Search results for the GEO ID: GSE42925  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1053485 | GPL570 |
|
macrophages at lacZ 30 hrs
|
macrophages infected with adenovirus expressing LacZ control for 30 hours
|
cell type: macrophages differentiated from monocytes
differentiation protocol: macrophages differentiated with G-MCSF
differentiation time: macrophages differentiated for 7 days
infection: adenovirus expressing LacZ control
infection time: 30 hrs
|
Gene expression data from lacz control
|
| Sample_geo_accession | GSM1053485
| | Sample_status | Public on Jun 01 2013
| | Sample_submission_date | Dec 14 2012
| | Sample_last_update_date | Jun 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were infected with 5 moi of adeno-lacZ or adeno-Tat for 30 hours or infected with HIVbal or medium alone as a control for 10 days.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation and then monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA). The monocytes were differentiated into macrophages by culturing them with human recombinant M-CSF for six days. THP-1 cells were differentiated into M2-polarized MDM with PHA.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected in Trizol® (Invitrogen, Carlsbad, CA), which was used to isolate total RNA according to the manufacturer’s instructions. The RNA was treated with 4 U of DNase I (Ambion, Austin, TX) and purified with Trizol® LS.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA, 0.1 ug was prepared for hybridization to HG U133 2.0 oligonucleotide array (Affymetrix, Memphis, Tennessee) according to the small sample expression protocol (Affymetrix). Hybridization was carried out overnight with 1.5 ug of labeled cRNA product, and arrays were scanned on Affymetrix scanners.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip human U133A plus 2.0 Affymetrix Array. 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 Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | NAYOUNG,,KIM
| | Sample_contact_email | nayoung.kim@childrens.harvard.edu
| | Sample_contact_department | MEDICINE
| | Sample_contact_institute | BOSTON CHILDREN'S HOSPITAL
| | Sample_contact_address | 61 BINNEY
| | Sample_contact_city | BOSTON
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053485/suppl/GSM1053485_M1_HG-U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053485/suppl/GSM1053485_M1_HG-U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE42925
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053486 | GPL570 |
|
macrophages at Tat 30 hrs
|
macrophages infected with adenovirus expressing Tat for 30 hours
|
cell type: macrophages differentiated from monocytes
differentiation protocol: macrophages differentiated with G-MCSF
differentiation time: macrophages differentiated for 7 days
infection: adenovirus expressing Tat
infection time: 30 hrs
|
Gene expression data from Tat
|
| Sample_geo_accession | GSM1053486
| | Sample_status | Public on Jun 01 2013
| | Sample_submission_date | Dec 14 2012
| | Sample_last_update_date | Jun 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were infected with 5 moi of adeno-lacZ or adeno-Tat for 30 hours or infected with HIVbal or medium alone as a control for 10 days.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation and then monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA). The monocytes were differentiated into macrophages by culturing them with human recombinant M-CSF for six days. THP-1 cells were differentiated into M2-polarized MDM with PHA.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected in Trizol® (Invitrogen, Carlsbad, CA), which was used to isolate total RNA according to the manufacturer’s instructions. The RNA was treated with 4 U of DNase I (Ambion, Austin, TX) and purified with Trizol® LS.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA, 0.1 ug was prepared for hybridization to HG U133 2.0 oligonucleotide array (Affymetrix, Memphis, Tennessee) according to the small sample expression protocol (Affymetrix). Hybridization was carried out overnight with 1.5 ug of labeled cRNA product, and arrays were scanned on Affymetrix scanners.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip human U133A plus 2.0 Affymetrix Array. 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 Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | NAYOUNG,,KIM
| | Sample_contact_email | nayoung.kim@childrens.harvard.edu
| | Sample_contact_department | MEDICINE
| | Sample_contact_institute | BOSTON CHILDREN'S HOSPITAL
| | Sample_contact_address | 61 BINNEY
| | Sample_contact_city | BOSTON
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053486/suppl/GSM1053486_M3_HG-U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053486/suppl/GSM1053486_M3_HG-U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE42925
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053487 | GPL570 |
|
macrophages at medium 7d
|
macrophages infected with medium control for 7 days
|
cell type: macrophages differentiated from monocytes
differentiation protocol: macrophages differentiated with G-MCSF
differentiation time: macrophages differentiated for 7 days
infection: medium control
infection time: 7 days
|
Gene expression data from medium 7d
|
| Sample_geo_accession | GSM1053487
| | Sample_status | Public on Jun 01 2013
| | Sample_submission_date | Dec 14 2012
| | Sample_last_update_date | Jun 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were infected with 5 moi of adeno-lacZ or adeno-Tat for 30 hours or infected with HIVbal or medium alone as a control for 10 days.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation and then monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA). The monocytes were differentiated into macrophages by culturing them with human recombinant M-CSF for six days. THP-1 cells were differentiated into M2-polarized MDM with PHA.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected in Trizol® (Invitrogen, Carlsbad, CA), which was used to isolate total RNA according to the manufacturer’s instructions. The RNA was treated with 4 U of DNase I (Ambion, Austin, TX) and purified with Trizol® LS.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA, 0.1 ug was prepared for hybridization to HG U133 2.0 oligonucleotide array (Affymetrix, Memphis, Tennessee) according to the small sample expression protocol (Affymetrix). Hybridization was carried out overnight with 1.5 ug of labeled cRNA product, and arrays were scanned on Affymetrix scanners.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip human U133A plus 2.0 Affymetrix Array. 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 Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | NAYOUNG,,KIM
| | Sample_contact_email | nayoung.kim@childrens.harvard.edu
| | Sample_contact_department | MEDICINE
| | Sample_contact_institute | BOSTON CHILDREN'S HOSPITAL
| | Sample_contact_address | 61 BINNEY
| | Sample_contact_city | BOSTON
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053487/suppl/GSM1053487_M4_HG-U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053487/suppl/GSM1053487_M4_HG-U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE42925
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053488 | GPL570 |
|
macrophages at HIV 7d
|
macrophages infected with HIVbal 7 days
|
cell type: macrophages differentiated from monocytes
differentiation protocol: macrophages differentiated with G-MCSF
differentiation time: macrophages differentiated for 7 days
infection: HIVbal
infection time: 7 days
|
Gene expression data from HIVbal 7d
|
| Sample_geo_accession | GSM1053488
| | Sample_status | Public on Jun 01 2013
| | Sample_submission_date | Dec 14 2012
| | Sample_last_update_date | Jun 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were infected with 5 moi of adeno-lacZ or adeno-Tat for 30 hours or infected with HIVbal or medium alone as a control for 10 days.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation and then monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA). The monocytes were differentiated into macrophages by culturing them with human recombinant M-CSF for six days. THP-1 cells were differentiated into M2-polarized MDM with PHA.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected in Trizol® (Invitrogen, Carlsbad, CA), which was used to isolate total RNA according to the manufacturer’s instructions. The RNA was treated with 4 U of DNase I (Ambion, Austin, TX) and purified with Trizol® LS.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA, 0.1 ug was prepared for hybridization to HG U133 2.0 oligonucleotide array (Affymetrix, Memphis, Tennessee) according to the small sample expression protocol (Affymetrix). Hybridization was carried out overnight with 1.5 ug of labeled cRNA product, and arrays were scanned on Affymetrix scanners.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip human U133A plus 2.0 Affymetrix Array. 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 Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | NAYOUNG,,KIM
| | Sample_contact_email | nayoung.kim@childrens.harvard.edu
| | Sample_contact_department | MEDICINE
| | Sample_contact_institute | BOSTON CHILDREN'S HOSPITAL
| | Sample_contact_address | 61 BINNEY
| | Sample_contact_city | BOSTON
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053488/suppl/GSM1053488_M5_HG-U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053488/suppl/GSM1053488_M5_HG-U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE42925
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053489 | GPL570 |
|
macrophages at medium 10d
|
macrophages infected with medium control for 10 days
|
cell type: macrophages differentiated from monocytes
differentiation protocol: macrophages differentiated with G-MCSF
differentiation time: macrophages differentiated for 7 days
infection: medium control
infection time: 10 days
|
Gene expression data from medium 10d
|
| Sample_geo_accession | GSM1053489
| | Sample_status | Public on Jun 01 2013
| | Sample_submission_date | Dec 14 2012
| | Sample_last_update_date | Jun 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were infected with 5 moi of adeno-lacZ or adeno-Tat for 30 hours or infected with HIVbal or medium alone as a control for 10 days.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation and then monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA). The monocytes were differentiated into macrophages by culturing them with human recombinant M-CSF for six days. THP-1 cells were differentiated into M2-polarized MDM with PHA.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected in Trizol® (Invitrogen, Carlsbad, CA), which was used to isolate total RNA according to the manufacturer’s instructions. The RNA was treated with 4 U of DNase I (Ambion, Austin, TX) and purified with Trizol® LS.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA, 0.1 ug was prepared for hybridization to HG U133 2.0 oligonucleotide array (Affymetrix, Memphis, Tennessee) according to the small sample expression protocol (Affymetrix). Hybridization was carried out overnight with 1.5 ug of labeled cRNA product, and arrays were scanned on Affymetrix scanners.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip human U133A plus 2.0 Affymetrix Array. 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 Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | NAYOUNG,,KIM
| | Sample_contact_email | nayoung.kim@childrens.harvard.edu
| | Sample_contact_department | MEDICINE
| | Sample_contact_institute | BOSTON CHILDREN'S HOSPITAL
| | Sample_contact_address | 61 BINNEY
| | Sample_contact_city | BOSTON
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053489/suppl/GSM1053489_M6_HG-U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053489/suppl/GSM1053489_M6_HG-U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE42925
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053490 | GPL570 |
|
macrophages at HIV 10d
|
macrophages infected with HIVbal 10 days
|
cell type: macrophages differentiated from monocytes
differentiation protocol: macrophages differentiated with G-MCSF
differentiation time: macrophages differentiated for 7 days
infection: HIVbal
infection time: 10 days
|
Gene expression data from HIVbal 10d
|
| Sample_geo_accession | GSM1053490
| | Sample_status | Public on Jun 01 2013
| | Sample_submission_date | Dec 14 2012
| | Sample_last_update_date | Jun 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were infected with 5 moi of adeno-lacZ or adeno-Tat for 30 hours or infected with HIVbal or medium alone as a control for 10 days.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation and then monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA). The monocytes were differentiated into macrophages by culturing them with human recombinant M-CSF for six days. THP-1 cells were differentiated into M2-polarized MDM with PHA.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected in Trizol® (Invitrogen, Carlsbad, CA), which was used to isolate total RNA according to the manufacturer’s instructions. The RNA was treated with 4 U of DNase I (Ambion, Austin, TX) and purified with Trizol® LS.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA, 0.1 ug was prepared for hybridization to HG U133 2.0 oligonucleotide array (Affymetrix, Memphis, Tennessee) according to the small sample expression protocol (Affymetrix). Hybridization was carried out overnight with 1.5 ug of labeled cRNA product, and arrays were scanned on Affymetrix scanners.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip human U133A plus 2.0 Affymetrix Array. 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 Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | NAYOUNG,,KIM
| | Sample_contact_email | nayoung.kim@childrens.harvard.edu
| | Sample_contact_department | MEDICINE
| | Sample_contact_institute | BOSTON CHILDREN'S HOSPITAL
| | Sample_contact_address | 61 BINNEY
| | Sample_contact_city | BOSTON
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053490/suppl/GSM1053490_M7_HG-U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053490/suppl/GSM1053490_M7_HG-U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE42925
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053491 | GPL570 |
|
THP-Mac at tTA control
|
THP-1 cells infected with adenovirus expressing tTA control for 24 hours
|
cell type: macrophages differentiated from THP-1 cells
differentiation protocol: THP-1 derived macrophages differentiated with PMA
differentiation time: macrophages differentiated for 3 days
infection: adenovirus expressing tTA control
infection time: 24 hrs
|
Gene expression data from lacz control
|
| Sample_geo_accession | GSM1053491
| | Sample_status | Public on Jun 01 2013
| | Sample_submission_date | Dec 14 2012
| | Sample_last_update_date | Jun 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were infected with 5 moi of adeno-lacZ or adeno-Tat for 30 hours or infected with HIVbal or medium alone as a control for 10 days.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation and then monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA). The monocytes were differentiated into macrophages by culturing them with human recombinant M-CSF for six days. THP-1 cells were differentiated into M2-polarized MDM with PHA.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected in Trizol® (Invitrogen, Carlsbad, CA), which was used to isolate total RNA according to the manufacturer’s instructions. The RNA was treated with 4 U of DNase I (Ambion, Austin, TX) and purified with Trizol® LS.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA, 0.1 ug was prepared for hybridization to HG U133 2.0 oligonucleotide array (Affymetrix, Memphis, Tennessee) according to the small sample expression protocol (Affymetrix). Hybridization was carried out overnight with 1.5 ug of labeled cRNA product, and arrays were scanned on Affymetrix scanners.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip human U133A plus 2.0 Affymetrix Array. 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 Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | NAYOUNG,,KIM
| | Sample_contact_email | nayoung.kim@childrens.harvard.edu
| | Sample_contact_department | MEDICINE
| | Sample_contact_institute | BOSTON CHILDREN'S HOSPITAL
| | Sample_contact_address | 61 BINNEY
| | Sample_contact_city | BOSTON
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053491/suppl/GSM1053491_T1_HG-U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053491/suppl/GSM1053491_T1_HG-U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE42925
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053492 | GPL570 |
|
THP-Mac at TatSF2 24 hrs
|
THP-1 cells infected with adenovirus expressing TatSF2 for 24 hours
|
cell type: macrophages differentiated from THP-1 cells
differentiation protocol: THP-1 derived macrophages differentiated with PMA
differentiation time: macrophages differentiated for 3 days
infection: adenovirus expressing TatSF2
infection time: 24 hrs
|
Gene expression data from Tat
|
| Sample_geo_accession | GSM1053492
| | Sample_status | Public on Jun 01 2013
| | Sample_submission_date | Dec 14 2012
| | Sample_last_update_date | Jun 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were infected with 5 moi of adeno-lacZ or adeno-Tat for 30 hours or infected with HIVbal or medium alone as a control for 10 days.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation and then monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA). The monocytes were differentiated into macrophages by culturing them with human recombinant M-CSF for six days. THP-1 cells were differentiated into M2-polarized MDM with PHA.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected in Trizol® (Invitrogen, Carlsbad, CA), which was used to isolate total RNA according to the manufacturer’s instructions. The RNA was treated with 4 U of DNase I (Ambion, Austin, TX) and purified with Trizol® LS.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA, 0.1 ug was prepared for hybridization to HG U133 2.0 oligonucleotide array (Affymetrix, Memphis, Tennessee) according to the small sample expression protocol (Affymetrix). Hybridization was carried out overnight with 1.5 ug of labeled cRNA product, and arrays were scanned on Affymetrix scanners.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip human U133A plus 2.0 Affymetrix Array. 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 Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | NAYOUNG,,KIM
| | Sample_contact_email | nayoung.kim@childrens.harvard.edu
| | Sample_contact_department | MEDICINE
| | Sample_contact_institute | BOSTON CHILDREN'S HOSPITAL
| | Sample_contact_address | 61 BINNEY
| | Sample_contact_city | BOSTON
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053492/suppl/GSM1053492_T2_HG-U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053492/suppl/GSM1053492_T2_HG-U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE42925
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
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GSM1053493 | GPL570 |
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THP-Mac at TatHXB2 24 hrs
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THP-1 cells infected with adenovirus expressing TatHXB2 for 24 hours
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cell type: macrophages differentiated from THP-1 cells
differentiation protocol: THP-1 derived macrophages differentiated with PMA
differentiation time: macrophages differentiated for 3 days
infection: adenovirus expressing TatHXB2
infection time: 24 hrs
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Gene expression data from medium 7d
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| Sample_geo_accession | GSM1053493
| | Sample_status | Public on Jun 01 2013
| | Sample_submission_date | Dec 14 2012
| | Sample_last_update_date | Jun 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were infected with 5 moi of adeno-lacZ or adeno-Tat for 30 hours or infected with HIVbal or medium alone as a control for 10 days.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation and then monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA). The monocytes were differentiated into macrophages by culturing them with human recombinant M-CSF for six days. THP-1 cells were differentiated into M2-polarized MDM with PHA.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected in Trizol® (Invitrogen, Carlsbad, CA), which was used to isolate total RNA according to the manufacturer’s instructions. The RNA was treated with 4 U of DNase I (Ambion, Austin, TX) and purified with Trizol® LS.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA, 0.1 ug was prepared for hybridization to HG U133 2.0 oligonucleotide array (Affymetrix, Memphis, Tennessee) according to the small sample expression protocol (Affymetrix). Hybridization was carried out overnight with 1.5 ug of labeled cRNA product, and arrays were scanned on Affymetrix scanners.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip human U133A plus 2.0 Affymetrix Array. 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 Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | NAYOUNG,,KIM
| | Sample_contact_email | nayoung.kim@childrens.harvard.edu
| | Sample_contact_department | MEDICINE
| | Sample_contact_institute | BOSTON CHILDREN'S HOSPITAL
| | Sample_contact_address | 61 BINNEY
| | Sample_contact_city | BOSTON
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053493/suppl/GSM1053493_T3_HG-U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053493/suppl/GSM1053493_T3_HG-U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE42925
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
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