Search results for the GEO ID: GSE24082  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM591440 | GPL3921 |
|
Jurkat-PD1_3-28-PD1_rep1
|
PD1-expressing Jurkat cells incubated for 18h with PD-1/CD3/CD38 beads
|
cell type: Jurkat cells
|
Gene expression data from Jurkat cells cultured with beads
|
| Sample_geo_accession | GSM591440
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 08 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PD-1 expressing Jurkat cells were cultured for 18 hours with beads coated with antibodies to CD3 and CD28, with our without an antibody to PD-1.
| | Sample_growth_protocol_ch1 | PD-1 expressing Jurkat cells were harvested in mid-log phase of growth.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591440/suppl/GSM591440.CEL.gz
| | Sample_series_id | GSE24026
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM591441 | GPL3921 |
|
Jurkat-PD1_3-28-PD1_rep2
|
PD1-expressing Jurkat cells incubated for 18h with PD-1/CD3/CD38 beads
|
cell type: Jurkat cells
|
Gene expression data from Jurkat cells cultured with beads
|
| Sample_geo_accession | GSM591441
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 08 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PD-1 expressing Jurkat cells were cultured for 18 hours with beads coated with antibodies to CD3 and CD28, with our without an antibody to PD-1.
| | Sample_growth_protocol_ch1 | PD-1 expressing Jurkat cells were harvested in mid-log phase of growth.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591441/suppl/GSM591441.CEL.gz
| | Sample_series_id | GSE24026
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM591442 | GPL3921 |
|
Jurkat-PD1_3-28-PD1_rep3
|
PD1-expressing Jurkat cells incubated for 18h with PD-1/CD3/CD38 beads
|
cell type: Jurkat cells
|
Gene expression data from Jurkat cells cultured with beads
|
| Sample_geo_accession | GSM591442
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 08 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PD-1 expressing Jurkat cells were cultured for 18 hours with beads coated with antibodies to CD3 and CD28, with our without an antibody to PD-1.
| | Sample_growth_protocol_ch1 | PD-1 expressing Jurkat cells were harvested in mid-log phase of growth.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591442/suppl/GSM591442.CEL.gz
| | Sample_series_id | GSE24026
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM591443 | GPL3921 |
|
Jurkat-PD1_3-28-PD1_rep4
|
PD1-expressing Jurkat cells incubated for 18h with PD-1/CD3/CD38 beads
|
cell type: Jurkat cells
|
Gene expression data from Jurkat cells cultured with beads
|
| Sample_geo_accession | GSM591443
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 08 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PD-1 expressing Jurkat cells were cultured for 18 hours with beads coated with antibodies to CD3 and CD28, with our without an antibody to PD-1.
| | Sample_growth_protocol_ch1 | PD-1 expressing Jurkat cells were harvested in mid-log phase of growth.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591443/suppl/GSM591443.CEL.gz
| | Sample_series_id | GSE24026
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM591444 | GPL3921 |
|
Jurkat-PD1_3-28-PD1_rep5
|
PD1-expressing Jurkat cells incubated for 18h with PD-1/CD3/CD38 beads
|
cell type: Jurkat cells
|
Gene expression data from Jurkat cells cultured with beads
|
| Sample_geo_accession | GSM591444
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 08 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PD-1 expressing Jurkat cells were cultured for 18 hours with beads coated with antibodies to CD3 and CD28, with our without an antibody to PD-1.
| | Sample_growth_protocol_ch1 | PD-1 expressing Jurkat cells were harvested in mid-log phase of growth.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591444/suppl/GSM591444.CEL.gz
| | Sample_series_id | GSE24026
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM591445 | GPL3921 |
|
Jurkat-PD1_3-28-PD1_rep6
|
PD1-expressing Jurkat cells incubated for 18h with PD-1/CD3/CD38 beads
|
cell type: Jurkat cells
|
Gene expression data from Jurkat cells cultured with beads
|
| Sample_geo_accession | GSM591445
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 08 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PD-1 expressing Jurkat cells were cultured for 18 hours with beads coated with antibodies to CD3 and CD28, with our without an antibody to PD-1.
| | Sample_growth_protocol_ch1 | PD-1 expressing Jurkat cells were harvested in mid-log phase of growth.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591445/suppl/GSM591445.CEL.gz
| | Sample_series_id | GSE24026
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM591446 | GPL3921 |
|
Jurkat-PD1_3-28_rep1
|
PD1-expressing Jurkat cells incubated for 18h with CD3/CD38 beads
|
cell type: Jurkat cells
|
Gene expression data from Jurkat cells cultured with beads
|
| Sample_geo_accession | GSM591446
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 08 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PD-1 expressing Jurkat cells were cultured for 18 hours with beads coated with antibodies to CD3 and CD28, with our without an antibody to PD-1.
| | Sample_growth_protocol_ch1 | PD-1 expressing Jurkat cells were harvested in mid-log phase of growth.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591446/suppl/GSM591446.CEL.gz
| | Sample_series_id | GSE24026
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM591447 | GPL3921 |
|
Jurkat-PD1_3-28_rep3
|
PD1-expressing Jurkat cells incubated for 18h with CD3/CD38 beads
|
cell type: Jurkat cells
|
Gene expression data from Jurkat cells cultured with beads
|
| Sample_geo_accession | GSM591447
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 08 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PD-1 expressing Jurkat cells were cultured for 18 hours with beads coated with antibodies to CD3 and CD28, with our without an antibody to PD-1.
| | Sample_growth_protocol_ch1 | PD-1 expressing Jurkat cells were harvested in mid-log phase of growth.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591447/suppl/GSM591447.CEL.gz
| | Sample_series_id | GSE24026
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM591448 | GPL3921 |
|
Jurkat-PD1_3-28_rep4
|
PD1-expressing Jurkat cells incubated for 18h with CD3/CD38 beads
|
cell type: Jurkat cells
|
Gene expression data from Jurkat cells cultured with beads
|
| Sample_geo_accession | GSM591448
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 08 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PD-1 expressing Jurkat cells were cultured for 18 hours with beads coated with antibodies to CD3 and CD28, with our without an antibody to PD-1.
| | Sample_growth_protocol_ch1 | PD-1 expressing Jurkat cells were harvested in mid-log phase of growth.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591448/suppl/GSM591448.CEL.gz
| | Sample_series_id | GSE24026
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM591449 | GPL3921 |
|
Jurkat-PD1_3-28_rep5
|
PD1-expressing Jurkat cells incubated for 18h with CD3/CD38 beads
|
cell type: Jurkat cells
|
Gene expression data from Jurkat cells cultured with beads
|
| Sample_geo_accession | GSM591449
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 08 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PD-1 expressing Jurkat cells were cultured for 18 hours with beads coated with antibodies to CD3 and CD28, with our without an antibody to PD-1.
| | Sample_growth_protocol_ch1 | PD-1 expressing Jurkat cells were harvested in mid-log phase of growth.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591449/suppl/GSM591449.CEL.gz
| | Sample_series_id | GSE24026
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM591450 | GPL3921 |
|
Jurkat-PD1_3-28_rep6
|
PD1-expressing Jurkat cells incubated for 18h with CD3/CD38 beads
|
cell type: Jurkat cells
|
Gene expression data from Jurkat cells cultured with beads
|
| Sample_geo_accession | GSM591450
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 08 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PD-1 expressing Jurkat cells were cultured for 18 hours with beads coated with antibodies to CD3 and CD28, with our without an antibody to PD-1.
| | Sample_growth_protocol_ch1 | PD-1 expressing Jurkat cells were harvested in mid-log phase of growth.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM591nnn/GSM591450/suppl/GSM591450.CEL.gz
| | Sample_series_id | GSE24026
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592950 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_940546
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592950
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592950/suppl/GSM592950.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592951 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_553064
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592951
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592951/suppl/GSM592951.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592952 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_632343
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592952
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592952/suppl/GSM592952.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592953 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_321797
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592953
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592953/suppl/GSM592953.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592954 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_756587
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592954
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592954/suppl/GSM592954.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592955 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_285873
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592955
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592955/suppl/GSM592955.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592956 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_535367
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592956
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592956/suppl/GSM592956.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592957 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_254912
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592957
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592957/suppl/GSM592957.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592958 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_319564
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592958
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592958/suppl/GSM592958.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592959 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_187891
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592959
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592959/suppl/GSM592959.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592960 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_518955
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592960
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592960/suppl/GSM592960.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592961 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_632723
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592961
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592961/suppl/GSM592961.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592962 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_109477
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592962
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592962/suppl/GSM592962.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592963 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_366356
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592963
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592963/suppl/GSM592963.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592964 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_719104
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592964
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592964/suppl/GSM592964.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592965 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_270245
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592965
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592965/suppl/GSM592965.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592966 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_711816
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592966
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592966/suppl/GSM592966.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592967 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_245487
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592967
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592967/suppl/GSM592967.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592968 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_832764
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592968
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592968/suppl/GSM592968.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592969 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_941849
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592969
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592969/suppl/GSM592969.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592970 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_927078
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592970
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592970/suppl/GSM592970.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592971 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_831969
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592971
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592971/suppl/GSM592971.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592972 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_366065
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592972
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592972/suppl/GSM592972.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592973 | GPL3921 |
|
HIV-specific CD8 T cells_Controller_950005
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Controller
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592973
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592973/suppl/GSM592973.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592974 | GPL3921 |
|
HIV-specific CD8 T cells_Progressor_583127
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Progressor
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592974
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592974/suppl/GSM592974.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592975 | GPL3921 |
|
HIV-specific CD8 T cells_Progressor_388555
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Progressor
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592975
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592975/suppl/GSM592975.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592976 | GPL3921 |
|
HIV-specific CD8 T cells_Progressor_177154
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Progressor
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592976
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592976/suppl/GSM592976.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592977 | GPL3921 |
|
HIV-specific CD8 T cells_Progressor_264783
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Progressor
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592977
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592977/suppl/GSM592977.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592978 | GPL3921 |
|
HIV-specific CD8 T cells_Progressor_350103
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Progressor
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592978
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592978/suppl/GSM592978.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592979 | GPL3921 |
|
HIV-specific CD8 T cells_Progressor_792092_B02
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Progressor
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592979
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592979/suppl/GSM592979.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592980 | GPL3921 |
|
HIV-specific CD8 T cells_Progressor_806270
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Progressor
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592980
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592980/suppl/GSM592980.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592981 | GPL3921 |
|
HIV-specific CD8 T cells_Progressor_139603
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Progressor
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592981
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592981/suppl/GSM592981.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592982 | GPL3921 |
|
HIV-specific CD8 T cells_Progressor_560306
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Progressor
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592982
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592982/suppl/GSM592982.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592983 | GPL3921 |
|
HIV-specific CD8 T cells_Progressor_308811
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Progressor
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592983
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592983/suppl/GSM592983.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592984 | GPL3921 |
|
HIV-specific CD8 T cells_Progressor_941359
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Progressor
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592984
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592984/suppl/GSM592984.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592985 | GPL3921 |
|
HIV-specific CD8 T cells_Progressor_792092_B09
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Progressor
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592985
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592985/suppl/GSM592985.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592986 | GPL3921 |
|
HIV-specific CD8 T cells_Progressor_752022
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Progressor
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592986
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592986/suppl/GSM592986.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592987 | GPL3921 |
|
HIV-specific CD8 T cells_Progressor_554271
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Progressor
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592987
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592987/suppl/GSM592987.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592988 | GPL3921 |
|
HIV-specific CD8 T cells_Progressor_280153
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Progressor
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592988
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592988/suppl/GSM592988.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592989 | GPL3921 |
|
HIV-specific CD8 T cells_Progressor_881658
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Progressor
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592989
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592989/suppl/GSM592989.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592990 | GPL3921 |
|
HIV-specific CD8 T cells_Progressor_981444
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Progressor
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592990
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592990/suppl/GSM592990.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
GSM592991 | GPL3921 |
|
HIV-specific CD8 T cells_Progressor_403998
|
HIV-specific CD8 T cells
|
cell type: CD8 T cells
clinical status: Progressor
|
Gene expression data from tetramer-sorted Gag-specific CD8 T cells
|
| Sample_geo_accession | GSM592991
| | Sample_status | Public on Oct 03 2010
| | Sample_submission_date | Sep 10 2010
| | Sample_last_update_date | Sep 16 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | PBMC were isolated via density centrifugation and were stained with a cocktail of antibodies chosen to exclude irrelevant lineages and dead cells, anti-CD8 and MHC Class I HIV-Gag-specific tetramers to identify the antigen-specific populations, and antibodies against CD62L and CD45RA to characterize the memory phenotype populations of the tetramer+ fraction. CD8+tetramer+ cells were sorted using a FACSAria Cell Sorter (BD Biosciences). Following sorting, cells were pelleted and resuspended in TRIzol reagent (Invitrogen, Carlsbad, CA). Experiments with Annexin V staining were carried out according to the manufacturer’s instructions (BD Biosciences).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | The data were processed using GenePattern (RMA), RenderCat (enrichment tests), and custom scripts (differential expression, collapsing genes to probes, etc).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | W.,Nicholas,Haining
| | Sample_contact_laboratory | Haining lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM592nnn/GSM592991/suppl/GSM592991.CEL.gz
| | Sample_series_id | GSE24081
| | Sample_series_id | GSE24082
| | Sample_data_row_count | 22277
| | |
|
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