Search results for the GEO ID: GSE13909  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM349879 | GPL570 |
|
healthy_donor_43_primary_T_lymphoblasts_before_IL-2_deprivation_biol_rep1
|
IL-2 dependent normal peripheral blood T lymphocytes from IL-2-containing cultures
|
Healthy, male donor, age 36, PBMC
|
healthy_donor_43_primary_T_lymphoblasts_before_IL-2_deprivation_biol_rep1
|
| Sample_geo_accession | GSM349879
| | Sample_status | Public on Aug 13 2009
| | Sample_submission_date | Dec 10 2008
| | Sample_last_update_date | Aug 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Immunology, Cancer Centre and Institute of Oncology, Warsaw, Poland
| | Sample_treatment_protocol_ch1 | Primary, IL-2-dependent T lymphoblast cell lines were generated and propagated as previously described (Siwicki et al., Leuk Res 2008). Briefly, peripheral blood mononuclear cells (PBMC) derived from a healthy donor were suspended in a standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma]), activated for 24 h with 20 μg/ml of wheat germ agglutinin (WGA, Pharmacia) and subsequently cultured in the standard medium supplemented with 20 U/ml of rIL-2 (R&D). Cells were collected after 7-8 population doublings.
| | Sample_growth_protocol_ch1 | As described in treatment protocol - standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma])
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Nucleospin RNA II kit (Macherey-Nagel, Germany).RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano Chip Kit (Agilent Technologies).
| | Sample_label_ch1 | Biotin-Phycoerythrin
| | Sample_label_protocol_ch1 | Affymetrix protocol: 4,5 μg of total RNA was used for cRNA synthesis and fragmented. Single round of amplification and labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation. (http://www.affymetrix.com/products/reagents/specific/one_cycle_target_control.affx)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol, arrays were stained using phycoerythrin and streptavidin complex (http://www.affymetrix.com/products/reagents/specific/eukhyb.affx)
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol: http://www.affymetrix.com/products/instruments/specific/scanner_3000.affx
| | Sample_data_processing | Expression data (.CEL files) were normalized with the GC-RMA algorithm, using Bioconductor gcrma package
| | Sample_platform_id | GPL570
| | Sample_contact_name | Magdalena,,Chechlinska
| | Sample_contact_email | chech@coi.waw.pl
| | Sample_contact_phone | +48225462256
| | Sample_contact_fax | +48226449085
| | Sample_contact_laboratory | Cellular Immunology Laboratory
| | Sample_contact_department | Department of Immunology
| | Sample_contact_institute | Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology
| | Sample_contact_address | Roentgena 5
| | Sample_contact_city | Warszawa
| | Sample_contact_zip/postal_code | 02-781
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM349nnn/GSM349879/suppl/GSM349879.CEL.gz
| | Sample_series_id | GSE13909
| | Sample_data_row_count | 54675
| | |
|
GSM350377 | GPL570 |
|
healthy_donor_43_primary_T_lymphoblasts_8_hours_after_IL-2_deprivation_biol_rep1
|
IL-2 dependent normal peripheral blood T lymphocytes after IL-2 withdrawal
|
Healthy, male donor, age 36, PBMC
|
healthy_donor_43_primary_T_lymphoblasts_8_hours_after_IL-2_deprivation_biol_rep1
|
| Sample_geo_accession | GSM350377
| | Sample_status | Public on Aug 13 2009
| | Sample_submission_date | Dec 11 2008
| | Sample_last_update_date | Aug 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Immunology, Cancer Centre and Institute of Oncology, Warsaw, Poland
| | Sample_treatment_protocol_ch1 | Primary, IL-2-dependent T lymphoblast cell lines were generated and propagated as previously described (Siwicki et al., Leuk Res 2008). Briefly, peripheral blood mononuclear cells (PBMC) derived from a healthy donor were suspended in a standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma]), activated for 24 h with 20 μg/ml of wheat germ agglutinin (WGA, Pharmacia) and subsequently cultured in the standard medium supplemented with 20 U/ml of rIL-2 (R&D). Cell samples were collected after 7-8 population doublings, after 8-hrs incubation without IL-2, following triple thorough washing of the cells.
| | Sample_growth_protocol_ch1 | As described in treatment protocol - standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma])
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Nucleospin RNA II kit (Macherey-Nagel, Germany).RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano Chip Kit (Agilent Technologies).
| | Sample_label_ch1 | Biotin-Phycoerythrin
| | Sample_label_protocol_ch1 | Affymetrix protocol: 4,5 μg of total RNA was used for cRNA synthesis and fragmented. Single round of amplification and labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation. (http://www.affymetrix.com/products/reagents/specific/one_cycle_target_control.affx)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol, arrays were stained using phycoerythrin and streptavidin complex (http://www.affymetrix.com/products/reagents/specific/eukhyb.affx)
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol: http://www.affymetrix.com/products/instruments/specific/scanner_3000.affx
| | Sample_data_processing | Expression data (.CEL files) were normalized with the GC-RMA algorithm, using Bioconductor gcrma package
| | Sample_platform_id | GPL570
| | Sample_contact_name | Magdalena,,Chechlinska
| | Sample_contact_email | chech@coi.waw.pl
| | Sample_contact_phone | +48225462256
| | Sample_contact_fax | +48226449085
| | Sample_contact_laboratory | Cellular Immunology Laboratory
| | Sample_contact_department | Department of Immunology
| | Sample_contact_institute | Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology
| | Sample_contact_address | Roentgena 5
| | Sample_contact_city | Warszawa
| | Sample_contact_zip/postal_code | 02-781
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM350nnn/GSM350377/suppl/GSM350377.CEL.gz
| | Sample_series_id | GSE13909
| | Sample_data_row_count | 54675
| | |
|
GSM350378 | GPL570 |
|
healthy_donor_6_primary_T_lymphoblasts_before_IL-2_deprivation_biol_rep2
|
IL-2 dependent normal peripheral blood T lymphocytes from IL-2-containing cultures
|
Healthy, male donor, age 42, PBMC
|
healthy_donor_6_primary_T_lymphoblasts_before_IL-2_deprivation_biol_rep2
|
| Sample_geo_accession | GSM350378
| | Sample_status | Public on Aug 13 2009
| | Sample_submission_date | Dec 11 2008
| | Sample_last_update_date | Aug 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Immunology, Cancer Centre and Institute of Oncology, Warsaw, Poland
| | Sample_treatment_protocol_ch1 | Primary, IL-2-dependent T lymphoblast cell lines were generated and propagated as previously described (Siwicki et al., Leuk Res 2008). Briefly, peripheral blood mononuclear cells (PBMC) derived from a healthy donor were suspended in a standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma]), activated for 24 h with 20 μg/ml of wheat germ agglutinin (WGA, Pharmacia) and subsequently cultured in the standard medium supplemented with 20 U/ml of rIL-2 (R&D). Cells were collected after 4-5 population doublings.
| | Sample_growth_protocol_ch1 | As described in treatment protocol - standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma])
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Nucleospin RNA II kit (Macherey-Nagel, Germany).RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano Chip Kit (Agilent Technologies).
| | Sample_label_ch1 | Biotin-Phycoerythrin
| | Sample_label_protocol_ch1 | Affymetrix protocol: 4,5 μg of total RNA was used for cRNA synthesis and fragmented. Single round of amplification and labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation. (http://www.affymetrix.com/products/reagents/specific/one_cycle_target_control.affx)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol, arrays were stained using phycoerythrin and streptavidin complex (http://www.affymetrix.com/products/reagents/specific/eukhyb.affx)
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol: http://www.affymetrix.com/products/instruments/specific/scanner_3000.affx
| | Sample_data_processing | Expression data (.CEL files) were normalized with the GC-RMA algorithm, using Bioconductor gcrma package
| | Sample_platform_id | GPL570
| | Sample_contact_name | Magdalena,,Chechlinska
| | Sample_contact_email | chech@coi.waw.pl
| | Sample_contact_phone | +48225462256
| | Sample_contact_fax | +48226449085
| | Sample_contact_laboratory | Cellular Immunology Laboratory
| | Sample_contact_department | Department of Immunology
| | Sample_contact_institute | Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology
| | Sample_contact_address | Roentgena 5
| | Sample_contact_city | Warszawa
| | Sample_contact_zip/postal_code | 02-781
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM350nnn/GSM350378/suppl/GSM350378.CEL.gz
| | Sample_series_id | GSE13909
| | Sample_data_row_count | 54675
| | |
|
GSM350379 | GPL570 |
|
healthy_donor_6_primary_T_lymphoblasts_8_hours_after_IL-2_deprivation_biol_rep2
|
IL-2 dependent normal peripheral blood T lymphocytes after IL-2 withdrawal
|
Healthy, male donor, age 42, PBMC
|
healthy_donor_6_primary_T_lymphoblasts_8_hours_after_IL-2_deprivation_biol_rep2
|
| Sample_geo_accession | GSM350379
| | Sample_status | Public on Aug 13 2009
| | Sample_submission_date | Dec 11 2008
| | Sample_last_update_date | Aug 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Immunology, Cancer Centre and Institute of Oncology, Warsaw, Poland
| | Sample_treatment_protocol_ch1 | Primary, IL-2-dependent T lymphoblast cell lines were generated and propagated as previously described (Siwicki et al., Leuk Res 2008). Briefly, peripheral blood mononuclear cells (PBMC) derived from a healthy donor were suspended in a standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma]), activated for 24 h with 20 μg/ml of wheat germ agglutinin (WGA, Pharmacia) and subsequently cultured in the standard medium supplemented with 20 U/ml of rIL-2 (R&D). Cell samples were collected after 4-5 population doublings, after 8-hrs incubation without IL-2, following triple thorough washing of the cells.
| | Sample_growth_protocol_ch1 | As described in treatment protocol - standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma])
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Nucleospin RNA II kit (Macherey-Nagel, Germany).RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano Chip Kit (Agilent Technologies).
| | Sample_label_ch1 | Biotin-Phycoerythrin
| | Sample_label_protocol_ch1 | Affymetrix protocol: 4,5 μg of total RNA was used for cRNA synthesis and fragmented. Single round of amplification and labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation. (http://www.affymetrix.com/products/reagents/specific/one_cycle_target_control.affx)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol, arrays were stained using phycoerythrin and streptavidin complex (http://www.affymetrix.com/products/reagents/specific/eukhyb.affx)
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol: http://www.affymetrix.com/products/instruments/specific/scanner_3000.affx
| | Sample_data_processing | Expression data (.CEL files) were normalized with the GC-RMA algorithm, using Bioconductor gcrma package
| | Sample_platform_id | GPL570
| | Sample_contact_name | Magdalena,,Chechlinska
| | Sample_contact_email | chech@coi.waw.pl
| | Sample_contact_phone | +48225462256
| | Sample_contact_fax | +48226449085
| | Sample_contact_laboratory | Cellular Immunology Laboratory
| | Sample_contact_department | Department of Immunology
| | Sample_contact_institute | Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology
| | Sample_contact_address | Roentgena 5
| | Sample_contact_city | Warszawa
| | Sample_contact_zip/postal_code | 02-781
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM350nnn/GSM350379/suppl/GSM350379.CEL.gz
| | Sample_series_id | GSE13909
| | Sample_data_row_count | 54675
| | |
|
GSM350380 | GPL570 |
|
immortalised_line5_before_IL-2_deprivation_biol_rep1
|
spontaneously immortalised normal spleen-derived T lymphocytes from IL-2-containing cultures
|
Healthy male, age 56, spleen
|
immortalised_line5_before_IL-2_deprivation_biol_rep1
|
| Sample_geo_accession | GSM350380
| | Sample_status | Public on Aug 13 2009
| | Sample_submission_date | Dec 11 2008
| | Sample_last_update_date | Aug 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Immunology, Cancer Centre and Institute of Oncology, Warsaw, Poland
| | Sample_treatment_protocol_ch1 | Spontaneously immortalized IL-2-dependent T cell line was derived from normal spleen and established and cultured as previously described (Siwicki et al., Exp Gerontol 2000). The cells followed 222 population doublings.
| | Sample_growth_protocol_ch1 | As described in treatment protocol - standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma])
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Nucleospin RNA II kit (Macherey-Nagel, Germany).RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano Chip Kit (Agilent Technologies).
| | Sample_label_ch1 | Biotin-Phycoerythrin
| | Sample_label_protocol_ch1 | Affymetrix protocol: 5 μg of total RNA was used for cRNA synthesis and fragmented. Single round of amplification and labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation. (http://www.affymetrix.com/products/reagents/specific/one_cycle_target_control.affx)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol, arrays were stained using phycoerythrin and streptavidin complex (http://www.affymetrix.com/products/reagents/specific/eukhyb.affx)
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol: http://www.affymetrix.com/products/instruments/specific/scanner_3000.affx
| | Sample_data_processing | Expression data (.CEL files) were normalized with the GC-RMA algorithm, using Bioconductor gcrma package
| | Sample_platform_id | GPL570
| | Sample_contact_name | Magdalena,,Chechlinska
| | Sample_contact_email | chech@coi.waw.pl
| | Sample_contact_phone | +48225462256
| | Sample_contact_fax | +48226449085
| | Sample_contact_laboratory | Cellular Immunology Laboratory
| | Sample_contact_department | Department of Immunology
| | Sample_contact_institute | Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology
| | Sample_contact_address | Roentgena 5
| | Sample_contact_city | Warszawa
| | Sample_contact_zip/postal_code | 02-781
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM350nnn/GSM350380/suppl/GSM350380.CEL.gz
| | Sample_series_id | GSE13909
| | Sample_data_row_count | 54675
| | |
|
GSM350381 | GPL570 |
|
immortalised_line5_before_IL-2_deprivation_biol_rep2
|
spontaneously immortalised normal spleen-derived T lymphocytes from IL-2-containing cultures
|
Healthy male, age 56, spleen
|
immortalised_line5_before_IL-2_deprivation_biol_rep2
|
| Sample_geo_accession | GSM350381
| | Sample_status | Public on Aug 13 2009
| | Sample_submission_date | Dec 11 2008
| | Sample_last_update_date | Aug 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Immunology, Cancer Centre and Institute of Oncology, Warsaw, Poland
| | Sample_treatment_protocol_ch1 | Spontaneously immortalized IL-2-dependent T cell line was derived from normal spleen and established and cultured as previously described (Siwicki et al., Exp Gerontol 2000). The cells followed 222 population doublings.
| | Sample_growth_protocol_ch1 | As described in treatment protocol - standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma])
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Nucleospin RNA II kit (Macherey-Nagel, Germany).RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano Chip Kit (Agilent Technologies).
| | Sample_label_ch1 | Biotin-Phycoerythrin
| | Sample_label_protocol_ch1 | Affymetrix protocol: 5 μg of total RNA was used for cRNA synthesis and fragmented. Single round of amplification and labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation. (http://www.affymetrix.com/products/reagents/specific/one_cycle_target_control.affx)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol, arrays were stained using phycoerythrin and streptavidin complex (http://www.affymetrix.com/products/reagents/specific/eukhyb.affx)
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol: http://www.affymetrix.com/products/instruments/specific/scanner_3000.affx
| | Sample_data_processing | Expression data (.CEL files) were normalized with the GC-RMA algorithm, using Bioconductor gcrma package
| | Sample_platform_id | GPL570
| | Sample_contact_name | Magdalena,,Chechlinska
| | Sample_contact_email | chech@coi.waw.pl
| | Sample_contact_phone | +48225462256
| | Sample_contact_fax | +48226449085
| | Sample_contact_laboratory | Cellular Immunology Laboratory
| | Sample_contact_department | Department of Immunology
| | Sample_contact_institute | Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology
| | Sample_contact_address | Roentgena 5
| | Sample_contact_city | Warszawa
| | Sample_contact_zip/postal_code | 02-781
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM350nnn/GSM350381/suppl/GSM350381.CEL.gz
| | Sample_series_id | GSE13909
| | Sample_data_row_count | 54675
| | |
|
GSM350382 | GPL570 |
|
immortalised_line5_before_IL-2_deprivation_biol_rep3
|
spontaneously immortalised normal spleen-derived T lymphocytes from IL-2-containing cultures
|
Healthy male, age 56, spleen
|
immortalised_line5_before_IL-2_deprivation_biol_rep3
|
| Sample_geo_accession | GSM350382
| | Sample_status | Public on Aug 13 2009
| | Sample_submission_date | Dec 11 2008
| | Sample_last_update_date | Aug 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Immunology, Cancer Centre and Institute of Oncology, Warsaw, Poland
| | Sample_treatment_protocol_ch1 | Spontaneously immortalized IL-2-dependent T cell line was derived from normal spleen and established and cultured as previously described (Siwicki et al., Exp Gerontol 2000). The cells followed 222 population doublings.
| | Sample_growth_protocol_ch1 | As described in treatment protocol - standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma])
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Nucleospin RNA II kit (Macherey-Nagel, Germany).RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano Chip Kit (Agilent Technologies).
| | Sample_label_ch1 | Biotin-Phycoerythrin
| | Sample_label_protocol_ch1 | Affymetrix protocol: 5 μg of total RNA was used for cRNA synthesis and fragmented. Single round of amplification and labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation. (http://www.affymetrix.com/products/reagents/specific/one_cycle_target_control.affx)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol, arrays were stained using phycoerythrin and streptavidin complex (http://www.affymetrix.com/products/reagents/specific/eukhyb.affx)
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol: http://www.affymetrix.com/products/instruments/specific/scanner_3000.affx
| | Sample_data_processing | Expression data (.CEL files) were normalized with the GC-RMA algorithm, using Bioconductor gcrma package
| | Sample_platform_id | GPL570
| | Sample_contact_name | Magdalena,,Chechlinska
| | Sample_contact_email | chech@coi.waw.pl
| | Sample_contact_phone | +48225462256
| | Sample_contact_fax | +48226449085
| | Sample_contact_laboratory | Cellular Immunology Laboratory
| | Sample_contact_department | Department of Immunology
| | Sample_contact_institute | Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology
| | Sample_contact_address | Roentgena 5
| | Sample_contact_city | Warszawa
| | Sample_contact_zip/postal_code | 02-781
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM350nnn/GSM350382/suppl/GSM350382.CEL.gz
| | Sample_series_id | GSE13909
| | Sample_data_row_count | 54675
| | |
|
GSM350383 | GPL570 |
|
immortalised_line5_8_hours_after_IL-2_deprivation_biol_rep1
|
spontaneously immortalised normal spleen-derived T lymphocytes after IL-2 withdrawal
|
Healthy male, age 56, spleen
|
immortalised_line5_8_hours_after_IL-2_deprivation_biol_rep1
|
| Sample_geo_accession | GSM350383
| | Sample_status | Public on Aug 13 2009
| | Sample_submission_date | Dec 11 2008
| | Sample_last_update_date | Aug 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Immunology, Cancer Centre and Institute of Oncology, Warsaw, Poland
| | Sample_treatment_protocol_ch1 | Spontaneously immortalized IL-2-dependent T cell line was derived from normal spleen and established and cultured as previously described (Siwicki et al., Exp Gerontol 2000). The cells followed 222 population doublings. Sample was collected 8 hours following IL-2 withdrawal.
| | Sample_growth_protocol_ch1 | As described in treatment protocol - standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma])
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Nucleospin RNA II kit (Macherey-Nagel, Germany).RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano Chip Kit (Agilent Technologies).
| | Sample_label_ch1 | Biotin-Phycoerythrin
| | Sample_label_protocol_ch1 | Affymetrix protocol: 5 μg of total RNA was used for cRNA synthesis and fragmented. Single round of amplification and labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation. (http://www.affymetrix.com/products/reagents/specific/one_cycle_target_control.affx)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol, arrays were stained using phycoerythrin and streptavidin complex (http://www.affymetrix.com/products/reagents/specific/eukhyb.affx)
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol: http://www.affymetrix.com/products/instruments/specific/scanner_3000.affx
| | Sample_data_processing | Expression data (.CEL files) were normalized with the GC-RMA algorithm, using Bioconductor gcrma package
| | Sample_platform_id | GPL570
| | Sample_contact_name | Magdalena,,Chechlinska
| | Sample_contact_email | chech@coi.waw.pl
| | Sample_contact_phone | +48225462256
| | Sample_contact_fax | +48226449085
| | Sample_contact_laboratory | Cellular Immunology Laboratory
| | Sample_contact_department | Department of Immunology
| | Sample_contact_institute | Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology
| | Sample_contact_address | Roentgena 5
| | Sample_contact_city | Warszawa
| | Sample_contact_zip/postal_code | 02-781
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM350nnn/GSM350383/suppl/GSM350383.CEL.gz
| | Sample_series_id | GSE13909
| | Sample_data_row_count | 54675
| | |
|
GSM350384 | GPL570 |
|
immortalised_line5_8_hours_after_IL-2_deprivation_biol_rep2
|
spontaneously immortalised normal spleen-derived T lymphocytes after IL-2 withdrawal
|
Healthy male, age 56, spleen
|
immortalised_line5_8_hours_after_IL-2_deprivation_biol_rep2
|
| Sample_geo_accession | GSM350384
| | Sample_status | Public on Aug 13 2009
| | Sample_submission_date | Dec 11 2008
| | Sample_last_update_date | Aug 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Immunology, Cancer Centre and Institute of Oncology, Warsaw, Poland
| | Sample_treatment_protocol_ch1 | Spontaneously immortalized IL-2-dependent T cell line was derived from normal spleen and established and cultured as previously described (Siwicki et al., Exp Gerontol 2000). The cells followed 222 population doublings. Sample was collected 8 hours following IL-2 withdrawal.
| | Sample_growth_protocol_ch1 | As described in treatment protocol - standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma])
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Nucleospin RNA II kit (Macherey-Nagel, Germany).RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano Chip Kit (Agilent Technologies).
| | Sample_label_ch1 | Biotin-Phycoerythrin
| | Sample_label_protocol_ch1 | Affymetrix protocol: 5 μg of total RNA was used for cRNA synthesis and fragmented. Single round of amplification and labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation. (http://www.affymetrix.com/products/reagents/specific/one_cycle_target_control.affx)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol, arrays were stained using phycoerythrin and streptavidin complex (http://www.affymetrix.com/products/reagents/specific/eukhyb.affx)
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol: http://www.affymetrix.com/products/instruments/specific/scanner_3000.affx
| | Sample_data_processing | Expression data (.CEL files) were normalized with the GC-RMA algorithm, using Bioconductor gcrma package
| | Sample_platform_id | GPL570
| | Sample_contact_name | Magdalena,,Chechlinska
| | Sample_contact_email | chech@coi.waw.pl
| | Sample_contact_phone | +48225462256
| | Sample_contact_fax | +48226449085
| | Sample_contact_laboratory | Cellular Immunology Laboratory
| | Sample_contact_department | Department of Immunology
| | Sample_contact_institute | Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology
| | Sample_contact_address | Roentgena 5
| | Sample_contact_city | Warszawa
| | Sample_contact_zip/postal_code | 02-781
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM350nnn/GSM350384/suppl/GSM350384.CEL.gz
| | Sample_series_id | GSE13909
| | Sample_data_row_count | 54675
| | |
|
GSM350385 | GPL570 |
|
immortalised_line5_8_hours_after_IL-2_deprivation_biol_rep3
|
spontaneously immortalised normal spleen-derived T lymphocytes after IL-2 withdrawal
|
Healthy male, age 56, spleen
|
immortalised_line5_8_hours_after_IL-2_deprivation_biol_rep3
|
| Sample_geo_accession | GSM350385
| | Sample_status | Public on Aug 13 2009
| | Sample_submission_date | Dec 11 2008
| | Sample_last_update_date | Aug 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Immunology, Cancer Centre and Institute of Oncology, Warsaw, Poland
| | Sample_treatment_protocol_ch1 | Spontaneously immortalized IL-2-dependent T cell line was derived from normal spleen and established and cultured as previously described (Siwicki et al., Exp Gerontol 2000). The cells followed 222 population doublings. Sample was collected 8 hours following IL-2 withdrawal.
| | Sample_growth_protocol_ch1 | As described in treatment protocol - standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma])
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Nucleospin RNA II kit (Macherey-Nagel, Germany).RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano Chip Kit (Agilent Technologies).
| | Sample_label_ch1 | Biotin-Phycoerythrin
| | Sample_label_protocol_ch1 | Affymetrix protocol: 5 μg of total RNA was used for cRNA synthesis and fragmented. Single round of amplification and labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation. (http://www.affymetrix.com/products/reagents/specific/one_cycle_target_control.affx)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol, arrays were stained using phycoerythrin and streptavidin complex (http://www.affymetrix.com/products/reagents/specific/eukhyb.affx)
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol: http://www.affymetrix.com/products/instruments/specific/scanner_3000.affx
| | Sample_data_processing | Expression data (.CEL files) were normalized with the GC-RMA algorithm, using Bioconductor gcrma package
| | Sample_platform_id | GPL570
| | Sample_contact_name | Magdalena,,Chechlinska
| | Sample_contact_email | chech@coi.waw.pl
| | Sample_contact_phone | +48225462256
| | Sample_contact_fax | +48226449085
| | Sample_contact_laboratory | Cellular Immunology Laboratory
| | Sample_contact_department | Department of Immunology
| | Sample_contact_institute | Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology
| | Sample_contact_address | Roentgena 5
| | Sample_contact_city | Warszawa
| | Sample_contact_zip/postal_code | 02-781
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM350nnn/GSM350385/suppl/GSM350385.CEL.gz
| | Sample_series_id | GSE13909
| | Sample_data_row_count | 54675
| | |
|
GSM350386 | GPL570 |
|
immortalised_lineS9_before_IL-2_deprivation_biol_rep1
|
spontaneously immortalised PBMC-derived T lymphocytes of NBS patient, from IL-2-containing cultures
|
NBS patient, male, age 11, PBMC
|
immortalised_lineS9_before_IL-2_deprivation_biol_rep1
|
| Sample_geo_accession | GSM350386
| | Sample_status | Public on Aug 13 2009
| | Sample_submission_date | Dec 11 2008
| | Sample_last_update_date | Aug 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Immunology, Cancer Centre and Institute of Oncology, Warsaw, Poland
| | Sample_treatment_protocol_ch1 | Spontaneously immortalized IL-2-dependent T cell line was derived from PBMC of Nijmegen Breakage Syndrome patient and established and cultured as previously described (Siwicki et al., Exp Cell Res 2003). The cells followed 125 population doublings.
| | Sample_growth_protocol_ch1 | As described in treatment protocol - standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma])
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Nucleospin RNA II kit (Macherey-Nagel, Germany).RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano Chip Kit (Agilent Technologies).
| | Sample_label_ch1 | Biotin-Phycoerythrin
| | Sample_label_protocol_ch1 | Affymetrix protocol: 5 μg of total RNA was used for cRNA synthesis and fragmented. Single round of amplification and labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation. (http://www.affymetrix.com/products/reagents/specific/one_cycle_target_control.affx)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol, arrays were stained using phycoerythrin and streptavidin complex (http://www.affymetrix.com/products/reagents/specific/eukhyb.affx)
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol: http://www.affymetrix.com/products/instruments/specific/scanner_3000.affx
| | Sample_data_processing | Expression data (.CEL files) were normalized with the GC-RMA algorithm, using Bioconductor gcrma package
| | Sample_platform_id | GPL570
| | Sample_contact_name | Magdalena,,Chechlinska
| | Sample_contact_email | chech@coi.waw.pl
| | Sample_contact_phone | +48225462256
| | Sample_contact_fax | +48226449085
| | Sample_contact_laboratory | Cellular Immunology Laboratory
| | Sample_contact_department | Department of Immunology
| | Sample_contact_institute | Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology
| | Sample_contact_address | Roentgena 5
| | Sample_contact_city | Warszawa
| | Sample_contact_zip/postal_code | 02-781
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM350nnn/GSM350386/suppl/GSM350386.CEL.gz
| | Sample_series_id | GSE13909
| | Sample_data_row_count | 54675
| | |
|
GSM350387 | GPL570 |
|
immortalised_lineS9_before_IL-2_deprivation_biol_rep2
|
spontaneously immortalised PBMC-derived T lymphocytes of NBS patient, from IL-2-containing cultures
|
NBS patient, male, age 11, PBMC
|
immortalised_lineS9_before_IL-2_deprivation_biol_rep2
|
| Sample_geo_accession | GSM350387
| | Sample_status | Public on Aug 13 2009
| | Sample_submission_date | Dec 11 2008
| | Sample_last_update_date | Aug 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Immunology, Cancer Centre and Institute of Oncology, Warsaw, Poland
| | Sample_treatment_protocol_ch1 | Spontaneously immortalized IL-2-dependent T cell line was derived from PBMC of Nijmegen Breakage Syndrome patient and established and cultured as previously described (Siwicki et al., Exp Cell Res 2003). The cells followed 125 population doublings. Sample was collected 8 hours following IL-2 withdrawal.
| | Sample_growth_protocol_ch1 | As described in treatment protocol - standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma])
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Nucleospin RNA II kit (Macherey-Nagel, Germany).RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano Chip Kit (Agilent Technologies).
| | Sample_label_ch1 | Biotin-Phycoerythrin
| | Sample_label_protocol_ch1 | Affymetrix protocol: 5 μg of total RNA was used for cRNA synthesis and fragmented. Single round of amplification and labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation. (http://www.affymetrix.com/products/reagents/specific/one_cycle_target_control.affx)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol, arrays were stained using phycoerythrin and streptavidin complex (http://www.affymetrix.com/products/reagents/specific/eukhyb.affx)
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol: http://www.affymetrix.com/products/instruments/specific/scanner_3000.affx
| | Sample_data_processing | Expression data (.CEL files) were normalized with the GC-RMA algorithm, using Bioconductor gcrma package
| | Sample_platform_id | GPL570
| | Sample_contact_name | Magdalena,,Chechlinska
| | Sample_contact_email | chech@coi.waw.pl
| | Sample_contact_phone | +48225462256
| | Sample_contact_fax | +48226449085
| | Sample_contact_laboratory | Cellular Immunology Laboratory
| | Sample_contact_department | Department of Immunology
| | Sample_contact_institute | Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology
| | Sample_contact_address | Roentgena 5
| | Sample_contact_city | Warszawa
| | Sample_contact_zip/postal_code | 02-781
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM350nnn/GSM350387/suppl/GSM350387.CEL.gz
| | Sample_series_id | GSE13909
| | Sample_data_row_count | 54675
| | |
|
GSM350388 | GPL570 |
|
immortalised_lineS9_before_IL-2_deprivation_biol_rep3
|
spontaneously immortalised PBMC-derived T lymphocytes of NBS patient, from IL-2-containing cultures
|
NBS patient, male, age 11, PBMC
|
immortalised_lineS9_before_IL-2_deprivation_biol_rep3
|
| Sample_geo_accession | GSM350388
| | Sample_status | Public on Aug 13 2009
| | Sample_submission_date | Dec 11 2008
| | Sample_last_update_date | Aug 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Immunology, Cancer Centre and Institute of Oncology, Warsaw, Poland
| | Sample_treatment_protocol_ch1 | Spontaneously immortalized IL-2-dependent T cell line was derived from PBMC of Nijmegen Breakage Syndrome patient and established and cultured as previously described (Siwicki et al., Exp Cell Res 2003). The cells followed 125 population doublings.
| | Sample_growth_protocol_ch1 | As described in treatment protocol - standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma])
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Nucleospin RNA II kit (Macherey-Nagel, Germany).RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano Chip Kit (Agilent Technologies).
| | Sample_label_ch1 | Biotin-Phycoerythrin
| | Sample_label_protocol_ch1 | Affymetrix protocol: 5 μg of total RNA was used for cRNA synthesis and fragmented. Single round of amplification and labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation. (http://www.affymetrix.com/products/reagents/specific/one_cycle_target_control.affx)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol, arrays were stained using phycoerythrin and streptavidin complex (http://www.affymetrix.com/products/reagents/specific/eukhyb.affx)
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol: http://www.affymetrix.com/products/instruments/specific/scanner_3000.affx
| | Sample_data_processing | Expression data (.CEL files) were normalized with the GC-RMA algorithm, using Bioconductor gcrma package
| | Sample_platform_id | GPL570
| | Sample_contact_name | Magdalena,,Chechlinska
| | Sample_contact_email | chech@coi.waw.pl
| | Sample_contact_phone | +48225462256
| | Sample_contact_fax | +48226449085
| | Sample_contact_laboratory | Cellular Immunology Laboratory
| | Sample_contact_department | Department of Immunology
| | Sample_contact_institute | Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology
| | Sample_contact_address | Roentgena 5
| | Sample_contact_city | Warszawa
| | Sample_contact_zip/postal_code | 02-781
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM350nnn/GSM350388/suppl/GSM350388.CEL.gz
| | Sample_series_id | GSE13909
| | Sample_data_row_count | 54675
| | |
|
GSM350389 | GPL570 |
|
immortalised_lineS9_8_hours_after_IL-2_deprivation_biol_rep1
|
spontaneously immortalised PBMC-derived T lymphocytes of NBS patient, after IL-2 withdrawal
|
NBS patient, male, age 11, PBMC
|
immortalised_lineS9_8_hours_after_IL-2_deprivation_biol_rep1
|
| Sample_geo_accession | GSM350389
| | Sample_status | Public on Aug 13 2009
| | Sample_submission_date | Dec 11 2008
| | Sample_last_update_date | Aug 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Immunology, Cancer Centre and Institute of Oncology, Warsaw, Poland
| | Sample_treatment_protocol_ch1 | Spontaneously immortalized IL-2-dependent T cell line was derived from PBMC of Nijmegen Breakage Syndrome patient and established and cultured as previously described (Siwicki et al., Exp Cell Res 2003). The cells followed 125 population doublings. Sample was collected 8 hours following IL-2 withdrawal.
| | Sample_growth_protocol_ch1 | As described in treatment protocol - standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma])
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Nucleospin RNA II kit (Macherey-Nagel, Germany).RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano Chip Kit (Agilent Technologies).
| | Sample_label_ch1 | Biotin-Phycoerythrin
| | Sample_label_protocol_ch1 | Affymetrix protocol: 5 μg of total RNA was used for cRNA synthesis and fragmented. Single round of amplification and labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation. (http://www.affymetrix.com/products/reagents/specific/one_cycle_target_control.affx)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol, arrays were stained using phycoerythrin and streptavidin complex (http://www.affymetrix.com/products/reagents/specific/eukhyb.affx)
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol: http://www.affymetrix.com/products/instruments/specific/scanner_3000.affx
| | Sample_data_processing | Expression data (.CEL files) were normalized with the GC-RMA algorithm, using Bioconductor gcrma package
| | Sample_platform_id | GPL570
| | Sample_contact_name | Magdalena,,Chechlinska
| | Sample_contact_email | chech@coi.waw.pl
| | Sample_contact_phone | +48225462256
| | Sample_contact_fax | +48226449085
| | Sample_contact_laboratory | Cellular Immunology Laboratory
| | Sample_contact_department | Department of Immunology
| | Sample_contact_institute | Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology
| | Sample_contact_address | Roentgena 5
| | Sample_contact_city | Warszawa
| | Sample_contact_zip/postal_code | 02-781
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM350nnn/GSM350389/suppl/GSM350389.CEL.gz
| | Sample_series_id | GSE13909
| | Sample_data_row_count | 54675
| | |
|
GSM350390 | GPL570 |
|
immortalised_lineS9_8_hours_after_IL-2_deprivation_biol_rep2
|
spontaneously immortalised PBMC-derived T lymphocytes of NBS patient, after IL-2 withdrawal
|
NBS patient, male, age 11, PBMC
|
immortalised_lineS9_8_hours_after_IL-2_deprivation_biol_rep2
|
| Sample_geo_accession | GSM350390
| | Sample_status | Public on Aug 13 2009
| | Sample_submission_date | Dec 11 2008
| | Sample_last_update_date | Aug 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Immunology, Cancer Centre and Institute of Oncology, Warsaw, Poland
| | Sample_treatment_protocol_ch1 | Spontaneously immortalized IL-2-dependent T cell line was derived from PBMC of Nijmegen Breakage Syndrome patient and established and cultured as previously described (Siwicki et al., Exp Cell Res 2003). The cells followed 125 population doublings. Sample was collected 8 hours following IL-2 withdrawal.
| | Sample_growth_protocol_ch1 | As described in treatment protocol - standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma])
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Nucleospin RNA II kit (Macherey-Nagel, Germany).RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano Chip Kit (Agilent Technologies).
| | Sample_label_ch1 | Biotin-Phycoerythrin
| | Sample_label_protocol_ch1 | Affymetrix protocol: 5 μg of total RNA was used for cRNA synthesis and fragmented. Single round of amplification and labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation. (http://www.affymetrix.com/products/reagents/specific/one_cycle_target_control.affx)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol, arrays were stained using phycoerythrin and streptavidin complex (http://www.affymetrix.com/products/reagents/specific/eukhyb.affx)
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol: http://www.affymetrix.com/products/instruments/specific/scanner_3000.affx
| | Sample_data_processing | Expression data (.CEL files) were normalized with the GC-RMA algorithm, using Bioconductor gcrma package
| | Sample_platform_id | GPL570
| | Sample_contact_name | Magdalena,,Chechlinska
| | Sample_contact_email | chech@coi.waw.pl
| | Sample_contact_phone | +48225462256
| | Sample_contact_fax | +48226449085
| | Sample_contact_laboratory | Cellular Immunology Laboratory
| | Sample_contact_department | Department of Immunology
| | Sample_contact_institute | Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology
| | Sample_contact_address | Roentgena 5
| | Sample_contact_city | Warszawa
| | Sample_contact_zip/postal_code | 02-781
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM350nnn/GSM350390/suppl/GSM350390.CEL.gz
| | Sample_series_id | GSE13909
| | Sample_data_row_count | 54675
| | |
|
GSM350391 | GPL570 |
|
immortalised_lineS9_8_hours_after_IL-2_deprivation_biol_rep3
|
spontaneously immortalised PBMC-derived T lymphocytes of NBS patient, after IL-2 withdrawal
|
NBS patient, male, age 11, PBMC
|
immortalised_lineS9_8_hours_after_IL-2_deprivation_biol_rep3
|
| Sample_geo_accession | GSM350391
| | Sample_status | Public on Aug 13 2009
| | Sample_submission_date | Dec 11 2008
| | Sample_last_update_date | Aug 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Immunology, Cancer Centre and Institute of Oncology, Warsaw, Poland
| | Sample_treatment_protocol_ch1 | Spontaneously immortalized IL-2-dependent T cell line was derived from PBMC of Nijmegen Breakage Syndrome patient and established and cultured as previously described (Siwicki et al., Exp Cell Res 2003). The cells followed 125 population doublings. Sample was collected 8 hours following IL-2 withdrawal.
| | Sample_growth_protocol_ch1 | As described in treatment protocol - standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma])
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Nucleospin RNA II kit (Macherey-Nagel, Germany).RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano Chip Kit (Agilent Technologies).
| | Sample_label_ch1 | Biotin-Phycoerythrin
| | Sample_label_protocol_ch1 | Affymetrix protocol: 5 μg of total RNA was used for cRNA synthesis and fragmented. Single round of amplification and labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation. (http://www.affymetrix.com/products/reagents/specific/one_cycle_target_control.affx)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol, arrays were stained using phycoerythrin and streptavidin complex (http://www.affymetrix.com/products/reagents/specific/eukhyb.affx)
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol: http://www.affymetrix.com/products/instruments/specific/scanner_3000.affx
| | Sample_data_processing | Expression data (.CEL files) were normalized with the GC-RMA algorithm, using Bioconductor gcrma package
| | Sample_platform_id | GPL570
| | Sample_contact_name | Magdalena,,Chechlinska
| | Sample_contact_email | chech@coi.waw.pl
| | Sample_contact_phone | +48225462256
| | Sample_contact_fax | +48226449085
| | Sample_contact_laboratory | Cellular Immunology Laboratory
| | Sample_contact_department | Department of Immunology
| | Sample_contact_institute | Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology
| | Sample_contact_address | Roentgena 5
| | Sample_contact_city | Warszawa
| | Sample_contact_zip/postal_code | 02-781
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM350nnn/GSM350391/suppl/GSM350391.CEL.gz
| | Sample_series_id | GSE13909
| | Sample_data_row_count | 54675
| | |
|
GSM350392 | GPL570 |
|
healthy_donor_j_primary_T_lymphoblasts_before_IL-2_deprivation_biol_rep3
|
IL-2 dependent normal peripheral blood T lymphocytes from IL-2-containing cultures
|
Healthy, male donor, age 48, PBMC
|
healthy_donor_j_primary_T_lymphoblasts_before_IL-2_deprivation_biol_rep3
|
| Sample_geo_accession | GSM350392
| | Sample_status | Public on Aug 13 2009
| | Sample_submission_date | Dec 11 2008
| | Sample_last_update_date | Aug 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Immunology, Cancer Centre and Institute of Oncology, Warsaw, Poland
| | Sample_treatment_protocol_ch1 | Primary, IL-2-dependent T lymphoblast cell lines were generated and propagated as previously described (Siwicki et al., Leuk Res 2008). Briefly, peripheral blood mononuclear cells (PBMC) derived from a healthy donor were suspended in a standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma]), activated for 24 h with 20 μg/ml of wheat germ agglutinin (WGA, Pharmacia) and subsequently cultured in the standard medium supplemented with 20 U/ml of rIL-2 (R&D). Cells were collected after 6-7 population doublings.
| | Sample_growth_protocol_ch1 | As described in treatment protocol - standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma])
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Nucleospin RNA II kit (Macherey-Nagel, Germany).RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano Chip Kit (Agilent Technologies).
| | Sample_label_ch1 | Biotin-Phycoerythrin
| | Sample_label_protocol_ch1 | Affymetrix protocol: 4,5 μg of total RNA was used for cRNA synthesis and fragmented. Single round of amplification and labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation. (http://www.affymetrix.com/products/reagents/specific/one_cycle_target_control.affx)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol, arrays were stained using phycoerythrin and streptavidin complex (http://www.affymetrix.com/products/reagents/specific/eukhyb.affx)
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol: http://www.affymetrix.com/products/instruments/specific/scanner_3000.affx
| | Sample_data_processing | Expression data (.CEL files) were normalized with the GC-RMA algorithm, using Bioconductor gcrma package
| | Sample_platform_id | GPL570
| | Sample_contact_name | Magdalena,,Chechlinska
| | Sample_contact_email | chech@coi.waw.pl
| | Sample_contact_phone | +48225462256
| | Sample_contact_fax | +48226449085
| | Sample_contact_laboratory | Cellular Immunology Laboratory
| | Sample_contact_department | Department of Immunology
| | Sample_contact_institute | Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology
| | Sample_contact_address | Roentgena 5
| | Sample_contact_city | Warszawa
| | Sample_contact_zip/postal_code | 02-781
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM350nnn/GSM350392/suppl/GSM350392.CEL.gz
| | Sample_series_id | GSE13909
| | Sample_data_row_count | 54675
| | |
|
GSM350393 | GPL570 |
|
healthy_donor_j_primary_T_lymphoblasts_8_hours_after_IL-2_deprivation_biol_rep3
|
IL-2 dependent normal peripheral blood T lymphocytes after IL-2 withdrawal
|
Healthy, male donor, age 48, PBMC
|
healthy_donor_j_primary_T_lymphoblasts_8_hours_after_IL-2_deprivation_biol_rep3
|
| Sample_geo_accession | GSM350393
| | Sample_status | Public on Aug 13 2009
| | Sample_submission_date | Dec 11 2008
| | Sample_last_update_date | Aug 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of Immunology, Cancer Centre and Institute of Oncology, Warsaw, Poland
| | Sample_treatment_protocol_ch1 | Primary, IL-2-dependent T lymphoblast cell lines were generated and propagated as previously described (Siwicki et al., Leuk Res 2008). Briefly, peripheral blood mononuclear cells (PBMC) derived from a healthy donor were suspended in a standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma]), activated for 24 h with 20 μg/ml of wheat germ agglutinin (WGA, Pharmacia) and subsequently cultured in the standard medium supplemented with 20 U/ml of rIL-2 (R&D). Cell samples were collected after 6-7 population doublings, 8-hrs incubation without IL-2, following triple thorough washing of the cells.
| | Sample_growth_protocol_ch1 | As described in treatment protocol - standard medium (RPMI 1640, 10–12% FCS, 50 μg/ml gentamycin [Sigma])
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Nucleospin RNA II kit (Macherey-Nagel, Germany).RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano Chip Kit (Agilent Technologies).
| | Sample_label_ch1 | Biotin-Phycoerythrin
| | Sample_label_protocol_ch1 | Affymetrix protocol: 4,5 μg of total RNA was used for cRNA synthesis and fragmented. Single round of amplification and labelling was performed with One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation. (http://www.affymetrix.com/products/reagents/specific/one_cycle_target_control.affx)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol, arrays were stained using phycoerythrin and streptavidin complex (http://www.affymetrix.com/products/reagents/specific/eukhyb.affx)
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocol: http://www.affymetrix.com/products/instruments/specific/scanner_3000.affx
| | Sample_data_processing | Expression data (.CEL files) were normalized with the GC-RMA algorithm, using Bioconductor gcrma package
| | Sample_platform_id | GPL570
| | Sample_contact_name | Magdalena,,Chechlinska
| | Sample_contact_email | chech@coi.waw.pl
| | Sample_contact_phone | +48225462256
| | Sample_contact_fax | +48226449085
| | Sample_contact_laboratory | Cellular Immunology Laboratory
| | Sample_contact_department | Department of Immunology
| | Sample_contact_institute | Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology
| | Sample_contact_address | Roentgena 5
| | Sample_contact_city | Warszawa
| | Sample_contact_zip/postal_code | 02-781
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM350nnn/GSM350393/suppl/GSM350393.CEL.gz
| | Sample_series_id | GSE13909
| | Sample_data_row_count | 54675
| | |
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