA samples using Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The one-cycle target labeling assay was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 5 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration, quality and to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Affymetrix Human HG-U133A GeneChip array hybridization and staining was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). The fragmented cRNA were hybridized to an identical lot of Affymetrix Human HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 enabled for High-Resolution Scanning.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Data analysis was performed using GeneSpring® GX 7.3.1 version (Agilent Technologies).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alessandro,,Aiuti
| | Sample_contact_email | a.aiuti@hsr.it
| | Sample_contact_phone | +39-02-26434435
| | Sample_contact_fax | +39-02-26434668
| | Sample_contact_institute | San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET)
| | Sample_contact_address | via olgettina 58
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433812/suppl/GSM433812.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433812/suppl/GSM433812.CHP.gz
| | Sample_series_id | GSE17354
| | Sample_data_row_count | 22283
| | |
|
GSM433813 | GPL96 |
|
CD4+ T-cells_gene therapy treated ADA-SCID_patient3
|
CD4+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the ADA-SCID patient Pt3
|
tissue: peripheral blood
cell type: CD4+ T-cells
treatment type: gene therapy treated patient
|
Gene expression data from CD4+ T-cells isolated from ADA-SCID patient after autologous transplantation with genetically corrected CD34+cells
|
| Sample_geo_accession | GSM433813
| | Sample_status | Public on Jul 29 2009
| | Sample_submission_date | Jul 27 2009
| | Sample_last_update_date | Oct 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Mononuclear cells from peripheral blood were isolated by density gradient centrifugation on Ficoll-Hypaque (Nycomed Pharma A/S). Thereafter, the CD4 and CD8 T-cell subsets were purified with positive selection by immunomagnetic technique using anti-CD4 and anti-CD8 antibody-coated microbeads (Miltenyi Biotec). Two steps of purification were performed to increase the purity to greater than 98%-99%. RNA was directly extracted from cell pellets.
| | Sample_growth_protocol_ch1 | Heparinized blood samples were obtained from patients with ADA-SCID and age-matched healthy controls after parents of patients gave informed consent following standard ethical procedures and with the approval of the Institutional Ethical Committee and immediately processed for mononuclear cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from 1x10^6 cells using Eurozol reagent (Euroclone S.p.A., Italy) according to the manufacturer's instructions. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration, purity, and integrity of RNA samples using Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The one-cycle target labeling assay was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 5 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration, quality and to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Affymetrix Human HG-U133A GeneChip array hybridization and staining was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). The fragmented cRNA were hybridized to an identical lot of Affymetrix Human HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 enabled for High-Resolution Scanning.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Data analysis was performed using GeneSpring® GX 7.3.1 version (Agilent Technologies).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alessandro,,Aiuti
| | Sample_contact_email | a.aiuti@hsr.it
| | Sample_contact_phone | +39-02-26434435
| | Sample_contact_fax | +39-02-26434668
| | Sample_contact_institute | San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET)
| | Sample_contact_address | via olgettina 58
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433813/suppl/GSM433813.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433813/suppl/GSM433813.CHP.gz
| | Sample_series_id | GSE17354
| | Sample_data_row_count | 22283
| | |
|
GSM433814 | GPL96 |
|
CD8+ T-cells_gene therapy treated ADA-SCID_patient3
|
CD8+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the ADA-SCID patient Pt3
|
tissue: peripheral blood
cell type: CD8+ T-cells
treatment type: gene therapy treated patient
|
Gene expression data from CD8+ T-cells isolated from ADA-SCID patient after autologous transplantation with genetically corrected CD34+cells
|
| Sample_geo_accession | GSM433814
| | Sample_status | Public on Jul 29 2009
| | Sample_submission_date | Jul 27 2009
| | Sample_last_update_date | Oct 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Mononuclear cells from peripheral blood were isolated by density gradient centrifugation on Ficoll-Hypaque (Nycomed Pharma A/S). Thereafter, the CD4 and CD8 T-cell subsets were purified with positive selection by immunomagnetic technique using anti-CD4 and anti-CD8 antibody-coated microbeads (Miltenyi Biotec). Two steps of purification were performed to increase the purity to greater than 98%-99%. RNA was directly extracted from cell pellets.
| | Sample_growth_protocol_ch1 | Heparinized blood samples were obtained from patients with ADA-SCID and age-matched healthy controls after parents of patients gave informed consent following standard ethical procedures and with the approval of the Institutional Ethical Committee and immediately processed for mononuclear cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from 1x10^6 cells using Eurozol reagent (Euroclone S.p.A., Italy) according to the manufacturer's instructions. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration, purity, and integrity of RNA samples using Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The one-cycle target labeling assay was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 5 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration, quality and to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Affymetrix Human HG-U133A GeneChip array hybridization and staining was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). The fragmented cRNA were hybridized to an identical lot of Affymetrix Human HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 enabled for High-Resolution Scanning.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Data analysis was performed using GeneSpring® GX 7.3.1 version (Agilent Technologies).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alessandro,,Aiuti
| | Sample_contact_email | a.aiuti@hsr.it
| | Sample_contact_phone | +39-02-26434435
| | Sample_contact_fax | +39-02-26434668
| | Sample_contact_institute | San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET)
| | Sample_contact_address | via olgettina 58
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433814/suppl/GSM433814.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433814/suppl/GSM433814.CHP.gz
| | Sample_series_id | GSE17354
| | Sample_data_row_count | 22283
| | |
|
GSM433815 | GPL96 |
|
CD4+ T-cells_gene therapy treated ADA-SCID_patient4
|
CD4+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the ADA-SCID patient Pt4
|
tissue: peripheral blood
cell type: CD4+ T-cells
treatment type: gene therapy treated patient
|
Gene expression data from CD4+ T-cells isolated from ADA-SCID patient after autologous transplantation with genetically corrected CD34+cells
|
| Sample_geo_accession | GSM433815
| | Sample_status | Public on Jul 29 2009
| | Sample_submission_date | Jul 27 2009
| | Sample_last_update_date | Oct 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Mononuclear cells from peripheral blood were isolated by density gradient centrifugation on Ficoll-Hypaque (Nycomed Pharma A/S). Thereafter, the CD4 and CD8 T-cell subsets were purified with positive selection by immunomagnetic technique using anti-CD4 and anti-CD8 antibody-coated microbeads (Miltenyi Biotec). Two steps of purification were performed to increase the purity to greater than 98%-99%. RNA was directly extracted from cell pellets.
| | Sample_growth_protocol_ch1 | Heparinized blood samples were obtained from patients with ADA-SCID and age-matched healthy controls after parents of patients gave informed consent following standard ethical procedures and with the approval of the Institutional Ethical Committee and immediately processed for mononuclear cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from 1x10^6 cells using Eurozol reagent (Euroclone S.p.A., Italy) according to the manufacturer's instructions. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration, purity, and integrity of RNA samples using Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The one-cycle target labeling assay was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 5 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration, quality and to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Affymetrix Human HG-U133A GeneChip array hybridization and staining was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). The fragmented cRNA were hybridized to an identical lot of Affymetrix Human HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 enabled for High-Resolution Scanning.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Data analysis was performed using GeneSpring® GX 7.3.1 version (Agilent Technologies).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alessandro,,Aiuti
| | Sample_contact_email | a.aiuti@hsr.it
| | Sample_contact_phone | +39-02-26434435
| | Sample_contact_fax | +39-02-26434668
| | Sample_contact_institute | San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET)
| | Sample_contact_address | via olgettina 58
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433815/suppl/GSM433815.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433815/suppl/GSM433815.CHP.gz
| | Sample_series_id | GSE17354
| | Sample_data_row_count | 22283
| | |
|
GSM433816 | GPL96 |
|
CD8+ T-cells_gene therapy treated ADA-SCID_patient4
|
CD8+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the ADA-SCID patient Pt4
|
tissue: peripheral blood
cell type: CD8+ T-cells
treatment type: gene therapy treated patient
|
Gene expression data from CD8+ T-cells isolated from ADA-SCID patient after autologous transplantation with genetically corrected CD34+cells
|
| Sample_geo_accession | GSM433816
| | Sample_status | Public on Jul 29 2009
| | Sample_submission_date | Jul 27 2009
| | Sample_last_update_date | Oct 19 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Mononuclear cells from peripheral blood were isolated by density gradient centrifugation on Ficoll-Hypaque (Nycomed Pharma A/S). Thereafter, the CD4 and CD8 T-cell subsets were purified with positive selection by immunomagnetic technique using anti-CD4 and anti-CD8 antibody-coated microbeads (Miltenyi Biotec). Two steps of purification were performed to increase the purity to greater than 98%-99%. RNA was directly extracted from cell pellets.
| | Sample_growth_protocol_ch1 | Heparinized blood samples were obtained from patients with ADA-SCID and age-matched healthy controls after parents of patients gave informed consent following standard ethical procedures and with the approval of the Institutional Ethical Committee and immediately processed for mononuclear cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from 1x10^6 cells using Eurozol reagent (Euroclone S.p.A., Italy) according to the manufacturer's instructions. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration, purity, and integrity of RNA samples using Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The one-cycle target labeling assay was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 5 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration, quality and to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Affymetrix Human HG-U133A GeneChip array hybridization and staining was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). The fragmented cRNA were hybridized to an identical lot of Affymetrix Human HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 enabled for High-Resolution Scanning.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Data analysis was performed using GeneSpring® GX 7.3.1 version (Agilent Technologies).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alessandro,,Aiuti
| | Sample_contact_email | a.aiuti@hsr.it
| | Sample_contact_phone | +39-02-26434435
| | Sample_contact_fax | +39-02-26434668
| | Sample_contact_institute | San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET)
| | Sample_contact_address | via olgettina 58
| | Sample_contact_city | Milan
| | Sample_contact_zip/postal_code | 20132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433816/suppl/GSM433816.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM433nnn/GSM433816/suppl/GSM433816.CHP.gz
| | Sample_series_id | GSE17354
| | Sample_data_row_count | 22283
| | |
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