Search results for the GEO ID: GSE48237  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1173210 | GPL570 |
|
IRIS patient 22
|
IRIS patient, PBMC stimulated for 6 hours with heat-killed H37Rv
|
individual: HIV-infected patient placed on antiretroviral treatment
case or control: IRIS case
cell type: PBMC
protocol: stimulated for 6 hours with heat killed H37Rv
|
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
IRIS_022_2
|
| Sample_geo_accession | GSM1173210
| | Sample_status | Public on Jun 24 2013
| | Sample_submission_date | Jun 24 2013
| | Sample_last_update_date | Jun 24 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 = stimulated with heat killed kH37Rv (multiplicity of infection MOI | 1:1, H37Rv to PBMC) for 6 hours
| | Sample_growth_protocol_ch1 | fresh PBMC were plated at 1x10^6 cells per ml, 5ml per well, rested overnight
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using RNeasy Mini Kit Spin protocol as per the manufacturer’s instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133+. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were analyzed with using the PLIER algorithm on ArrayAssist Lite using default analysis settings
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mark,,Nicol
| | Sample_contact_email | mark.nicol@uct.ac.za
| | Sample_contact_institute | University of Cape Town
| | Sample_contact_address | Anzio Road, Observatory,
| | Sample_contact_city | Cape Town
| | Sample_contact_zip/postal_code | 7925
| | Sample_contact_country | South Africa
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173210/suppl/GSM1173210_IRIS_022_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173210/suppl/GSM1173210_IRIS_022_2_PLIER.CHP.gz
| | Sample_series_id | GSE48237
| | Sample_data_row_count | 54675
| | |
|
GSM1173211 | GPL570 |
|
IRIS patient 24
|
IRIS patient, PBMC stimulated for 6 hours with heat-killed H37Rv
|
individual: HIV-infected patient placed on antiretroviral treatment
case or control: IRIS case
cell type: PBMC
protocol: stimulated for 6 hours with heat killed H37Rv
|
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
IRIS_024_2
|
| Sample_geo_accession | GSM1173211
| | Sample_status | Public on Jun 24 2013
| | Sample_submission_date | Jun 24 2013
| | Sample_last_update_date | Jun 24 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 = stimulated with heat killed kH37Rv (multiplicity of infection MOI | 1:1, H37Rv to PBMC) for 6 hours
| | Sample_growth_protocol_ch1 | fresh PBMC were plated at 1x10^6 cells per ml, 5ml per well, rested overnight
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using RNeasy Mini Kit Spin protocol as per the manufacturer’s instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133+. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were analyzed with using the PLIER algorithm on ArrayAssist Lite using default analysis settings
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mark,,Nicol
| | Sample_contact_email | mark.nicol@uct.ac.za
| | Sample_contact_institute | University of Cape Town
| | Sample_contact_address | Anzio Road, Observatory,
| | Sample_contact_city | Cape Town
| | Sample_contact_zip/postal_code | 7925
| | Sample_contact_country | South Africa
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173211/suppl/GSM1173211_IRIS_024_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173211/suppl/GSM1173211_IRIS_024_2_PLIER.CHP.gz
| | Sample_series_id | GSE48237
| | Sample_data_row_count | 54675
| | |
|
GSM1173212 | GPL570 |
|
IRIS patient 44
|
IRIS patient, PBMC stimulated for 6 hours with heat-killed H37Rv
|
individual: HIV-infected patient placed on antiretroviral treatment
case or control: IRIS case
cell type: PBMC
protocol: stimulated for 6 hours with heat killed H37Rv
|
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
IRIS_044_2
|
| Sample_geo_accession | GSM1173212
| | Sample_status | Public on Jun 24 2013
| | Sample_submission_date | Jun 24 2013
| | Sample_last_update_date | Jun 24 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 = stimulated with heat killed kH37Rv (multiplicity of infection MOI | 1:1, H37Rv to PBMC) for 6 hours
| | Sample_growth_protocol_ch1 | fresh PBMC were plated at 1x10^6 cells per ml, 5ml per well, rested overnight
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using RNeasy Mini Kit Spin protocol as per the manufacturer’s instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133+. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were analyzed with using the PLIER algorithm on ArrayAssist Lite using default analysis settings
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mark,,Nicol
| | Sample_contact_email | mark.nicol@uct.ac.za
| | Sample_contact_institute | University of Cape Town
| | Sample_contact_address | Anzio Road, Observatory,
| | Sample_contact_city | Cape Town
| | Sample_contact_zip/postal_code | 7925
| | Sample_contact_country | South Africa
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173212/suppl/GSM1173212_IRIS_044_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173212/suppl/GSM1173212_IRIS_044_2_PLIER.CHP.gz
| | Sample_series_id | GSE48237
| | Sample_data_row_count | 54675
| | |
|
GSM1173213 | GPL570 |
|
IRIS patient 48
|
IRIS patient, PBMC stimulated for 6 hours with heat-killed H37Rv
|
individual: HIV-infected patient placed on antiretroviral treatment
case or control: IRIS case
cell type: PBMC
protocol: stimulated for 6 hours with heat killed H37Rv
|
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
IRIS_048_2
|
| Sample_geo_accession | GSM1173213
| | Sample_status | Public on Jun 24 2013
| | Sample_submission_date | Jun 24 2013
| | Sample_last_update_date | Jun 24 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 = stimulated with heat killed kH37Rv (multiplicity of infection MOI | 1:1, H37Rv to PBMC) for 6 hours
| | Sample_growth_protocol_ch1 | fresh PBMC were plated at 1x10^6 cells per ml, 5ml per well, rested overnight
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using RNeasy Mini Kit Spin protocol as per the manufacturer’s instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133+. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were analyzed with using the PLIER algorithm on ArrayAssist Lite using default analysis settings
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mark,,Nicol
| | Sample_contact_email | mark.nicol@uct.ac.za
| | Sample_contact_institute | University of Cape Town
| | Sample_contact_address | Anzio Road, Observatory,
| | Sample_contact_city | Cape Town
| | Sample_contact_zip/postal_code | 7925
| | Sample_contact_country | South Africa
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173213/suppl/GSM1173213_IRIS_048_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173213/suppl/GSM1173213_IRIS_048_2_PLIER.CHP.gz
| | Sample_series_id | GSE48237
| | Sample_data_row_count | 54675
| | |
|
GSM1173214 | GPL570 |
|
IRIS patient 98
|
IRIS patient, PBMC stimulated for 6 hours with heat-killed H37Rv
|
individual: HIV-infected patient placed on antiretroviral treatment
case or control: IRIS case
cell type: PBMC
protocol: stimulated for 6 hours with heat killed H37Rv
|
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
IRIS_098_2
|
| Sample_geo_accession | GSM1173214
| | Sample_status | Public on Jun 24 2013
| | Sample_submission_date | Jun 24 2013
| | Sample_last_update_date | Jun 24 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 = stimulated with heat killed kH37Rv (multiplicity of infection MOI | 1:1, H37Rv to PBMC) for 6 hours
| | Sample_growth_protocol_ch1 | fresh PBMC were plated at 1x10^6 cells per ml, 5ml per well, rested overnight
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using RNeasy Mini Kit Spin protocol as per the manufacturer’s instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133+. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were analyzed with using the PLIER algorithm on ArrayAssist Lite using default analysis settings
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mark,,Nicol
| | Sample_contact_email | mark.nicol@uct.ac.za
| | Sample_contact_institute | University of Cape Town
| | Sample_contact_address | Anzio Road, Observatory,
| | Sample_contact_city | Cape Town
| | Sample_contact_zip/postal_code | 7925
| | Sample_contact_country | South Africa
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173214/suppl/GSM1173214_IRIS_098_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173214/suppl/GSM1173214_IRIS_098_2_PLIER.CHP.gz
| | Sample_series_id | GSE48237
| | Sample_data_row_count | 54675
| | |
|
GSM1173215 | GPL570 |
|
IRIS patient 113
|
IRIS patient, PBMC stimulated for 6 hours with heat-killed H37Rv
|
individual: HIV-infected patient placed on antiretroviral treatment
case or control: IRIS case
cell type: PBMC
protocol: stimulated for 6 hours with heat killed H37Rv
|
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
IRIS_113_2
|
| Sample_geo_accession | GSM1173215
| | Sample_status | Public on Jun 24 2013
| | Sample_submission_date | Jun 24 2013
| | Sample_last_update_date | Jun 24 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 = stimulated with heat killed kH37Rv (multiplicity of infection MOI | 1:1, H37Rv to PBMC) for 6 hours
| | Sample_growth_protocol_ch1 | fresh PBMC were plated at 1x10^6 cells per ml, 5ml per well, rested overnight
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using RNeasy Mini Kit Spin protocol as per the manufacturer’s instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133+. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were analyzed with using the PLIER algorithm on ArrayAssist Lite using default analysis settings
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mark,,Nicol
| | Sample_contact_email | mark.nicol@uct.ac.za
| | Sample_contact_institute | University of Cape Town
| | Sample_contact_address | Anzio Road, Observatory,
| | Sample_contact_city | Cape Town
| | Sample_contact_zip/postal_code | 7925
| | Sample_contact_country | South Africa
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173215/suppl/GSM1173215_IRIS_113_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173215/suppl/GSM1173215_IRIS_113_2_PLIER.CHP.gz
| | Sample_series_id | GSE48237
| | Sample_data_row_count | 54675
| | |
|
GSM1173216 | GPL570 |
|
IRIS patient 116
|
IRIS patient, PBMC stimulated for 6 hours with heat-killed H37Rv
|
individual: HIV-infected patient placed on antiretroviral treatment
case or control: IRIS case
cell type: PBMC
protocol: stimulated for 6 hours with heat killed H37Rv
|
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
IRIS_116_2
|
| Sample_geo_accession | GSM1173216
| | Sample_status | Public on Jun 24 2013
| | Sample_submission_date | Jun 24 2013
| | Sample_last_update_date | Jun 24 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 = stimulated with heat killed kH37Rv (multiplicity of infection MOI | 1:1, H37Rv to PBMC) for 6 hours
| | Sample_growth_protocol_ch1 | fresh PBMC were plated at 1x10^6 cells per ml, 5ml per well, rested overnight
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using RNeasy Mini Kit Spin protocol as per the manufacturer’s instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133+. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were analyzed with using the PLIER algorithm on ArrayAssist Lite using default analysis settings
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mark,,Nicol
| | Sample_contact_email | mark.nicol@uct.ac.za
| | Sample_contact_institute | University of Cape Town
| | Sample_contact_address | Anzio Road, Observatory,
| | Sample_contact_city | Cape Town
| | Sample_contact_zip/postal_code | 7925
| | Sample_contact_country | South Africa
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173216/suppl/GSM1173216_IRIS_116_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173216/suppl/GSM1173216_IRIS_116_2_PLIER.CHP.gz
| | Sample_series_id | GSE48237
| | Sample_data_row_count | 54675
| | |
|
GSM1173217 | GPL570 |
|
TBART control patient 001_6
|
IRIS patient, PBMC stimulated for 6 hours with heat-killed H37Rv
|
individual: HIV-infected patient placed on antiretroviral treatment
case or control: Control
cell type: PBMC
protocol: stimulated for 6 hours with heat killed H37Rv
|
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
TBART_001_6
|
| Sample_geo_accession | GSM1173217
| | Sample_status | Public on Jun 24 2013
| | Sample_submission_date | Jun 24 2013
| | Sample_last_update_date | Jun 24 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 = stimulated with heat killed kH37Rv (multiplicity of infection MOI | 1:1, H37Rv to PBMC) for 6 hours
| | Sample_growth_protocol_ch1 | fresh PBMC were plated at 1x10^6 cells per ml, 5ml per well, rested overnight
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using RNeasy Mini Kit Spin protocol as per the manufacturer’s instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133+. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were analyzed with using the PLIER algorithm on ArrayAssist Lite using default analysis settings
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mark,,Nicol
| | Sample_contact_email | mark.nicol@uct.ac.za
| | Sample_contact_institute | University of Cape Town
| | Sample_contact_address | Anzio Road, Observatory,
| | Sample_contact_city | Cape Town
| | Sample_contact_zip/postal_code | 7925
| | Sample_contact_country | South Africa
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173217/suppl/GSM1173217_TBART_001_6.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173217/suppl/GSM1173217_TBART_001_6_PLIER.CHP.gz
| | Sample_series_id | GSE48237
| | Sample_data_row_count | 54675
| | |
|
GSM1173218 | GPL570 |
|
TBART control patient15_6
|
TBART control patient, PBMC stimulated for 6 hours with heat-killed H37Rv
|
individual: HIV-infected patient placed on antiretroviral treatment
case or control: Control
cell type: PBMC
protocol: stimulated for 6 hours with heat killed H37Rv
|
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
TBART_15_6
|
| Sample_geo_accession | GSM1173218
| | Sample_status | Public on Jun 24 2013
| | Sample_submission_date | Jun 24 2013
| | Sample_last_update_date | Jun 24 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 = stimulated with heat killed kH37Rv (multiplicity of infection MOI | 1:1, H37Rv to PBMC) for 6 hours
| | Sample_growth_protocol_ch1 | fresh PBMC were plated at 1x10^6 cells per ml, 5ml per well, rested overnight
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using RNeasy Mini Kit Spin protocol as per the manufacturer’s instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133+. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were analyzed with using the PLIER algorithm on ArrayAssist Lite using default analysis settings
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mark,,Nicol
| | Sample_contact_email | mark.nicol@uct.ac.za
| | Sample_contact_institute | University of Cape Town
| | Sample_contact_address | Anzio Road, Observatory,
| | Sample_contact_city | Cape Town
| | Sample_contact_zip/postal_code | 7925
| | Sample_contact_country | South Africa
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173218/suppl/GSM1173218_TBART_15_6.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173218/suppl/GSM1173218_TBART_15_6_PLIER.CHP.gz
| | Sample_series_id | GSE48237
| | Sample_data_row_count | 54675
| | |
|
GSM1173219 | GPL570 |
|
TBART control patient 27
|
TBART control patient, PBMC stimulated for 6 hours with heat-killed H37Rv
|
individual: HIV-infected patient placed on antiretroviral treatment
case or control: Control
cell type: PBMC
protocol: stimulated for 6 hours with heat killed H37Rv
|
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
TBART_27
|
| Sample_geo_accession | GSM1173219
| | Sample_status | Public on Jun 24 2013
| | Sample_submission_date | Jun 24 2013
| | Sample_last_update_date | Jun 24 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 = stimulated with heat killed kH37Rv (multiplicity of infection MOI | 1:1, H37Rv to PBMC) for 6 hours
| | Sample_growth_protocol_ch1 | fresh PBMC were plated at 1x10^6 cells per ml, 5ml per well, rested overnight
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using RNeasy Mini Kit Spin protocol as per the manufacturer’s instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133+. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were analyzed with using the PLIER algorithm on ArrayAssist Lite using default analysis settings
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mark,,Nicol
| | Sample_contact_email | mark.nicol@uct.ac.za
| | Sample_contact_institute | University of Cape Town
| | Sample_contact_address | Anzio Road, Observatory,
| | Sample_contact_city | Cape Town
| | Sample_contact_zip/postal_code | 7925
| | Sample_contact_country | South Africa
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173219/suppl/GSM1173219_TBART_27.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173219/suppl/GSM1173219_TBART_27_PLIER.CHP.gz
| | Sample_series_id | GSE48237
| | Sample_data_row_count | 54675
| | |
|
GSM1173220 | GPL570 |
|
TBART control patient 32
|
TBART control patient, PBMC stimulated for 6 hours with heat-killed H37Rv
|
individual: HIV-infected patient placed on antiretroviral treatment
case or control: Control
cell type: PBMC
protocol: stimulated for 6 hours with heat killed H37Rv
|
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
TBART_32
|
| Sample_geo_accession | GSM1173220
| | Sample_status | Public on Jun 24 2013
| | Sample_submission_date | Jun 24 2013
| | Sample_last_update_date | Jun 24 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 = stimulated with heat killed kH37Rv (multiplicity of infection MOI | 1:1, H37Rv to PBMC) for 6 hours
| | Sample_growth_protocol_ch1 | fresh PBMC were plated at 1x10^6 cells per ml, 5ml per well, rested overnight
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using RNeasy Mini Kit Spin protocol as per the manufacturer’s instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133+. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were analyzed with using the PLIER algorithm on ArrayAssist Lite using default analysis settings
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mark,,Nicol
| | Sample_contact_email | mark.nicol@uct.ac.za
| | Sample_contact_institute | University of Cape Town
| | Sample_contact_address | Anzio Road, Observatory,
| | Sample_contact_city | Cape Town
| | Sample_contact_zip/postal_code | 7925
| | Sample_contact_country | South Africa
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173220/suppl/GSM1173220_TBART_32.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173220/suppl/GSM1173220_TBART_32_PLIER.CHP.gz
| | Sample_series_id | GSE48237
| | Sample_data_row_count | 54675
| | |
|
GSM1173221 | GPL570 |
|
TBART control patient 35
|
TBART control patient, PBMC stimulated for 6 hours with heat-killed H37Rv
|
individual: HIV-infected patient placed on antiretroviral treatment
case or control: Control
cell type: PBMC
protocol: stimulated for 6 hours with heat killed H37Rv
|
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
TBART_35
|
| Sample_geo_accession | GSM1173221
| | Sample_status | Public on Jun 24 2013
| | Sample_submission_date | Jun 24 2013
| | Sample_last_update_date | Jun 24 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 = stimulated with heat killed kH37Rv (multiplicity of infection MOI | 1:1, H37Rv to PBMC) for 6 hours
| | Sample_growth_protocol_ch1 | fresh PBMC were plated at 1x10^6 cells per ml, 5ml per well, rested overnight
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using RNeasy Mini Kit Spin protocol as per the manufacturer’s instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133+. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were analyzed with using the PLIER algorithm on ArrayAssist Lite using default analysis settings
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mark,,Nicol
| | Sample_contact_email | mark.nicol@uct.ac.za
| | Sample_contact_institute | University of Cape Town
| | Sample_contact_address | Anzio Road, Observatory,
| | Sample_contact_city | Cape Town
| | Sample_contact_zip/postal_code | 7925
| | Sample_contact_country | South Africa
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173221/suppl/GSM1173221_TBART_35.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173221/suppl/GSM1173221_TBART_35_PLIER.CHP.gz
| | Sample_series_id | GSE48237
| | Sample_data_row_count | 54675
| | |
|
GSM1173222 | GPL570 |
|
TBART control patient 36
|
TBART control patient, PBMC stimulated for 6 hours with heat-killed H37Rv
|
individual: HIV-infected patient placed on antiretroviral treatment
case or control: Control
cell type: PBMC
protocol: stimulated for 6 hours with heat killed H37Rv
|
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
TBART_36
|
| Sample_geo_accession | GSM1173222
| | Sample_status | Public on Jun 24 2013
| | Sample_submission_date | Jun 24 2013
| | Sample_last_update_date | Jun 24 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 = stimulated with heat killed kH37Rv (multiplicity of infection MOI | 1:1, H37Rv to PBMC) for 6 hours
| | Sample_growth_protocol_ch1 | fresh PBMC were plated at 1x10^6 cells per ml, 5ml per well, rested overnight
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using RNeasy Mini Kit Spin protocol as per the manufacturer’s instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133+. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were analyzed with using the PLIER algorithm on ArrayAssist Lite using default analysis settings
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mark,,Nicol
| | Sample_contact_email | mark.nicol@uct.ac.za
| | Sample_contact_institute | University of Cape Town
| | Sample_contact_address | Anzio Road, Observatory,
| | Sample_contact_city | Cape Town
| | Sample_contact_zip/postal_code | 7925
| | Sample_contact_country | South Africa
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173222/suppl/GSM1173222_TBART_36.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173222/suppl/GSM1173222_TBART_36_PLIER.CHP.gz
| | Sample_series_id | GSE48237
| | Sample_data_row_count | 54675
| | |
|
GSM1173223 | GPL570 |
|
TBART control patient 37
|
TBART control patient, PBMC stimulated for 6 hours with heat-killed H37Rv
|
individual: HIV-infected patient placed on antiretroviral treatment
case or control: Control
cell type: PBMC
protocol: stimulated for 6 hours with heat killed H37Rv
|
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
TBART_37
|
| Sample_geo_accession | GSM1173223
| | Sample_status | Public on Jun 24 2013
| | Sample_submission_date | Jun 24 2013
| | Sample_last_update_date | Jun 24 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 = stimulated with heat killed kH37Rv (multiplicity of infection MOI | 1:1, H37Rv to PBMC) for 6 hours
| | Sample_growth_protocol_ch1 | fresh PBMC were plated at 1x10^6 cells per ml, 5ml per well, rested overnight
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using RNeasy Mini Kit Spin protocol as per the manufacturer’s instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133+. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were analyzed with using the PLIER algorithm on ArrayAssist Lite using default analysis settings
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mark,,Nicol
| | Sample_contact_email | mark.nicol@uct.ac.za
| | Sample_contact_institute | University of Cape Town
| | Sample_contact_address | Anzio Road, Observatory,
| | Sample_contact_city | Cape Town
| | Sample_contact_zip/postal_code | 7925
| | Sample_contact_country | South Africa
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173223/suppl/GSM1173223_TBART_37.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1173nnn/GSM1173223/suppl/GSM1173223_TBART_37_PLIER.CHP.gz
| | Sample_series_id | GSE48237
| | Sample_data_row_count | 54675
| | |
|
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