Search results for the GEO ID: GSE42924  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1053464 | GPL570 |
|
Ad-TatHXB2 10 h p.i.
|
iDC expressing TatHXB2, collected 10 h p.i.
|
cell type: Immature dendritic cells differentiated from monocytes
infection: Ad-TatHXB2
time (hpi): 10 hr
|
Gene expression data from iDC 10 h p.i.
|
| Sample_geo_accession | GSM1053464
| | 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 | 10e6 DC cells were infected with 5 plaque-forming units per cell of both Ad-tTA and the Ad-Tat constructs or Ad-LacZ as a control.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation. Monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA) according to the manufacturer’s instructions. The monocytes were differentiated into immature dendritic cells by culturing them with human recombinant GM-CSF and IL-4 (R&D Systems, Minneapolis, MN) for six days (Bender et al. 1996).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected 0 h, 5 h, 10 h and 20 h post infection. 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_Plus_2 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 | Values in the raw data below 100, were floored to 100. Expression levels were compared to RNA from uninfected cells and cells infected with Ad-LacZ as a control. Gene up-regulation was examined only for transcripts from Ad-Tat infected cells that were present according to the detection call and down-regulation only for genes that were present in the uninfected and Ad-tTA-infected controls.
| | 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/GSM1053464/suppl/GSM1053464_Kukkonen_HX10.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053464/suppl/GSM1053464_Kukkonen_HX10.CHP.gz
| | Sample_series_id | GSE42924
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053465 | GPL570 |
|
Ad-TatSF2 10 h p.i.
|
iDC expressing TatSF2, collected 10 h p.i.
|
cell type: Immature dendritic cells differentiated from monocytes
infection: Ad-TatSF2
time (hpi): 10 hr
|
Gene expression data from iDC 10 h p.i.
|
| Sample_geo_accession | GSM1053465
| | 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 | 10e6 DC cells were infected with 5 plaque-forming units per cell of both Ad-tTA and the Ad-Tat constructs or Ad-LacZ as a control.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation. Monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA) according to the manufacturer’s instructions. The monocytes were differentiated into immature dendritic cells by culturing them with human recombinant GM-CSF and IL-4 (R&D Systems, Minneapolis, MN) for six days (Bender et al. 1996).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected 0 h, 5 h, 10 h and 20 h post infection. 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_Plus_2 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 | Values in the raw data below 100, were floored to 100. Expression levels were compared to RNA from uninfected cells and cells infected with Ad-LacZ as a control. Gene up-regulation was examined only for transcripts from Ad-Tat infected cells that were present according to the detection call and down-regulation only for genes that were present in the uninfected and Ad-tTA-infected controls.
| | 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/GSM1053465/suppl/GSM1053465_Kukkonen_SF10-A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053465/suppl/GSM1053465_Kukkonen_SF10-A.CHP.gz
| | Sample_series_id | GSE42924
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053466 | GPL570 |
|
Ad TatSF2A58T 10 h p.i.
|
iDC expressing TatSF2A58T, collected 10 h p.i.
|
cell type: Immature dendritic cells differentiated from monocytes
infection: Ad TatSF2A58T
time (hpi): 10 hr
|
Gene expression data from iDC 10 h p.i.
|
| Sample_geo_accession | GSM1053466
| | 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 | 10e6 DC cells were infected with 5 plaque-forming units per cell of both Ad-tTA and the Ad-Tat constructs or Ad-LacZ as a control.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation. Monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA) according to the manufacturer’s instructions. The monocytes were differentiated into immature dendritic cells by culturing them with human recombinant GM-CSF and IL-4 (R&D Systems, Minneapolis, MN) for six days (Bender et al. 1996).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected 0 h, 5 h, 10 h and 20 h post infection. 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_Plus_2 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 | Values in the raw data below 100, were floored to 100. Expression levels were compared to RNA from uninfected cells and cells infected with Ad-LacZ as a control. Gene up-regulation was examined only for transcripts from Ad-Tat infected cells that were present according to the detection call and down-regulation only for genes that were present in the uninfected and Ad-tTA-infected controls.
| | 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/GSM1053466/suppl/GSM1053466_Kukkonen_AT10.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053466/suppl/GSM1053466_Kukkonen_AT10.CHP.gz
| | Sample_series_id | GSE42924
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053467 | GPL570 |
|
Ad-TatSF2C25,30,34S 10 h p.i.
|
iDC expressing TatSF2C25,30,34S, collected 10 h p.i.
|
cell type: Immature dendritic cells differentiated from monocytes
infection: Ad-TatSF2C25,30,34S
time (hpi): 10 hr
|
Gene expression data from iDC 10 h p.i.
|
| Sample_geo_accession | GSM1053467
| | 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 | 10e6 DC cells were infected with 5 plaque-forming units per cell of both Ad-tTA and the Ad-Tat constructs or Ad-LacZ as a control.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation. Monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA) according to the manufacturer’s instructions. The monocytes were differentiated into immature dendritic cells by culturing them with human recombinant GM-CSF and IL-4 (R&D Systems, Minneapolis, MN) for six days (Bender et al. 1996).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected 0 h, 5 h, 10 h and 20 h post infection. 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_Plus_2 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 | Values in the raw data below 100, were floored to 100. Expression levels were compared to RNA from uninfected cells and cells infected with Ad-LacZ as a control. Gene up-regulation was examined only for transcripts from Ad-Tat infected cells that were present according to the detection call and down-regulation only for genes that were present in the uninfected and Ad-tTA-infected controls.
| | 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/GSM1053467/suppl/GSM1053467_Kukkonen_CS10.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053467/suppl/GSM1053467_Kukkonen_CS10.CHP.gz
| | Sample_series_id | GSE42924
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053468 | GPL570 |
|
Ad-LacZ 10 h p.i.
|
iDC expressing LacZ, collected 10 h p.i.
|
cell type: Immature dendritic cells differentiated from monocytes
infection: Ad-LacZ
time (hpi): 10 hr
|
Gene expression data from iDC 10 h p.i.
|
| Sample_geo_accession | GSM1053468
| | 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 | 10e6 DC cells were infected with 5 plaque-forming units per cell of both Ad-tTA and the Ad-Tat constructs or Ad-LacZ as a control.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation. Monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA) according to the manufacturer’s instructions. The monocytes were differentiated into immature dendritic cells by culturing them with human recombinant GM-CSF and IL-4 (R&D Systems, Minneapolis, MN) for six days (Bender et al. 1996).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected 0 h, 5 h, 10 h and 20 h post infection. 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_Plus_2 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 | Values in the raw data below 100, were floored to 100. Expression levels were compared to RNA from uninfected cells and cells infected with Ad-LacZ as a control. Gene up-regulation was examined only for transcripts from Ad-Tat infected cells that were present according to the detection call and down-regulation only for genes that were present in the uninfected and Ad-tTA-infected controls.
| | 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/GSM1053468/suppl/GSM1053468_Kukkonen_LZ10.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053468/suppl/GSM1053468_Kukkonen_LZ10.CHP.gz
| | Sample_series_id | GSE42924
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053469 | GPL570 |
|
Ad-TatHXB2 20 h p.i.
|
iDC expressing TatHXB2, collected 20 h p.i.
|
cell type: Immature dendritic cells differentiated from monocytes
infection: Ad-TatHXB2
time (hpi): 20 hr
|
Gene expression data from iDC 20 h p.i.
|
| Sample_geo_accession | GSM1053469
| | 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 | 10e6 DC cells were infected with 5 plaque-forming units per cell of both Ad-tTA and the Ad-Tat constructs or Ad-LacZ as a control.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation. Monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA) according to the manufacturer’s instructions. The monocytes were differentiated into immature dendritic cells by culturing them with human recombinant GM-CSF and IL-4 (R&D Systems, Minneapolis, MN) for six days (Bender et al. 1996).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected 0 h, 5 h, 10 h and 20 h post infection. 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_Plus_2 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 | Values in the raw data below 100, were floored to 100. Expression levels were compared to RNA from uninfected cells and cells infected with Ad-LacZ as a control. Gene up-regulation was examined only for transcripts from Ad-Tat infected cells that were present according to the detection call and down-regulation only for genes that were present in the uninfected and Ad-tTA-infected controls.
| | 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/GSM1053469/suppl/GSM1053469_Kukkonen_HX20.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053469/suppl/GSM1053469_Kukkonen_HX20.CHP.gz
| | Sample_series_id | GSE42924
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053470 | GPL570 |
|
Ad-TatSF2 20 h p.i.
|
iDC expressing TatSF2, collected 20 h p.i.
|
cell type: Immature dendritic cells differentiated from monocytes
infection: Ad-TatSF2
time (hpi): 20 hr
|
Gene expression data from iDC 20 h p.i.
|
| Sample_geo_accession | GSM1053470
| | 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 | 10e6 DC cells were infected with 5 plaque-forming units per cell of both Ad-tTA and the Ad-Tat constructs or Ad-LacZ as a control.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation. Monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA) according to the manufacturer’s instructions. The monocytes were differentiated into immature dendritic cells by culturing them with human recombinant GM-CSF and IL-4 (R&D Systems, Minneapolis, MN) for six days (Bender et al. 1996).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected 0 h, 5 h, 10 h and 20 h post infection. 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_Plus_2 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 | Values in the raw data below 100, were floored to 100. Expression levels were compared to RNA from uninfected cells and cells infected with Ad-LacZ as a control. Gene up-regulation was examined only for transcripts from Ad-Tat infected cells that were present according to the detection call and down-regulation only for genes that were present in the uninfected and Ad-tTA-infected controls.
| | 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/GSM1053470/suppl/GSM1053470_Kukkonen_SF20.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053470/suppl/GSM1053470_Kukkonen_SF20.CHP.gz
| | Sample_series_id | GSE42924
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053471 | GPL570 |
|
Ad TatSF2A58T 20 h p.i.
|
iDC expressing TatSF2A58T, collected 20 h p.i.
|
cell type: Immature dendritic cells differentiated from monocytes
infection: Ad TatSF2A58T
time (hpi): 20 hr
|
Gene expression data from iDC 20 h p.i.
|
| Sample_geo_accession | GSM1053471
| | 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 | 10e6 DC cells were infected with 5 plaque-forming units per cell of both Ad-tTA and the Ad-Tat constructs or Ad-LacZ as a control.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation. Monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA) according to the manufacturer’s instructions. The monocytes were differentiated into immature dendritic cells by culturing them with human recombinant GM-CSF and IL-4 (R&D Systems, Minneapolis, MN) for six days (Bender et al. 1996).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected 0 h, 5 h, 10 h and 20 h post infection. 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_Plus_2 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 | Values in the raw data below 100, were floored to 100. Expression levels were compared to RNA from uninfected cells and cells infected with Ad-LacZ as a control. Gene up-regulation was examined only for transcripts from Ad-Tat infected cells that were present according to the detection call and down-regulation only for genes that were present in the uninfected and Ad-tTA-infected controls.
| | 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/GSM1053471/suppl/GSM1053471_Kukkonen_AT20.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053471/suppl/GSM1053471_Kukkonen_AT20.CHP.gz
| | Sample_series_id | GSE42924
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053472 | GPL570 |
|
Ad-TatSF2C25,30,34S 20 h p.i.
|
iDC expressing TatSF2C25,30,34S, collected 20 h p.i.
|
cell type: Immature dendritic cells differentiated from monocytes
infection: Ad-TatSF2C25,30,34S
time (hpi): 20 hr
|
Gene expression data from iDC 20 h p.i.
|
| Sample_geo_accession | GSM1053472
| | 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 | 10e6 DC cells were infected with 5 plaque-forming units per cell of both Ad-tTA and the Ad-Tat constructs or Ad-LacZ as a control.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation. Monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA) according to the manufacturer’s instructions. The monocytes were differentiated into immature dendritic cells by culturing them with human recombinant GM-CSF and IL-4 (R&D Systems, Minneapolis, MN) for six days (Bender et al. 1996).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected 0 h, 5 h, 10 h and 20 h post infection. 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_Plus_2 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 | Values in the raw data below 100, were floored to 100. Expression levels were compared to RNA from uninfected cells and cells infected with Ad-LacZ as a control. Gene up-regulation was examined only for transcripts from Ad-Tat infected cells that were present according to the detection call and down-regulation only for genes that were present in the uninfected and Ad-tTA-infected controls.
| | 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/GSM1053472/suppl/GSM1053472_Kukkonen_CS20.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053472/suppl/GSM1053472_Kukkonen_CS20.CHP.gz
| | Sample_series_id | GSE42924
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053473 | GPL570 |
|
Ad-LacZ 20 h p.i.
|
iDC expressing LacZ, collected 20 h p.i.
|
cell type: Immature dendritic cells differentiated from monocytes
infection: Ad-LacZ
time (hpi): 20 hr
|
Gene expression data from iDC 20 h p.i.
|
| Sample_geo_accession | GSM1053473
| | 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 | 10e6 DC cells were infected with 5 plaque-forming units per cell of both Ad-tTA and the Ad-Tat constructs or Ad-LacZ as a control.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation. Monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA) according to the manufacturer’s instructions. The monocytes were differentiated into immature dendritic cells by culturing them with human recombinant GM-CSF and IL-4 (R&D Systems, Minneapolis, MN) for six days (Bender et al. 1996).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected 0 h, 5 h, 10 h and 20 h post infection. 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_Plus_2 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 | Values in the raw data below 100, were floored to 100. Expression levels were compared to RNA from uninfected cells and cells infected with Ad-LacZ as a control. Gene up-regulation was examined only for transcripts from Ad-Tat infected cells that were present according to the detection call and down-regulation only for genes that were present in the uninfected and Ad-tTA-infected controls.
| | 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/GSM1053473/suppl/GSM1053473_Kukkonen_LZ20.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053473/suppl/GSM1053473_Kukkonen_LZ20.CHP.gz
| | Sample_series_id | GSE42924
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053474 | GPL570 |
|
0 control
|
Uninfected iDC
|
cell type: Immature dendritic cells differentiated from monocytes
infection: Uninfected
time (hpi): control
|
Gene expression data from uninfected iDC.
|
| Sample_geo_accession | GSM1053474
| | 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 | 10e6 DC cells were infected with 5 plaque-forming units per cell of both Ad-tTA and the Ad-Tat constructs or Ad-LacZ as a control.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation. Monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA) according to the manufacturer’s instructions. The monocytes were differentiated into immature dendritic cells by culturing them with human recombinant GM-CSF and IL-4 (R&D Systems, Minneapolis, MN) for six days (Bender et al. 1996).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected 0 h, 5 h, 10 h and 20 h post infection. 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_Plus_2 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 | Values in the raw data below 100, were floored to 100. Expression levels were compared to RNA from uninfected cells and cells infected with Ad-LacZ as a control. Gene up-regulation was examined only for transcripts from Ad-Tat infected cells that were present according to the detection call and down-regulation only for genes that were present in the uninfected and Ad-tTA-infected controls.
| | 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/GSM1053474/suppl/GSM1053474_Kukkonen_1002.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053474/suppl/GSM1053474_Kukkonen_1002.CHP.gz
| | Sample_series_id | GSE42924
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053475 | GPL570 |
|
Ad-TatSF2
|
iDC expressing TatSF2
|
cell type: Immature dendritic cells differentiated from monocytes
infection: Ad-TatSF2
time (hpi): 10 hr
|
Gene expression data from iDC 10 h p.i.
|
| Sample_geo_accession | GSM1053475
| | 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 | 10e6 DC cells were infected with 5 plaque-forming units per cell of both Ad-tTA and the Ad-Tat constructs or Ad-LacZ as a control.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation. Monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA) according to the manufacturer’s instructions. The monocytes were differentiated into immature dendritic cells by culturing them with human recombinant GM-CSF and IL-4 (R&D Systems, Minneapolis, MN) for six days (Bender et al. 1996).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected 0 h, 5 h, 10 h and 20 h post infection. 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_Plus_2 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 | Values in the raw data below 100, were floored to 100. Expression levels were compared to RNA from uninfected cells and cells infected with Ad-LacZ as a control. Gene up-regulation was examined only for transcripts from Ad-Tat infected cells that were present according to the detection call and down-regulation only for genes that were present in the uninfected and Ad-tTA-infected controls.
| | 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/GSM1053475/suppl/GSM1053475_Kukkonen_10SF.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053475/suppl/GSM1053475_Kukkonen_10SF.CHP.gz
| | Sample_series_id | GSE42924
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053476 | GPL570 |
|
Ad-LacZ
|
iDC expressing LacZ
|
cell type: Immature dendritic cells differentiated from monocytes
infection: Ad-LacZ
time (hpi): 10 hr
|
Gene expression data from iDC 10 h p.i.
|
| Sample_geo_accession | GSM1053476
| | 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 | 10e6 DC cells were infected with 5 plaque-forming units per cell of both Ad-tTA and the Ad-Tat constructs or Ad-LacZ as a control.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation. Monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA) according to the manufacturer’s instructions. The monocytes were differentiated into immature dendritic cells by culturing them with human recombinant GM-CSF and IL-4 (R&D Systems, Minneapolis, MN) for six days (Bender et al. 1996).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected 0 h, 5 h, 10 h and 20 h post infection. 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_Plus_2 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 | Values in the raw data below 100, were floored to 100. Expression levels were compared to RNA from uninfected cells and cells infected with Ad-LacZ as a control. Gene up-regulation was examined only for transcripts from Ad-Tat infected cells that were present according to the detection call and down-regulation only for genes that were present in the uninfected and Ad-tTA-infected controls.
| | 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/GSM1053476/suppl/GSM1053476_Kukkonen_10LZ.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053476/suppl/GSM1053476_Kukkonen_10LZ.CHP.gz
| | Sample_series_id | GSE42924
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053477 | GPL570 |
|
Ad-TatSF258
|
iDC expressing TatSF258
|
cell type: Immature dendritic cells differentiated from monocytes
infection: Ad-TatSF258
time (hpi): 10 hr
|
Gene expression data from iDC 10 h p.i.
|
| Sample_geo_accession | GSM1053477
| | 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 | 10e6 DC cells were infected with 5 plaque-forming units per cell of both Ad-tTA and the Ad-Tat constructs or Ad-LacZ as a control.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation. Monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA) according to the manufacturer’s instructions. The monocytes were differentiated into immature dendritic cells by culturing them with human recombinant GM-CSF and IL-4 (R&D Systems, Minneapolis, MN) for six days (Bender et al. 1996).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected 0 h, 5 h, 10 h and 20 h post infection. 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_Plus_2 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 | Values in the raw data below 100, were floored to 100. Expression levels were compared to RNA from uninfected cells and cells infected with Ad-LacZ as a control. Gene up-regulation was examined only for transcripts from Ad-Tat infected cells that were present according to the detection call and down-regulation only for genes that were present in the uninfected and Ad-tTA-infected controls.
| | 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/GSM1053477/suppl/GSM1053477_Kukkonen_1058.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053477/suppl/GSM1053477_Kukkonen_1058.CHP.gz
| | Sample_series_id | GSE42924
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053478 | GPL570 |
|
Ad-TatSF272
|
iDC expressing TatSF272
|
cell type: Immature dendritic cells differentiated from monocytes
infection: Ad-TatSF272
time (hpi): 10 hr
|
Gene expression data from iDC 10 h p.i.
|
| Sample_geo_accession | GSM1053478
| | 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 | 10e6 DC cells were infected with 5 plaque-forming units per cell of both Ad-tTA and the Ad-Tat constructs or Ad-LacZ as a control.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation. Monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA) according to the manufacturer’s instructions. The monocytes were differentiated into immature dendritic cells by culturing them with human recombinant GM-CSF and IL-4 (R&D Systems, Minneapolis, MN) for six days (Bender et al. 1996).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected 0 h, 5 h, 10 h and 20 h post infection. 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_Plus_2 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 | Values in the raw data below 100, were floored to 100. Expression levels were compared to RNA from uninfected cells and cells infected with Ad-LacZ as a control. Gene up-regulation was examined only for transcripts from Ad-Tat infected cells that were present according to the detection call and down-regulation only for genes that were present in the uninfected and Ad-tTA-infected controls.
| | 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/GSM1053478/suppl/GSM1053478_Kukkonen_1072.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053478/suppl/GSM1053478_Kukkonen_1072.CHP.gz
| | Sample_series_id | GSE42924
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053479 | GPL570 |
|
Ad-TatSF2E86-E92A
|
iDC expressing TatSF2E86-E92A
|
cell type: Immature dendritic cells differentiated from monocytes
infection: Ad-TatSF2E86-E92A
time (hpi): 10 hr
|
Gene expression data from iDC 10 h p.i.
|
| Sample_geo_accession | GSM1053479
| | 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 | 10e6 DC cells were infected with 5 plaque-forming units per cell of both Ad-tTA and the Ad-Tat constructs or Ad-LacZ as a control.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation. Monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA) according to the manufacturer’s instructions. The monocytes were differentiated into immature dendritic cells by culturing them with human recombinant GM-CSF and IL-4 (R&D Systems, Minneapolis, MN) for six days (Bender et al. 1996).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected 0 h, 5 h, 10 h and 20 h post infection. 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_Plus_2 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 | Values in the raw data below 100, were floored to 100. Expression levels were compared to RNA from uninfected cells and cells infected with Ad-LacZ as a control. Gene up-regulation was examined only for transcripts from Ad-Tat infected cells that were present according to the detection call and down-regulation only for genes that were present in the uninfected and Ad-tTA-infected controls.
| | 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/GSM1053479/suppl/GSM1053479_Kukkonen_10EA.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053479/suppl/GSM1053479_Kukkonen_10EA.CHP.gz
| | Sample_series_id | GSE42924
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053480 | GPL570 |
|
Ad-TatSF2K28,50A
|
iDC expressing TatSF2K28,50A
|
cell type: Immature dendritic cells differentiated from monocytes
infection: Ad-TatSF2K28,50A
time (hpi): 10 hr
|
Gene expression data from iDC 10 h p.i.
|
| Sample_geo_accession | GSM1053480
| | 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 | 10e6 DC cells were infected with 5 plaque-forming units per cell of both Ad-tTA and the Ad-Tat constructs or Ad-LacZ as a control.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation. Monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA) according to the manufacturer’s instructions. The monocytes were differentiated into immature dendritic cells by culturing them with human recombinant GM-CSF and IL-4 (R&D Systems, Minneapolis, MN) for six days (Bender et al. 1996).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected 0 h, 5 h, 10 h and 20 h post infection. 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_Plus_2 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 | Values in the raw data below 100, were floored to 100. Expression levels were compared to RNA from uninfected cells and cells infected with Ad-LacZ as a control. Gene up-regulation was examined only for transcripts from Ad-Tat infected cells that were present according to the detection call and down-regulation only for genes that were present in the uninfected and Ad-tTA-infected controls.
| | 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/GSM1053480/suppl/GSM1053480_Kukkonen_1028.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053480/suppl/GSM1053480_Kukkonen_1028.CHP.gz
| | Sample_series_id | GSE42924
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053481 | GPL570 |
|
Ad-TatSF2K51A
|
iDC expressing TatSF2K51A
|
cell type: Immature dendritic cells differentiated from monocytes
infection: Ad-TatSF2K51A
time (hpi): 10 hr
|
Gene expression data from iDC 10 h p.i.
|
| Sample_geo_accession | GSM1053481
| | 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 | 10e6 DC cells were infected with 5 plaque-forming units per cell of both Ad-tTA and the Ad-Tat constructs or Ad-LacZ as a control.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation. Monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA) according to the manufacturer’s instructions. The monocytes were differentiated into immature dendritic cells by culturing them with human recombinant GM-CSF and IL-4 (R&D Systems, Minneapolis, MN) for six days (Bender et al. 1996).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected 0 h, 5 h, 10 h and 20 h post infection. 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_Plus_2 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 | Values in the raw data below 100, were floored to 100. Expression levels were compared to RNA from uninfected cells and cells infected with Ad-LacZ as a control. Gene up-regulation was examined only for transcripts from Ad-Tat infected cells that were present according to the detection call and down-regulation only for genes that were present in the uninfected and Ad-tTA-infected controls.
| | 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/GSM1053481/suppl/GSM1053481_Kukkonen_1051.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053481/suppl/GSM1053481_Kukkonen_1051.CHP.gz
| | Sample_series_id | GSE42924
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053482 | GPL570 |
|
10^2 U/ml IFN-alpha
|
10^2 U/ml IFN-alpha
|
cell type: Immature dendritic cells differentiated from monocytes
treatment: 10^2 U/ml IFN-alpha
time (post-treatment): 10 hr
|
Gene expression data from iDC 10 h after treatment.
|
| Sample_geo_accession | GSM1053482
| | 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 | 10e6 DC cells were infected with 5 plaque-forming units per cell of both Ad-tTA and the Ad-Tat constructs or Ad-LacZ as a control.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation. Monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA) according to the manufacturer’s instructions. The monocytes were differentiated into immature dendritic cells by culturing them with human recombinant GM-CSF and IL-4 (R&D Systems, Minneapolis, MN) for six days (Bender et al. 1996).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected 0 h, 5 h, 10 h and 20 h post infection. 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_Plus_2 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 | Values in the raw data below 100, were floored to 100. Expression levels were compared to RNA from uninfected cells and cells infected with Ad-LacZ as a control. Gene up-regulation was examined only for transcripts from Ad-Tat infected cells that were present according to the detection call and down-regulation only for genes that were present in the uninfected and Ad-tTA-infected controls.
| | 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/GSM1053482/suppl/GSM1053482_Kukkonen_10A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053482/suppl/GSM1053482_Kukkonen_10A.CHP.gz
| | Sample_series_id | GSE42924
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053483 | GPL570 |
|
10^2 U/ml IFN-beta
|
10^2 U/ml IFN-beta
|
cell type: Immature dendritic cells differentiated from monocytes
treatment: 10^2 U/ml IFN-beta
time (post-treatment): 10 hr
|
Gene expression data from iDC 10 h after treatment.
|
| Sample_geo_accession | GSM1053483
| | 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 | 10e6 DC cells were infected with 5 plaque-forming units per cell of both Ad-tTA and the Ad-Tat constructs or Ad-LacZ as a control.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation. Monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA) according to the manufacturer’s instructions. The monocytes were differentiated into immature dendritic cells by culturing them with human recombinant GM-CSF and IL-4 (R&D Systems, Minneapolis, MN) for six days (Bender et al. 1996).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected 0 h, 5 h, 10 h and 20 h post infection. 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_Plus_2 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 | Values in the raw data below 100, were floored to 100. Expression levels were compared to RNA from uninfected cells and cells infected with Ad-LacZ as a control. Gene up-regulation was examined only for transcripts from Ad-Tat infected cells that were present according to the detection call and down-regulation only for genes that were present in the uninfected and Ad-tTA-infected controls.
| | 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/GSM1053483/suppl/GSM1053483_Kukkonen_10B.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053483/suppl/GSM1053483_Kukkonen_10B.CHP.gz
| | Sample_series_id | GSE42924
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
GSM1053484 | GPL570 |
|
10^2 U/ml IFN-gamma
|
10^2 U/ml IFN-gamma
|
cell type: Immature dendritic cells differentiated from monocytes
treatment: 10^2 U/ml IFN-gamma
time (post-treatment): 10 hr
|
Gene expression data from iDC 10 h after treatment.
|
| Sample_geo_accession | GSM1053484
| | 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 | 10e6 DC cells were infected with 5 plaque-forming units per cell of both Ad-tTA and the Ad-Tat constructs or Ad-LacZ as a control.
| | Sample_growth_protocol_ch1 | Peripheral blood mononuclear cells were isolated from blood by Ficoll-gradient centrifugation. Monocytes were isolated by negative selection with Monocyte Isolation Kit II (Miltenyi Biotec, Auburn, CA) according to the manufacturer’s instructions. The monocytes were differentiated into immature dendritic cells by culturing them with human recombinant GM-CSF and IL-4 (R&D Systems, Minneapolis, MN) for six days (Bender et al. 1996).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were collected 0 h, 5 h, 10 h and 20 h post infection. 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_Plus_2 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 | Values in the raw data below 100, were floored to 100. Expression levels were compared to RNA from uninfected cells and cells infected with Ad-LacZ as a control. Gene up-regulation was examined only for transcripts from Ad-Tat infected cells that were present according to the detection call and down-regulation only for genes that were present in the uninfected and Ad-tTA-infected controls.
| | 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/GSM1053484/suppl/GSM1053484_Kukkonen_10G.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053484/suppl/GSM1053484_Kukkonen_10G.CHP.gz
| | Sample_series_id | GSE42924
| | Sample_series_id | GSE42926
| | Sample_data_row_count | 54675
| | |
|
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