Search results for the GEO ID: GSE9927 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM251101 | GPL570 |
|
Normal Control C-10a
|
Normal Control C-10a
|
CD4+ T-cells from normal HIV- donor
|
Activated CD4+ T cells were similarly isolated by positive
selection from CD4+ T cells using CD25 microbeads (Miltenyi Biotec, Auburn, CA). In order to ensure isolation of CD25lo cells, the manufacturer’s protocol was altered such that 2 μL of CD25 microbeads and 8 μL of wash media (PBS pH 7.2-7.4, 2% newborn calf serum, 0.1% glucose, 1% pen/strep, 12mM HEPES pH 7.2) were used per million CD4+ T cells. Purity of isolated CD25+ cells was almost always greater than 95%.
|
Sample_geo_accession | GSM251101
| Sample_status | Public on Feb 19 2008
| Sample_submission_date | Dec 17 2007
| Sample_last_update_date | Feb 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | JHMI volunteers
| Sample_treatment_protocol_ch1 | CD4+ T cells were positively selected to >98% purity from freshly
| Sample_treatment_protocol_ch1 | isolated peripheral blood mononuclear cells (PBMCs) using magnetic microbeads and subsequent column purification according to the manufacturer’s protocol (MiltenyiBiotec, Auburn, CA).
| Sample_growth_protocol_ch1 | RNA was isolated from fresh cells.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN).
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | The two-round RNA amplification protocol described by Affymetrix (Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II).
| Sample_hyb_protocol | 15μg of the biotinylated labeled cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10μg of total fragmented cRNA were hybridized to the Affymetrix Human Genome GeneChip array U133Plus 2.0 for 16hr at 45°C with constant rotation (60 rpm). The Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| Sample_scan_protocol | After washing and staining, all arrays were scanned with the Affymetrix GeneChip Scanner and data collected with GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA).
| Sample_data_processing | Image analysis by GCOS using the MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.
| Sample_platform_id | GPL570
| Sample_contact_name | Ahmad,,Sedaghat
| Sample_contact_laboratory | Robert Siliciano Lab
| Sample_contact_department | School of Medicine
| Sample_contact_institute | The Johns Hopkins University
| Sample_contact_address | 733 North Broadway
| Sample_contact_city | Baltimore
| Sample_contact_state | MD
| Sample_contact_zip/postal_code | 21205
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM251nnn/GSM251101/suppl/GSM251101.CEL.gz
| Sample_series_id | GSE9927
| Sample_data_row_count | 54675
| |
|
GSM251105 | GPL570 |
|
Normal Control C-1a
|
Normal Control
|
CD4+ T-cells from normal HIV- donor
|
Activated CD4+ T cells were similarly isolated by positive
selection from CD4+ T cells using CD25 microbeads (Miltenyi Biotec, Auburn, CA). In order to ensure isolation of CD25lo cells, the manufacturer’s protocol was altered such that 2 μL of CD25 microbeads and 8 μL of wash media (PBS pH 7.2-7.4, 2% newborn calf serum, 0.1% glucose, 1% pen/strep, 12mM HEPES pH 7.2) were used per million CD4+ T cells. Purity of isolated CD25+ cells was almost always greater than 95%.
|
Sample_geo_accession | GSM251105
| Sample_status | Public on Feb 19 2008
| Sample_submission_date | Dec 17 2007
| Sample_last_update_date | Feb 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | JHMI volunteers
| Sample_treatment_protocol_ch1 | CD4+ T cells were positively selected to >98% purity from freshly
| Sample_treatment_protocol_ch1 | isolated peripheral blood mononuclear cells (PBMCs) using magnetic microbeads and subsequent column purification according to the manufacturer’s protocol (MiltenyiBiotec, Auburn, CA).
| Sample_growth_protocol_ch1 | RNA was isolated from fresh cells.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN).
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | The two-round RNA amplification protocol described by Affymetrix (Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II).
| Sample_hyb_protocol | 15μg of the biotinylated labeled cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10μg of total fragmented cRNA were hybridized to the Affymetrix Human Genome GeneChip array U133Plus 2.0 for 16hr at 45°C with constant rotation (60 rpm). The Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| Sample_scan_protocol | After washing and staining, all arrays were scanned with the Affymetrix GeneChip Scanner and data collected with GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA).
| Sample_data_processing | Image analysis by GCOS using the MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.
| Sample_platform_id | GPL570
| Sample_contact_name | Ahmad,,Sedaghat
| Sample_contact_laboratory | Robert Siliciano Lab
| Sample_contact_department | School of Medicine
| Sample_contact_institute | The Johns Hopkins University
| Sample_contact_address | 733 North Broadway
| Sample_contact_city | Baltimore
| Sample_contact_state | MD
| Sample_contact_zip/postal_code | 21205
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM251nnn/GSM251105/suppl/GSM251105.CEL.gz
| Sample_series_id | GSE9927
| Sample_data_row_count | 54675
| |
|
GSM251110 | GPL570 |
|
Normal Control C-2a
|
Normal Control C-2a
|
CD4+ T-cells from normal HIV- donor
|
Activated CD4+ T cells were similarly isolated by positive
selection from CD4+ T cells using CD25 microbeads (Miltenyi Biotec, Auburn, CA). In order to ensure isolation of CD25lo cells, the manufacturer’s protocol was altered such that 2 μL of CD25 microbeads and 8 μL of wash media (PBS pH 7.2-7.4, 2% newborn calf serum, 0.1% glucose, 1% pen/strep, 12mM HEPES pH 7.2) were used per million CD4+ T cells. Purity of isolated CD25+ cells was almost always greater than 95%.
|
Sample_geo_accession | GSM251110
| Sample_status | Public on Feb 19 2008
| Sample_submission_date | Dec 17 2007
| Sample_last_update_date | Feb 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | JHMI volunteers
| Sample_treatment_protocol_ch1 | CD4+ T cells were positively selected to >98% purity from freshly
| Sample_treatment_protocol_ch1 | isolated peripheral blood mononuclear cells (PBMCs) using magnetic microbeads and subsequent column purification according to the manufacturer’s protocol (MiltenyiBiotec, Auburn, CA).
| Sample_growth_protocol_ch1 | RNA was isolated from fresh cells.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN).
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | The two-round RNA amplification protocol described by Affymetrix (Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II).
| Sample_hyb_protocol | 15μg of the biotinylated labeled cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10μg of total fragmented cRNA were hybridized to the Affymetrix Human Genome GeneChip array U133Plus 2.0 for 16hr at 45°C with constant rotation (60 rpm). The Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| Sample_scan_protocol | After washing and staining, all arrays were scanned with the Affymetrix GeneChip Scanner and data collected with GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA).
| Sample_data_processing | Image analysis by GCOS using the MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.
| Sample_platform_id | GPL570
| Sample_contact_name | Ahmad,,Sedaghat
| Sample_contact_laboratory | Robert Siliciano Lab
| Sample_contact_department | School of Medicine
| Sample_contact_institute | The Johns Hopkins University
| Sample_contact_address | 733 North Broadway
| Sample_contact_city | Baltimore
| Sample_contact_state | MD
| Sample_contact_zip/postal_code | 21205
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM251nnn/GSM251110/suppl/GSM251110.CEL.gz
| Sample_series_id | GSE9927
| Sample_data_row_count | 54675
| |
|
GSM251111 | GPL570 |
|
Normal Control C-3a
|
Control C-3a
|
CD4+ T-cells from normal HIV- donor
|
Activated CD4+ T cells were similarly isolated by positive
selection from CD4+ T cells using CD25 microbeads (Miltenyi Biotec, Auburn, CA). In order to ensure isolation of CD25lo cells, the manufacturer’s protocol was altered such that 2 μL of CD25 microbeads and 8 μL of wash media (PBS pH 7.2-7.4, 2% newborn calf serum, 0.1% glucose, 1% pen/strep, 12mM HEPES pH 7.2) were used per million CD4+ T cells. Purity of isolated CD25+ cells was almost always greater than 95%.
|
Sample_geo_accession | GSM251111
| Sample_status | Public on Feb 19 2008
| Sample_submission_date | Dec 17 2007
| Sample_last_update_date | Feb 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | JHMI volunteers
| Sample_treatment_protocol_ch1 | CD4+ T cells were positively selected to >98% purity from freshly
| Sample_treatment_protocol_ch1 | isolated peripheral blood mononuclear cells (PBMCs) using magnetic microbeads and subsequent column purification according to the manufacturer’s protocol (MiltenyiBiotec, Auburn, CA).
| Sample_growth_protocol_ch1 | RNA was isolated from fresh cells.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN).
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | The two-round RNA amplification protocol described by Affymetrix (Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II).
| Sample_hyb_protocol | 15μg of the biotinylated labeled cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10μg of total fragmented cRNA were hybridized to the Affymetrix Human Genome GeneChip array U133Plus 2.0 for 16hr at 45°C with constant rotation (60 rpm). The Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| Sample_scan_protocol | After washing and staining, all arrays were scanned with the Affymetrix GeneChip Scanner and data collected with GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA).
| Sample_data_processing | Image analysis by GCOS using the MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.
| Sample_platform_id | GPL570
| Sample_contact_name | Ahmad,,Sedaghat
| Sample_contact_laboratory | Robert Siliciano Lab
| Sample_contact_department | School of Medicine
| Sample_contact_institute | The Johns Hopkins University
| Sample_contact_address | 733 North Broadway
| Sample_contact_city | Baltimore
| Sample_contact_state | MD
| Sample_contact_zip/postal_code | 21205
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM251nnn/GSM251111/suppl/GSM251111.CEL.gz
| Sample_series_id | GSE9927
| Sample_data_row_count | 54675
| |
|
GSM251114 | GPL570 |
|
Normal Control C-4a
|
Normal Control C-4a
|
CD4+ T-cells from normal HIV- donor
|
Activated CD4+ T cells were similarly isolated by positive
selection from CD4+ T cells using CD25 microbeads (Miltenyi Biotec, Auburn, CA). In order to ensure isolation of CD25lo cells, the manufacturer’s protocol was altered such that 2 μL of CD25 microbeads and 8 μL of wash media (PBS pH 7.2-7.4, 2% newborn calf serum, 0.1% glucose, 1% pen/strep, 12mM HEPES pH 7.2) were used per million CD4+ T cells. Purity of isolated CD25+ cells was almost always greater than 95%.
|
Sample_geo_accession | GSM251114
| Sample_status | Public on Feb 19 2008
| Sample_submission_date | Dec 17 2007
| Sample_last_update_date | Feb 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | JHMI volunteers
| Sample_treatment_protocol_ch1 | CD4+ T cells were positively selected to >98% purity from freshly
| Sample_treatment_protocol_ch1 | isolated peripheral blood mononuclear cells (PBMCs) using magnetic microbeads and subsequent column purification according to the manufacturer’s protocol (MiltenyiBiotec, Auburn, CA).
| Sample_growth_protocol_ch1 | RNA was isolated from fresh cells.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN).
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | The two-round RNA amplification protocol described by Affymetrix (Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II).
| Sample_hyb_protocol | 15μg of the biotinylated labeled cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10μg of total fragmented cRNA were hybridized to the Affymetrix Human Genome GeneChip array U133Plus 2.0 for 16hr at 45°C with constant rotation (60 rpm). The Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| Sample_scan_protocol | After washing and staining, all arrays were scanned with the Affymetrix GeneChip Scanner and data collected with GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA).
| Sample_data_processing | Image analysis by GCOS using the MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.
| Sample_platform_id | GPL570
| Sample_contact_name | Ahmad,,Sedaghat
| Sample_contact_laboratory | Robert Siliciano Lab
| Sample_contact_department | School of Medicine
| Sample_contact_institute | The Johns Hopkins University
| Sample_contact_address | 733 North Broadway
| Sample_contact_city | Baltimore
| Sample_contact_state | MD
| Sample_contact_zip/postal_code | 21205
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM251nnn/GSM251114/suppl/GSM251114.CEL.gz
| Sample_series_id | GSE9927
| Sample_data_row_count | 54675
| |
|
GSM251126 | GPL570 |
|
Normal Control C-5a
|
Normal Control C-5a
|
CD4+ T-cells from normal HIV- donor
|
Activated CD4+ T cells were similarly isolated by positive
selection from CD4+ T cells using CD25 microbeads (Miltenyi Biotec, Auburn, CA). In order to ensure isolation of CD25lo cells, the manufacturer’s protocol was altered such that 2 μL of CD25 microbeads and 8 μL of wash media (PBS pH 7.2-7.4, 2% newborn calf serum, 0.1% glucose, 1% pen/strep, 12mM HEPES pH 7.2) were used per million CD4+ T cells. Purity of isolated CD25+ cells was almost always greater than 95%.
|
Sample_geo_accession | GSM251126
| Sample_status | Public on Feb 19 2008
| Sample_submission_date | Dec 17 2007
| Sample_last_update_date | Feb 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | JHMI volunteers
| Sample_treatment_protocol_ch1 | CD4+ T cells were positively selected to >98% purity from freshly
| Sample_treatment_protocol_ch1 | isolated peripheral blood mononuclear cells (PBMCs) using magnetic microbeads and subsequent column purification according to the manufacturer’s protocol (MiltenyiBiotec, Auburn, CA).
| Sample_growth_protocol_ch1 | RNA was isolated from fresh cells.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN).
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | The two-round RNA amplification protocol described by Affymetrix (Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II).
| Sample_hyb_protocol | 15μg of the biotinylated labeled cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10μg of total fragmented cRNA were hybridized to the Affymetrix Human Genome GeneChip array U133Plus 2.0 for 16hr at 45°C with constant rotation (60 rpm). The Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| Sample_scan_protocol | After washing and staining, all arrays were scanned with the Affymetrix GeneChip Scanner and data collected with GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA).
| Sample_data_processing | Image analysis by GCOS using the MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.
| Sample_platform_id | GPL570
| Sample_contact_name | Ahmad,,Sedaghat
| Sample_contact_laboratory | Robert Siliciano Lab
| Sample_contact_department | School of Medicine
| Sample_contact_institute | The Johns Hopkins University
| Sample_contact_address | 733 North Broadway
| Sample_contact_city | Baltimore
| Sample_contact_state | MD
| Sample_contact_zip/postal_code | 21205
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM251nnn/GSM251126/suppl/GSM251126.CEL.gz
| Sample_series_id | GSE9927
| Sample_data_row_count | 54675
| |
|
GSM251129 | GPL570 |
|
Normal Control C-6a
|
Normal Control C-6a
|
CD4+ T-cells from normal HIV- donor
|
Activated CD4+ T cells were similarly isolated by positive
selection from CD4+ T cells using CD25 microbeads (Miltenyi Biotec, Auburn, CA). In order to ensure isolation of CD25lo cells, the manufacturer’s protocol was altered such that 2 μL of CD25 microbeads and 8 μL of wash media (PBS pH 7.2-7.4, 2% newborn calf serum, 0.1% glucose, 1% pen/strep, 12mM HEPES pH 7.2) were used per million CD4+ T cells. Purity of isolated CD25+ cells was almost always greater than 95%.
|
Sample_geo_accession | GSM251129
| Sample_status | Public on Feb 19 2008
| Sample_submission_date | Dec 17 2007
| Sample_last_update_date | Feb 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | JHMI volunteers
| Sample_treatment_protocol_ch1 | CD4+ T cells were positively selected to >98% purity from freshly
| Sample_treatment_protocol_ch1 | isolated peripheral blood mononuclear cells (PBMCs) using magnetic microbeads and subsequent column purification according to the manufacturer’s protocol (MiltenyiBiotec, Auburn, CA).
| Sample_growth_protocol_ch1 | RNA was isolated from fresh cells.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN).
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | The two-round RNA amplification protocol described by Affymetrix (Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II).
| Sample_hyb_protocol | 15μg of the biotinylated labeled cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10μg of total fragmented cRNA were hybridized to the Affymetrix Human Genome GeneChip array U133Plus 2.0 for 16hr at 45°C with constant rotation (60 rpm). The Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| Sample_scan_protocol | After washing and staining, all arrays were scanned with the Affymetrix GeneChip Scanner and data collected with GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA).
| Sample_data_processing | Image analysis by GCOS using the MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.
| Sample_platform_id | GPL570
| Sample_contact_name | Ahmad,,Sedaghat
| Sample_contact_laboratory | Robert Siliciano Lab
| Sample_contact_department | School of Medicine
| Sample_contact_institute | The Johns Hopkins University
| Sample_contact_address | 733 North Broadway
| Sample_contact_city | Baltimore
| Sample_contact_state | MD
| Sample_contact_zip/postal_code | 21205
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM251nnn/GSM251129/suppl/GSM251129.CEL.gz
| Sample_series_id | GSE9927
| Sample_data_row_count | 54675
| |
|
GSM251192 | GPL570 |
|
Normal Control C-7a
|
Normal Control C-7a
|
CD4+ T-cells from normal HIV- donor
|
Activated CD4+ T cells were similarly isolated by positive
selection from CD4+ T cells using CD25 microbeads (Miltenyi Biotec, Auburn, CA). In order to ensure isolation of CD25lo cells, the manufacturer’s protocol was altered such that 2 μL of CD25 microbeads and 8 μL of wash media (PBS pH 7.2-7.4, 2% newborn calf serum, 0.1% glucose, 1% pen/strep, 12mM HEPES pH 7.2) were used per million CD4+ T cells. Purity of isolated CD25+ cells was almost always greater than 95%.
|
Sample_geo_accession | GSM251192
| Sample_status | Public on Feb 19 2008
| Sample_submission_date | Dec 17 2007
| Sample_last_update_date | Feb 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | JHMI volunteers
| Sample_treatment_protocol_ch1 | CD4+ T cells were positively selected to >98% purity from freshly
| Sample_treatment_protocol_ch1 | isolated peripheral blood mononuclear cells (PBMCs) using magnetic microbeads and subsequent column purification according to the manufacturer’s protocol (MiltenyiBiotec, Auburn, CA).
| Sample_growth_protocol_ch1 | RNA was isolated from fresh cells.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN).
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | The two-round RNA amplification protocol described by Affymetrix (Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II).
| Sample_hyb_protocol | 15μg of the biotinylated labeled cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10μg of total fragmented cRNA were hybridized to the Affymetrix Human Genome GeneChip array U133Plus 2.0 for 16hr at 45°C with constant rotation (60 rpm). The Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| Sample_scan_protocol | After washing and staining, all arrays were scanned with the Affymetrix GeneChip Scanner and data collected with GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA).
| Sample_data_processing | Image analysis by GCOS using the MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.
| Sample_platform_id | GPL570
| Sample_contact_name | Ahmad,,Sedaghat
| Sample_contact_laboratory | Robert Siliciano Lab
| Sample_contact_department | School of Medicine
| Sample_contact_institute | The Johns Hopkins University
| Sample_contact_address | 733 North Broadway
| Sample_contact_city | Baltimore
| Sample_contact_state | MD
| Sample_contact_zip/postal_code | 21205
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM251nnn/GSM251192/suppl/GSM251192.CEL.gz
| Sample_series_id | GSE9927
| Sample_data_row_count | 54675
| |
|
GSM251194 | GPL570 |
|
Normal Control C-8a
|
Normal Control C-8a
|
CD4+ T-cells from normal HIV- donor
|
Activated CD4+ T cells were similarly isolated by positive
selection from CD4+ T cells using CD25 microbeads (Miltenyi Biotec, Auburn, CA). In order to ensure isolation of CD25lo cells, the manufacturer’s protocol was altered such that 2 μL of CD25 microbeads and 8 μL of wash media (PBS pH 7.2-7.4, 2% newborn calf serum, 0.1% glucose, 1% pen/strep, 12mM HEPES pH 7.2) were used per million CD4+ T cells. Purity of isolated CD25+ cells was almost always greater than 95%.
|
Sample_geo_accession | GSM251194
| Sample_status | Public on Feb 19 2008
| Sample_submission_date | Dec 17 2007
| Sample_last_update_date | Feb 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | JHMI volunteers
| Sample_treatment_protocol_ch1 | CD4+ T cells were positively selected to >98% purity from freshly
| Sample_treatment_protocol_ch1 | isolated peripheral blood mononuclear cells (PBMCs) using magnetic microbeads and subsequent column purification according to the manufacturer’s protocol (MiltenyiBiotec, Auburn, CA).
| Sample_growth_protocol_ch1 | RNA was isolated from fresh cells.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN).
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | The two-round RNA amplification protocol described by Affymetrix (Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II).
| Sample_hyb_protocol | 15μg of the biotinylated labeled cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10μg of total fragmented cRNA were hybridized to the Affymetrix Human Genome GeneChip array U133Plus 2.0 for 16hr at 45°C with constant rotation (60 rpm). The Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| Sample_scan_protocol | After washing and staining, all arrays were scanned with the Affymetrix GeneChip Scanner and data collected with GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA).
| Sample_data_processing | Image analysis by GCOS using the MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.
| Sample_platform_id | GPL570
| Sample_contact_name | Ahmad,,Sedaghat
| Sample_contact_laboratory | Robert Siliciano Lab
| Sample_contact_department | School of Medicine
| Sample_contact_institute | The Johns Hopkins University
| Sample_contact_address | 733 North Broadway
| Sample_contact_city | Baltimore
| Sample_contact_state | MD
| Sample_contact_zip/postal_code | 21205
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM251nnn/GSM251194/suppl/GSM251194.CEL.gz
| Sample_series_id | GSE9927
| Sample_data_row_count | 54675
| |
|
GSM251195 | GPL570 |
|
HIV+ Individual HIV-10a
|
HIV+ Individual HIV-10a
|
CD4+ T-cells from HIV+ donor
|
Activated CD4+ T cells were similarly isolated by positive
selection from CD4+ T cells using CD25 microbeads (Miltenyi Biotec, Auburn, CA). In order to ensure isolation of CD25lo cells, the manufacturer’s protocol was altered such that 2 μL of CD25 microbeads and 8 μL of wash media (PBS pH 7.2-7.4, 2% newborn calf serum, 0.1% glucose, 1% pen/strep, 12mM HEPES pH 7.2) were used per million CD4+ T cells. Purity of isolated CD25+ cells was almost always greater than 95%.
|
Sample_geo_accession | GSM251195
| Sample_status | Public on Feb 19 2008
| Sample_submission_date | Dec 17 2007
| Sample_last_update_date | Feb 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | JHMI volunteers
| Sample_treatment_protocol_ch1 | CD4+ T cells were positively selected to >98% purity from freshly
| Sample_treatment_protocol_ch1 | isolated peripheral blood mononuclear cells (PBMCs) using magnetic microbeads and subsequent column purification according to the manufacturer’s protocol (MiltenyiBiotec, Auburn, CA).
| Sample_growth_protocol_ch1 | RNA was isolated from fresh cells.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN).
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | The two-round RNA amplification protocol described by Affymetrix (Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II).
| Sample_hyb_protocol | 15μg of the biotinylated labeled cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10μg of total fragmented cRNA were hybridized to the Affymetrix Human
| Sample_hyb_protocol | Genome GeneChip array U133Plus 2.0 for 16hr at 45°C with constant rotation (60 rpm).
| Sample_hyb_protocol | The Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| Sample_scan_protocol | After washing and staining, all arrays were scanned with the Affymetrix GeneChip Scanner and data collected with GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA).
| Sample_data_processing | Image analysis by GCOS using the MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.
| Sample_platform_id | GPL570
| Sample_contact_name | Ahmad,,Sedaghat
| Sample_contact_laboratory | Robert Siliciano Lab
| Sample_contact_department | School of Medicine
| Sample_contact_institute | The Johns Hopkins University
| Sample_contact_address | 733 North Broadway
| Sample_contact_city | Baltimore
| Sample_contact_state | MD
| Sample_contact_zip/postal_code | 21205
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM251nnn/GSM251195/suppl/GSM251195.CEL.gz
| Sample_series_id | GSE9927
| Sample_data_row_count | 54675
| |
|
GSM251196 | GPL570 |
|
HIV+ Individual HIV-11a
|
HIV+ Individual HIV-11a
|
CD4+ T-cells from HIV+ donor
|
Activated CD4+ T cells were similarly isolated by positive
selection from CD4+ T cells using CD25 microbeads (Miltenyi Biotec, Auburn, CA). In order to ensure isolation of CD25lo cells, the manufacturer’s protocol was altered such that 2 μL of CD25 microbeads and 8 μL of wash media (PBS pH 7.2-7.4, 2% newborn calf serum, 0.1% glucose, 1% pen/strep, 12mM HEPES pH 7.2) were used per million CD4+ T cells. Purity of isolated CD25+ cells was almost always greater than 95%.
|
Sample_geo_accession | GSM251196
| Sample_status | Public on Feb 19 2008
| Sample_submission_date | Dec 17 2007
| Sample_last_update_date | Feb 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | JHMI volunteers
| Sample_treatment_protocol_ch1 | CD4+ T cells were positively selected to >98% purity from freshly
| Sample_treatment_protocol_ch1 | isolated peripheral blood mononuclear cells (PBMCs) using magnetic microbeads and subsequent column purification according to the manufacturer’s protocol (MiltenyiBiotec, Auburn, CA).
| Sample_growth_protocol_ch1 | RNA was isolated from fresh cells.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN).
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | The two-round RNA amplification protocol described by Affymetrix (Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II).
| Sample_hyb_protocol | 15μg of the biotinylated labeled cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10μg of total fragmented cRNA were hybridized to the Affymetrix Human Genome GeneChip array U133Plus 2.0 for 16hr at 45°C with constant rotation (60 rpm). The Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| Sample_scan_protocol | After washing and staining, all arrays were scanned with the Affymetrix GeneChip Scanner and data collected with GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA).
| Sample_data_processing | Image analysis by GCOS using the MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.
| Sample_platform_id | GPL570
| Sample_contact_name | Ahmad,,Sedaghat
| Sample_contact_laboratory | Robert Siliciano Lab
| Sample_contact_department | School of Medicine
| Sample_contact_institute | The Johns Hopkins University
| Sample_contact_address | 733 North Broadway
| Sample_contact_city | Baltimore
| Sample_contact_state | MD
| Sample_contact_zip/postal_code | 21205
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM251nnn/GSM251196/suppl/GSM251196.CEL.gz
| Sample_series_id | GSE9927
| Sample_data_row_count | 54675
| |
|
GSM251197 | GPL570 |
|
HIV+ Individual HIV-1a
|
HIV+ Individual HIV-1a
|
CD4+ T-cells from HIV+ donor
|
Activated CD4+ T cells were similarly isolated by positive
selection from CD4+ T cells using CD25 microbeads (Miltenyi Biotec, Auburn, CA). In order to ensure isolation of CD25lo cells, the manufacturer’s protocol was altered such that 2 μL of CD25 microbeads and 8 μL of wash media (PBS pH 7.2-7.4, 2% newborn calf serum, 0.1% glucose, 1% pen/strep, 12mM HEPES pH 7.2) were used per million CD4+ T cells. Purity of isolated CD25+ cells was almost always greater than 95%.
|
Sample_geo_accession | GSM251197
| Sample_status | Public on Feb 19 2008
| Sample_submission_date | Dec 17 2007
| Sample_last_update_date | Feb 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | JHMI volunteers
| Sample_treatment_protocol_ch1 | CD4+ T cells were positively selected to >98% purity from freshly
| Sample_treatment_protocol_ch1 | isolated peripheral blood mononuclear cells (PBMCs) using magnetic microbeads and subsequent column purification according to the manufacturer’s protocol (MiltenyiBiotec, Auburn, CA).
| Sample_growth_protocol_ch1 | RNA was isolated from fresh cells.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN).
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | The two-round RNA amplification protocol described by Affymetrix (Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II).
| Sample_hyb_protocol | 15μg of the biotinylated labeled cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10μg of total fragmented cRNA were hybridized to the Affymetrix Human Genome GeneChip array U133Plus 2.0 for 16hr at 45°C with constant rotation (60 rpm). The Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| Sample_scan_protocol | After washing and staining, all arrays were scanned with the Affymetrix GeneChip Scanner and data collected with GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA).
| Sample_data_processing | Image analysis by GCOS using the MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.
| Sample_platform_id | GPL570
| Sample_contact_name | Ahmad,,Sedaghat
| Sample_contact_laboratory | Robert Siliciano Lab
| Sample_contact_department | School of Medicine
| Sample_contact_institute | The Johns Hopkins University
| Sample_contact_address | 733 North Broadway
| Sample_contact_city | Baltimore
| Sample_contact_state | MD
| Sample_contact_zip/postal_code | 21205
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM251nnn/GSM251197/suppl/GSM251197.CEL.gz
| Sample_series_id | GSE9927
| Sample_data_row_count | 54675
| |
|
GSM251198 | GPL570 |
|
HIV+ Individual HIV-2a
|
HIV+ Individual HIV-2a
|
CD4+ T-cells from HIV+ donor
|
Activated CD4+ T cells were similarly isolated by positive
selection from CD4+ T cells using CD25 microbeads (Miltenyi Biotec, Auburn, CA). In order to ensure isolation of CD25lo cells, the manufacturer’s protocol was altered such that 2 μL of CD25 microbeads and 8 μL of wash media (PBS pH 7.2-7.4, 2% newborn calf serum, 0.1% glucose, 1% pen/strep, 12mM HEPES pH 7.2) were used per million CD4+ T cells. Purity of isolated CD25+ cells was almost always greater than 95%.
|
Sample_geo_accession | GSM251198
| Sample_status | Public on Feb 19 2008
| Sample_submission_date | Dec 17 2007
| Sample_last_update_date | Feb 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | JHMI volunteers
| Sample_treatment_protocol_ch1 | CD4+ T cells were positively selected to >98% purity from freshly
| Sample_treatment_protocol_ch1 | isolated peripheral blood mononuclear cells (PBMCs) using magnetic microbeads and subsequent column purification according to the manufacturer’s protocol (MiltenyiBiotec, Auburn, CA).
| Sample_growth_protocol_ch1 | RNA was isolated from fresh cells.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN).
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | The two-round RNA amplification protocol described by Affymetrix (Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II).
| Sample_hyb_protocol | 15μg of the biotinylated labeled cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10μg of total fragmented cRNA were hybridized to the Affymetrix Human Genome GeneChip array U133Plus 2.0 for 16hr at 45°C with constant rotation (60 rpm). The Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| Sample_scan_protocol | After washing and staining, all arrays were scanned with the Affymetrix GeneChip Scanner and data collected with GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA).
| Sample_data_processing | Image analysis by GCOS using the MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.
| Sample_platform_id | GPL570
| Sample_contact_name | Ahmad,,Sedaghat
| Sample_contact_laboratory | Robert Siliciano Lab
| Sample_contact_department | School of Medicine
| Sample_contact_institute | The Johns Hopkins University
| Sample_contact_address | 733 North Broadway
| Sample_contact_city | Baltimore
| Sample_contact_state | MD
| Sample_contact_zip/postal_code | 21205
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM251nnn/GSM251198/suppl/GSM251198.CEL.gz
| Sample_series_id | GSE9927
| Sample_data_row_count | 54675
| |
|
GSM251199 | GPL570 |
|
HIV+ Individual HIV-3a
|
HIV+ Individual HIV-3a
|
CD4+ T-cells from HIV+ donor
|
Activated CD4+ T cells were similarly isolated by positive
selection from CD4+ T cells using CD25 microbeads (Miltenyi Biotec, Auburn, CA). In order to ensure isolation of CD25lo cells, the manufacturer’s protocol was altered such that 2 μL of CD25 microbeads and 8 μL of wash media (PBS pH 7.2-7.4, 2% newborn calf serum, 0.1% glucose, 1% pen/strep, 12mM HEPES pH 7.2) were used per million CD4+ T cells. Purity of isolated CD25+ cells was almost always greater than 95%.
|
Sample_geo_accession | GSM251199
| Sample_status | Public on Feb 19 2008
| Sample_submission_date | Dec 17 2007
| Sample_last_update_date | Feb 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | JHMI volunteers
| Sample_treatment_protocol_ch1 | CD4+ T cells were positively selected to >98% purity from freshly
| Sample_treatment_protocol_ch1 | isolated peripheral blood mononuclear cells (PBMCs) using magnetic microbeads and subsequent column purification according to the manufacturer’s protocol (MiltenyiBiotec, Auburn, CA).
| Sample_growth_protocol_ch1 | RNA was isolated from fresh cells.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN).
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | The two-round RNA amplification protocol described by Affymetrix (Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II).
| Sample_hyb_protocol | 15μg of the biotinylated labeled cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10μg of total fragmented cRNA were hybridized to the Affymetrix Human Genome GeneChip array U133Plus 2.0 for 16hr at 45°C with constant rotation (60 rpm). The Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| Sample_scan_protocol | After washing and staining, all arrays were scanned with the Affymetrix GeneChip Scanner and data collected with GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA).
| Sample_data_processing | Image analysis by GCOS using the MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.
| Sample_platform_id | GPL570
| Sample_contact_name | Ahmad,,Sedaghat
| Sample_contact_laboratory | Robert Siliciano Lab
| Sample_contact_department | School of Medicine
| Sample_contact_institute | The Johns Hopkins University
| Sample_contact_address | 733 North Broadway
| Sample_contact_city | Baltimore
| Sample_contact_state | MD
| Sample_contact_zip/postal_code | 21205
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM251nnn/GSM251199/suppl/GSM251199.CEL.gz
| Sample_series_id | GSE9927
| Sample_data_row_count | 54675
| |
|
GSM251200 | GPL570 |
|
HIV+ Individual HIV-4a
|
HIV+ Individual HIV-4a
|
CD4+ T-cells from HIV+ donor
|
Activated CD4+ T cells were similarly isolated by positive
selection from CD4+ T cells using CD25 microbeads (Miltenyi Biotec, Auburn, CA). In order to ensure isolation of CD25lo cells, the manufacturer’s protocol was altered such that 2 μL of CD25 microbeads and 8 μL of wash media (PBS pH 7.2-7.4, 2% newborn calf serum, 0.1% glucose, 1% pen/strep, 12mM HEPES pH 7.2) were used per million CD4+ T cells. Purity of isolated CD25+ cells was almost always greater than 95%.
|
Sample_geo_accession | GSM251200
| Sample_status | Public on Feb 19 2008
| Sample_submission_date | Dec 17 2007
| Sample_last_update_date | Feb 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | JHMI volunteers
| Sample_treatment_protocol_ch1 | CD4+ T cells were positively selected to >98% purity from freshly
| Sample_treatment_protocol_ch1 | isolated peripheral blood mononuclear cells (PBMCs) using magnetic microbeads and subsequent column purification according to the manufacturer’s protocol (MiltenyiBiotec, Auburn, CA).
| Sample_growth_protocol_ch1 | RNA was isolated from fresh cells.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN).
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | The two-round RNA amplification protocol described by Affymetrix (Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II).
| Sample_hyb_protocol | 15μg of the biotinylated labeled cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10μg of total fragmented cRNA were hybridized to the Affymetrix Human Genome GeneChip array U133Plus 2.0 for 16hr at 45°C with constant rotation (60 rpm). The Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| Sample_scan_protocol | After washing and staining, all arrays were scanned with the Affymetrix GeneChip Scanner and data collected with GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA).
| Sample_data_processing | Image analysis by GCOS using the MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.
| Sample_platform_id | GPL570
| Sample_contact_name | Ahmad,,Sedaghat
| Sample_contact_laboratory | Robert Siliciano Lab
| Sample_contact_department | School of Medicine
| Sample_contact_institute | The Johns Hopkins University
| Sample_contact_address | 733 North Broadway
| Sample_contact_city | Baltimore
| Sample_contact_state | MD
| Sample_contact_zip/postal_code | 21205
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM251nnn/GSM251200/suppl/GSM251200.CEL.gz
| Sample_series_id | GSE9927
| Sample_data_row_count | 54675
| |
|
GSM251207 | GPL570 |
|
HIV+ Individual HIV-5a
|
HIV+ Individual HIV-5a
|
CD4+ T-cells from HIV+ donor
|
Activated CD4+ T cells were similarly isolated by positive
selection from CD4+ T cells using CD25 microbeads (Miltenyi Biotec, Auburn, CA). In order to ensure isolation of CD25lo cells, the manufacturer’s protocol was altered such that 2 μL of CD25 microbeads and 8 μL of wash media (PBS pH 7.2-7.4, 2% newborn calf serum, 0.1% glucose, 1% pen/strep, 12mM HEPES pH 7.2) were used per million CD4+ T cells. Purity of isolated CD25+ cells was almost always greater than 95%.
|
Sample_geo_accession | GSM251207
| Sample_status | Public on Feb 19 2008
| Sample_submission_date | Dec 17 2007
| Sample_last_update_date | Feb 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | JHMI volunteers
| Sample_treatment_protocol_ch1 | CD4+ T cells were positively selected to >98% purity from freshly
| Sample_treatment_protocol_ch1 | isolated peripheral blood mononuclear cells (PBMCs) using magnetic microbeads and subsequent column purification according to the manufacturer’s protocol (MiltenyiBiotec, Auburn, CA).
| Sample_growth_protocol_ch1 | RNA was isolated from fresh cells.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN).
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | The two-round RNA amplification protocol described by Affymetrix (Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II).
| Sample_hyb_protocol | 15μg of the biotinylated labeled cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10μg of total fragmented cRNA were hybridized to the Affymetrix Human Genome GeneChip array U133Plus 2.0 for 16hr at 45°C with constant rotation (60 rpm). The Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| Sample_scan_protocol | After washing and staining, all arrays were scanned with the Affymetrix GeneChip Scanner and data collected with GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA).
| Sample_data_processing | Image analysis by GCOS using the MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.
| Sample_platform_id | GPL570
| Sample_contact_name | Ahmad,,Sedaghat
| Sample_contact_laboratory | Robert Siliciano Lab
| Sample_contact_department | School of Medicine
| Sample_contact_institute | The Johns Hopkins University
| Sample_contact_address | 733 North Broadway
| Sample_contact_city | Baltimore
| Sample_contact_state | MD
| Sample_contact_zip/postal_code | 21205
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM251nnn/GSM251207/suppl/GSM251207.CEL.gz
| Sample_series_id | GSE9927
| Sample_data_row_count | 54675
| |
|
GSM251208 | GPL570 |
|
HIV+ Individual HIV-6a
|
HIV+ Individual HIV-6a
|
CD4+ T-cells from HIV+ donor
|
Activated CD4+ T cells were similarly isolated by positive
selection from CD4+ T cells using CD25 microbeads (Miltenyi Biotec, Auburn, CA). In order to ensure isolation of CD25lo cells, the manufacturer’s protocol was altered such that 2 μL of CD25 microbeads and 8 μL of wash media (PBS pH 7.2-7.4, 2% newborn calf serum, 0.1% glucose, 1% pen/strep, 12mM HEPES pH 7.2) were used per million CD4+ T cells. Purity of isolated CD25+ cells was almost always greater than 95%.
|
Sample_geo_accession | GSM251208
| Sample_status | Public on Feb 19 2008
| Sample_submission_date | Dec 17 2007
| Sample_last_update_date | Feb 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | JHMI volunteers
| Sample_treatment_protocol_ch1 | CD4+ T cells were positively selected to >98% purity from freshly
| Sample_treatment_protocol_ch1 | isolated peripheral blood mononuclear cells (PBMCs) using magnetic microbeads and subsequent column purification according to the manufacturer’s protocol (MiltenyiBiotec, Auburn, CA).
| Sample_growth_protocol_ch1 | RNA was isolated from fresh cells.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN).
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | The two-round RNA amplification protocol described by Affymetrix (Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II).
| Sample_hyb_protocol | 15μg of the biotinylated labeled cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10μg of total fragmented cRNA were hybridized to the Affymetrix Human Genome GeneChip array U133Plus 2.0 for 16hr at 45°C with constant rotation (60 rpm). The Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| Sample_scan_protocol | After washing and staining, all arrays were scanned with the Affymetrix GeneChip Scanner and data collected with GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA).
| Sample_data_processing | Image analysis by GCOS using the MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.
| Sample_platform_id | GPL570
| Sample_contact_name | Ahmad,,Sedaghat
| Sample_contact_laboratory | Robert Siliciano Lab
| Sample_contact_department | School of Medicine
| Sample_contact_institute | The Johns Hopkins University
| Sample_contact_address | 733 North Broadway
| Sample_contact_city | Baltimore
| Sample_contact_state | MD
| Sample_contact_zip/postal_code | 21205
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM251nnn/GSM251208/suppl/GSM251208.CEL.gz
| Sample_series_id | GSE9927
| Sample_data_row_count | 54675
| |
|
GSM251209 | GPL570 |
|
HIV+ Individual HIV-7a
|
HIV+ Individual HIV-7a
|
CD4+ T-cells from HIV+ donor
|
Activated CD4+ T cells were similarly isolated by positive
selection from CD4+ T cells using CD25 microbeads (Miltenyi Biotec, Auburn, CA). In order to ensure isolation of CD25lo cells, the manufacturer’s protocol was altered such that 2 μL of CD25 microbeads and 8 μL of wash media (PBS pH 7.2-7.4, 2% newborn calf serum, 0.1% glucose, 1% pen/strep, 12mM HEPES pH 7.2) were used per million CD4+ T cells. Purity of isolated CD25+ cells was almost always greater than 95%.
|
Sample_geo_accession | GSM251209
| Sample_status | Public on Feb 19 2008
| Sample_submission_date | Dec 17 2007
| Sample_last_update_date | Feb 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | JHMI volunteers
| Sample_treatment_protocol_ch1 | CD4+ T cells were positively selected to >98% purity from freshly
| Sample_treatment_protocol_ch1 | isolated peripheral blood mononuclear cells (PBMCs) using magnetic microbeads and subsequent column purification according to the manufacturer’s protocol (MiltenyiBiotec, Auburn, CA).
| Sample_growth_protocol_ch1 | RNA was isolated from fresh cells.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN).
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | The two-round RNA amplification protocol described by Affymetrix (Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II).
| Sample_hyb_protocol | 15μg of the biotinylated labeled cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10μg of total fragmented cRNA were hybridized to the Affymetrix Human Genome GeneChip array U133Plus 2.0 for 16hr at 45°C with constant rotation (60 rpm). The Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| Sample_scan_protocol | After washing and staining, all arrays were scanned with the Affymetrix GeneChip Scanner and data collected with GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA).
| Sample_data_processing | Image analysis by GCOS using the MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.
| Sample_platform_id | GPL570
| Sample_contact_name | Ahmad,,Sedaghat
| Sample_contact_laboratory | Robert Siliciano Lab
| Sample_contact_department | School of Medicine
| Sample_contact_institute | The Johns Hopkins University
| Sample_contact_address | 733 North Broadway
| Sample_contact_city | Baltimore
| Sample_contact_state | MD
| Sample_contact_zip/postal_code | 21205
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM251nnn/GSM251209/suppl/GSM251209.CEL.gz
| Sample_series_id | GSE9927
| Sample_data_row_count | 54675
| |
|
GSM251210 | GPL570 |
|
HIV+ Individual HIV-8a
|
HIV+ Individual HIV-8a
|
CD4+ T-cells from HIV+ donor
|
Activated CD4+ T cells were similarly isolated by positive
selection from CD4+ T cells using CD25 microbeads (Miltenyi Biotec, Auburn, CA). In order to ensure isolation of CD25lo cells, the manufacturer’s protocol was altered such that 2 μL of CD25 microbeads and 8 μL of wash media (PBS pH 7.2-7.4, 2% newborn calf serum, 0.1% glucose, 1% pen/strep, 12mM HEPES pH 7.2) were used per million CD4+ T cells. Purity of isolated CD25+ cells was almost always greater than 95%.
|
Sample_geo_accession | GSM251210
| Sample_status | Public on Feb 19 2008
| Sample_submission_date | Dec 17 2007
| Sample_last_update_date | Feb 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | JHMI volunteers
| Sample_treatment_protocol_ch1 | CD4+ T cells were positively selected to >98% purity from freshly
| Sample_treatment_protocol_ch1 | isolated peripheral blood mononuclear cells (PBMCs) using magnetic microbeads and subsequent column purification according to the manufacturer’s protocol (MiltenyiBiotec, Auburn, CA).
| Sample_growth_protocol_ch1 | RNA was isolated from fresh cells.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN).
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | The two-round RNA amplification protocol described by Affymetrix (Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II).
| Sample_hyb_protocol | 15μg of the biotinylated labeled cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10μg of total fragmented cRNA were hybridized to the Affymetrix Human Genome GeneChip array U133Plus 2.0 for 16hr at 45°C with constant rotation (60 rpm). The Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| Sample_scan_protocol | After washing and staining, all arrays were scanned with the Affymetrix GeneChip Scanner and data collected with GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA).
| Sample_data_processing | Image analysis by GCOS using the MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.
| Sample_platform_id | GPL570
| Sample_contact_name | Ahmad,,Sedaghat
| Sample_contact_laboratory | Robert Siliciano Lab
| Sample_contact_department | School of Medicine
| Sample_contact_institute | The Johns Hopkins University
| Sample_contact_address | 733 North Broadway
| Sample_contact_city | Baltimore
| Sample_contact_state | MD
| Sample_contact_zip/postal_code | 21205
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM251nnn/GSM251210/suppl/GSM251210.CEL.gz
| Sample_series_id | GSE9927
| Sample_data_row_count | 54675
| |
|
GSM251211 | GPL570 |
|
HIV+ Individual HIV-9a
|
HIV+ Individual HIV-9a
|
CD4+ T-cells from HIV+ donor
|
Activated CD4+ T cells were similarly isolated by positive
selection from CD4+ T cells using CD25 microbeads (Miltenyi Biotec, Auburn, CA). In order to ensure isolation of CD25lo cells, the manufacturer’s protocol was altered such that 2 μL of CD25 microbeads and 8 μL of wash media (PBS pH 7.2-7.4, 2% newborn calf serum, 0.1% glucose, 1% pen/strep, 12mM HEPES pH 7.2) were used per million CD4+ T cells. Purity of isolated CD25+ cells was almost always greater than 95%.
|
Sample_geo_accession | GSM251211
| Sample_status | Public on Feb 19 2008
| Sample_submission_date | Dec 17 2007
| Sample_last_update_date | Feb 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | JHMI volunteers
| Sample_treatment_protocol_ch1 | CD4+ T cells were positively selected to >98% purity from freshly
| Sample_treatment_protocol_ch1 | isolated peripheral blood mononuclear cells (PBMCs) using magnetic microbeads and subsequent column purification according to the manufacturer’s protocol (MiltenyiBiotec, Auburn, CA).
| Sample_growth_protocol_ch1 | RNA was isolated from fresh cells.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN).
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | The two-round RNA amplification protocol described by Affymetrix (Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II).
| Sample_hyb_protocol | 15μg of the biotinylated labeled cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10μg of total fragmented cRNA were hybridized to the Affymetrix Human Genome GeneChip array U133Plus 2.0 for 16hr at 45°C with constant rotation (60 rpm). The Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinylated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
| Sample_scan_protocol | After washing and staining, all arrays were scanned with the Affymetrix GeneChip Scanner and data collected with GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA).
| Sample_data_processing | Image analysis by GCOS using the MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.
| Sample_platform_id | GPL570
| Sample_contact_name | Ahmad,,Sedaghat
| Sample_contact_laboratory | Robert Siliciano Lab
| Sample_contact_department | School of Medicine
| Sample_contact_institute | The Johns Hopkins University
| Sample_contact_address | 733 North Broadway
| Sample_contact_city | Baltimore
| Sample_contact_state | MD
| Sample_contact_zip/postal_code | 21205
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM251nnn/GSM251211/suppl/GSM251211.CEL.gz
| Sample_series_id | GSE9927
| Sample_data_row_count | 54675
| |
|
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Make groups for comparisons |
(2 groups will be compared at a time) |
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Select GSMs and click on "Add groups" |
Enter the group name here: |
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