Search results for the GEO ID: GSE24132  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM594162 | GPL570 |
|
Adult donor 34 DCs mock infected
|
Adult dendritic cells, mock infected
|
age: adult
tissue: blood
cell types: isolated conventional and plasmacytoid dendritic cells
infection: mock infected
|
|
| Sample_geo_accession | GSM594162
| | Sample_status | Public on Nov 01 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells from each donor were divided in half, and were either infected at an MOI of 3.0 with RSV wild-type strain A2 grown in HEp-2 cells or mock infected with a supernatant from a parallel uninfected HEp-2 cell-culture monolayer.
| | Sample_growth_protocol_ch1 | Human peripheral blood was collected with the approval of the Vanderbilt University Institutional Review Board. Sixty mL of peripheral blood was collected from healthy adult donors or 10 – 25 mL blood was collected from umbilical cords. PBMCs and cord blood mononuclear cells (CBMCs) were isolated using Ficoll (Sigma Histopaque 1077). Mixed cultures of primary plasmacytoid and conventional DCs were enriched using Miltenyi blood dendritic cell isolation kit II (cat. 130-091-379) and a VarioMACS magnet, as directed by the manufacturer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mock- or RSV-infected DCs were pelleted 24 hours post-infection, washed once with PBS, and then RNA was extracted organically with Trizol and chloroform and further purified with RNeasy (Qiagen), as directed by the manufacturer. RNA was DNase treated (Qiagen), as directed by the manufacturer. RNA concentration was measured with a Nanodrop spectrophotometer and was sent to Vanderbilt Microarray Shared Resources (VMSR) core facility. RNA integrity was analyzed by the VMSR core on an Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs with RNA integrity numbers equal to or greater than 7.0 were used for further analysis, amplified with Nugen amplification kit as directed by the manufacturer, and hybridized to Affymetrix human U1.33 plus 2.0 3¢ UTR transcriptional profile array.
| | Sample_hyb_protocol | 15 μg of biotin-labeled aRNA was fragmented and hybridized on to the Affymetrix Human Genome U133 plus 2.0 GeneChip. After hybridization, the GeneChip was washed, stained with strepavidin/phycoerythrin conjugate and biotinylated antibody.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G with AutoLoader.
| | Sample_data_processing | Data from all 12 arrays were batch normalized with the RMA quantile algorithm using Expression Console software (Affymetrix)
| | Sample_platform_id | GPL570
| | Sample_contact_name | James,,Crowe
| | Sample_contact_email | james.crowe@vanderbilt.edu, natalie.thornburg@vanderbilt.edu, frances.house@vanderbilt.edu
| | Sample_contact_phone | 615-343-8064
| | Sample_contact_fax | 615-343-4456
| | Sample_contact_laboratory | Crowe laboratory
| | Sample_contact_department | Vanderbilt Vaccine Center
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | T2219 21st Avenue South,
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232-2905
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594162/suppl/GSM594162.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594162/suppl/GSM594162.chp.gz
| | Sample_series_id | GSE24132
| | Sample_data_row_count | 54675
| | |
|
GSM594163 | GPL570 |
|
Adult donor 34 DCs RSV infected
|
Adult dendritic cells, respiratory syncytial virus infected
|
age: adult
tissue: blood
cell types: isolated conventional and plasmacytoid dendritic cells
infection: respiratory syncytial virus infected
|
|
| Sample_geo_accession | GSM594163
| | Sample_status | Public on Nov 01 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells from each donor were divided in half, and were either infected at an MOI of 3.0 with RSV wild-type strain A2 grown in HEp-2 cells or mock infected with a supernatant from a parallel uninfected HEp-2 cell-culture monolayer.
| | Sample_growth_protocol_ch1 | Human peripheral blood was collected with the approval of the Vanderbilt University Institutional Review Board. Sixty mL of peripheral blood was collected from healthy adult donors or 10 – 25 mL blood was collected from umbilical cords. PBMCs and cord blood mononuclear cells (CBMCs) were isolated using Ficoll (Sigma Histopaque 1077). Mixed cultures of primary plasmacytoid and conventional DCs were enriched using Miltenyi blood dendritic cell isolation kit II (cat. 130-091-379) and a VarioMACS magnet, as directed by the manufacturer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mock- or RSV-infected DCs were pelleted 24 hours post-infection, washed once with PBS, and then RNA was extracted organically with Trizol and chloroform and further purified with RNeasy (Qiagen), as directed by the manufacturer. RNA was DNase treated (Qiagen), as directed by the manufacturer. RNA concentration was measured with a Nanodrop spectrophotometer and was sent to Vanderbilt Microarray Shared Resources (VMSR) core facility. RNA integrity was analyzed by the VMSR core on an Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs with RNA integrity numbers equal to or greater than 7.0 were used for further analysis, amplified with Nugen amplification kit as directed by the manufacturer, and hybridized to Affymetrix human U1.33 plus 2.0 3¢ UTR transcriptional profile array.
| | Sample_hyb_protocol | 15 μg of biotin-labeled aRNA was fragmented and hybridized on to the Affymetrix Human Genome U133 plus 2.0 GeneChip. After hybridization, the GeneChip was washed, stained with strepavidin/phycoerythrin conjugate and biotinylated antibody.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G with AutoLoader.
| | Sample_data_processing | Data from all 12 arrays were batch normalized with the RMA quantile algorithm using Expression Console software (Affymetrix)
| | Sample_platform_id | GPL570
| | Sample_contact_name | James,,Crowe
| | Sample_contact_email | james.crowe@vanderbilt.edu, natalie.thornburg@vanderbilt.edu, frances.house@vanderbilt.edu
| | Sample_contact_phone | 615-343-8064
| | Sample_contact_fax | 615-343-4456
| | Sample_contact_laboratory | Crowe laboratory
| | Sample_contact_department | Vanderbilt Vaccine Center
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | T2219 21st Avenue South,
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232-2905
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594163/suppl/GSM594163.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594163/suppl/GSM594163.chp.gz
| | Sample_series_id | GSE24132
| | Sample_data_row_count | 54675
| | |
|
GSM594164 | GPL570 |
|
Adult donor 90 DCs mock infected
|
Adult dendritic cells, mock infected
|
age: adult
tissue: blood
cell types: isolated conventional and plasmacytoid dendritic cells
infection: mock infected
|
|
| Sample_geo_accession | GSM594164
| | Sample_status | Public on Nov 01 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells from each donor were divided in half, and were either infected at an MOI of 3.0 with RSV wild-type strain A2 grown in HEp-2 cells or mock infected with a supernatant from a parallel uninfected HEp-2 cell-culture monolayer.
| | Sample_growth_protocol_ch1 | Human peripheral blood was collected with the approval of the Vanderbilt University Institutional Review Board. Sixty mL of peripheral blood was collected from healthy adult donors or 10 – 25 mL blood was collected from umbilical cords. PBMCs and cord blood mononuclear cells (CBMCs) were isolated using Ficoll (Sigma Histopaque 1077). Mixed cultures of primary plasmacytoid and conventional DCs were enriched using Miltenyi blood dendritic cell isolation kit II (cat. 130-091-379) and a VarioMACS magnet, as directed by the manufacturer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mock- or RSV-infected DCs were pelleted 24 hours post-infection, washed once with PBS, and then RNA was extracted organically with Trizol and chloroform and further purified with RNeasy (Qiagen), as directed by the manufacturer. RNA was DNase treated (Qiagen), as directed by the manufacturer. RNA concentration was measured with a Nanodrop spectrophotometer and was sent to Vanderbilt Microarray Shared Resources (VMSR) core facility. RNA integrity was analyzed by the VMSR core on an Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs with RNA integrity numbers equal to or greater than 7.0 were used for further analysis, amplified with Nugen amplification kit as directed by the manufacturer, and hybridized to Affymetrix human U1.33 plus 2.0 3¢ UTR transcriptional profile array.
| | Sample_hyb_protocol | 15 μg of biotin-labeled aRNA was fragmented and hybridized on to the Affymetrix Human Genome U133 plus 2.0 GeneChip. After hybridization, the GeneChip was washed, stained with strepavidin/phycoerythrin conjugate and biotinylated antibody.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G with AutoLoader.
| | Sample_data_processing | Data from all 12 arrays were batch normalized with the RMA quantile algorithm using Expression Console software (Affymetrix)
| | Sample_platform_id | GPL570
| | Sample_contact_name | James,,Crowe
| | Sample_contact_email | james.crowe@vanderbilt.edu, natalie.thornburg@vanderbilt.edu, frances.house@vanderbilt.edu
| | Sample_contact_phone | 615-343-8064
| | Sample_contact_fax | 615-343-4456
| | Sample_contact_laboratory | Crowe laboratory
| | Sample_contact_department | Vanderbilt Vaccine Center
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | T2219 21st Avenue South,
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232-2905
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594164/suppl/GSM594164.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594164/suppl/GSM594164.chp.gz
| | Sample_series_id | GSE24132
| | Sample_data_row_count | 54675
| | |
|
GSM594165 | GPL570 |
|
Adult donor 90 DCs RSV infected
|
Adult dendritic cells, respiratory syncytial virus infected
|
age: adult
tissue: blood
cell types: isolated conventional and plasmacytoid dendritic cells
infection: respiratory syncytial virus infected
|
|
| Sample_geo_accession | GSM594165
| | Sample_status | Public on Nov 01 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells from each donor were divided in half, and were either infected at an MOI of 3.0 with RSV wild-type strain A2 grown in HEp-2 cells or mock infected with a supernatant from a parallel uninfected HEp-2 cell-culture monolayer.
| | Sample_growth_protocol_ch1 | Human peripheral blood was collected with the approval of the Vanderbilt University Institutional Review Board. Sixty mL of peripheral blood was collected from healthy adult donors or 10 – 25 mL blood was collected from umbilical cords. PBMCs and cord blood mononuclear cells (CBMCs) were isolated using Ficoll (Sigma Histopaque 1077). Mixed cultures of primary plasmacytoid and conventional DCs were enriched using Miltenyi blood dendritic cell isolation kit II (cat. 130-091-379) and a VarioMACS magnet, as directed by the manufacturer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mock- or RSV-infected DCs were pelleted 24 hours post-infection, washed once with PBS, and then RNA was extracted organically with Trizol and chloroform and further purified with RNeasy (Qiagen), as directed by the manufacturer. RNA was DNase treated (Qiagen), as directed by the manufacturer. RNA concentration was measured with a Nanodrop spectrophotometer and was sent to Vanderbilt Microarray Shared Resources (VMSR) core facility. RNA integrity was analyzed by the VMSR core on an Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs with RNA integrity numbers equal to or greater than 7.0 were used for further analysis, amplified with Nugen amplification kit as directed by the manufacturer, and hybridized to Affymetrix human U1.33 plus 2.0 3¢ UTR transcriptional profile array.
| | Sample_hyb_protocol | 15 μg of biotin-labeled aRNA was fragmented and hybridized on to the Affymetrix Human Genome U133 plus 2.0 GeneChip. After hybridization, the GeneChip was washed, stained with strepavidin/phycoerythrin conjugate and biotinylated antibody.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G with AutoLoader.
| | Sample_data_processing | Data from all 12 arrays were batch normalized with the RMA quantile algorithm using Expression Console software (Affymetrix)
| | Sample_platform_id | GPL570
| | Sample_contact_name | James,,Crowe
| | Sample_contact_email | james.crowe@vanderbilt.edu, natalie.thornburg@vanderbilt.edu, frances.house@vanderbilt.edu
| | Sample_contact_phone | 615-343-8064
| | Sample_contact_fax | 615-343-4456
| | Sample_contact_laboratory | Crowe laboratory
| | Sample_contact_department | Vanderbilt Vaccine Center
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | T2219 21st Avenue South,
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232-2905
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594165/suppl/GSM594165.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594165/suppl/GSM594165.chp.gz
| | Sample_series_id | GSE24132
| | Sample_data_row_count | 54675
| | |
|
GSM594166 | GPL570 |
|
Adult donor 88 DCs mock infected
|
Adult dendritic cells, mock infected
|
age: adult
tissue: blood
cell types: isolated conventional and plasmacytoid dendritic cells
infection: mock infected
|
|
| Sample_geo_accession | GSM594166
| | Sample_status | Public on Nov 01 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells from each donor were divided in half, and were either infected at an MOI of 3.0 with RSV wild-type strain A2 grown in HEp-2 cells or mock infected with a supernatant from a parallel uninfected HEp-2 cell-culture monolayer.
| | Sample_growth_protocol_ch1 | Human peripheral blood was collected with the approval of the Vanderbilt University Institutional Review Board. Sixty mL of peripheral blood was collected from healthy adult donors or 10 – 25 mL blood was collected from umbilical cords. PBMCs and cord blood mononuclear cells (CBMCs) were isolated using Ficoll (Sigma Histopaque 1077). Mixed cultures of primary plasmacytoid and conventional DCs were enriched using Miltenyi blood dendritic cell isolation kit II (cat. 130-091-379) and a VarioMACS magnet, as directed by the manufacturer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mock- or RSV-infected DCs were pelleted 24 hours post-infection, washed once with PBS, and then RNA was extracted organically with Trizol and chloroform and further purified with RNeasy (Qiagen), as directed by the manufacturer. RNA was DNase treated (Qiagen), as directed by the manufacturer. RNA concentration was measured with a Nanodrop spectrophotometer and was sent to Vanderbilt Microarray Shared Resources (VMSR) core facility. RNA integrity was analyzed by the VMSR core on an Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs with RNA integrity numbers equal to or greater than 7.0 were used for further analysis, amplified with Nugen amplification kit as directed by the manufacturer, and hybridized to Affymetrix human U1.33 plus 2.0 3¢ UTR transcriptional profile array.
| | Sample_hyb_protocol | 15 μg of biotin-labeled aRNA was fragmented and hybridized on to the Affymetrix Human Genome U133 plus 2.0 GeneChip. After hybridization, the GeneChip was washed, stained with strepavidin/phycoerythrin conjugate and biotinylated antibody.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G with AutoLoader.
| | Sample_data_processing | Data from all 12 arrays were batch normalized with the RMA quantile algorithm using Expression Console software (Affymetrix)
| | Sample_platform_id | GPL570
| | Sample_contact_name | James,,Crowe
| | Sample_contact_email | james.crowe@vanderbilt.edu, natalie.thornburg@vanderbilt.edu, frances.house@vanderbilt.edu
| | Sample_contact_phone | 615-343-8064
| | Sample_contact_fax | 615-343-4456
| | Sample_contact_laboratory | Crowe laboratory
| | Sample_contact_department | Vanderbilt Vaccine Center
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | T2219 21st Avenue South,
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232-2905
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594166/suppl/GSM594166.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594166/suppl/GSM594166.chp.gz
| | Sample_series_id | GSE24132
| | Sample_data_row_count | 54675
| | |
|
GSM594167 | GPL570 |
|
Adult donor 88 DCs RSV infected
|
Adult dendritic cells, respiratory syncytial virus infected
|
age: adult
tissue: blood
cell types: isolated conventional and plasmacytoid dendritic cells
infection: respiratory syncytial virus infected
|
|
| Sample_geo_accession | GSM594167
| | Sample_status | Public on Nov 01 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells from each donor were divided in half, and were either infected at an MOI of 3.0 with RSV wild-type strain A2 grown in HEp-2 cells or mock infected with a supernatant from a parallel uninfected HEp-2 cell-culture monolayer.
| | Sample_growth_protocol_ch1 | Human peripheral blood was collected with the approval of the Vanderbilt University Institutional Review Board. Sixty mL of peripheral blood was collected from healthy adult donors or 10 – 25 mL blood was collected from umbilical cords. PBMCs and cord blood mononuclear cells (CBMCs) were isolated using Ficoll (Sigma Histopaque 1077). Mixed cultures of primary plasmacytoid and conventional DCs were enriched using Miltenyi blood dendritic cell isolation kit II (cat. 130-091-379) and a VarioMACS magnet, as directed by the manufacturer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mock- or RSV-infected DCs were pelleted 24 hours post-infection, washed once with PBS, and then RNA was extracted organically with Trizol and chloroform and further purified with RNeasy (Qiagen), as directed by the manufacturer. RNA was DNase treated (Qiagen), as directed by the manufacturer. RNA concentration was measured with a Nanodrop spectrophotometer and was sent to Vanderbilt Microarray Shared Resources (VMSR) core facility. RNA integrity was analyzed by the VMSR core on an Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs with RNA integrity numbers equal to or greater than 7.0 were used for further analysis, amplified with Nugen amplification kit as directed by the manufacturer, and hybridized to Affymetrix human U1.33 plus 2.0 3¢ UTR transcriptional profile array.
| | Sample_hyb_protocol | 15 μg of biotin-labeled aRNA was fragmented and hybridized on to the Affymetrix Human Genome U133 plus 2.0 GeneChip. After hybridization, the GeneChip was washed, stained with strepavidin/phycoerythrin conjugate and biotinylated antibody.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G with AutoLoader.
| | Sample_data_processing | Data from all 12 arrays were batch normalized with the RMA quantile algorithm using Expression Console software (Affymetrix)
| | Sample_platform_id | GPL570
| | Sample_contact_name | James,,Crowe
| | Sample_contact_email | james.crowe@vanderbilt.edu, natalie.thornburg@vanderbilt.edu, frances.house@vanderbilt.edu
| | Sample_contact_phone | 615-343-8064
| | Sample_contact_fax | 615-343-4456
| | Sample_contact_laboratory | Crowe laboratory
| | Sample_contact_department | Vanderbilt Vaccine Center
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | T2219 21st Avenue South,
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232-2905
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594167/suppl/GSM594167.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594167/suppl/GSM594167.chp.gz
| | Sample_series_id | GSE24132
| | Sample_data_row_count | 54675
| | |
|
GSM594168 | GPL570 |
|
Cord donor 052808 DCs mock infected
|
Umbillical cord blood dendritic cells, mock infected
|
age: neonatal
tissue: blood
cell types: isolated conventional and plasmacytoid dendritic cells
infection: mock infected
|
|
| Sample_geo_accession | GSM594168
| | Sample_status | Public on Nov 01 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells from each donor were divided in half, and were either infected at an MOI of 3.0 with RSV wild-type strain A2 grown in HEp-2 cells or mock infected with a supernatant from a parallel uninfected HEp-2 cell-culture monolayer.
| | Sample_growth_protocol_ch1 | Human peripheral blood was collected with the approval of the Vanderbilt University Institutional Review Board. Sixty mL of peripheral blood was collected from healthy adult donors or 10 – 25 mL blood was collected from umbilical cords. PBMCs and cord blood mononuclear cells (CBMCs) were isolated using Ficoll (Sigma Histopaque 1077). Mixed cultures of primary plasmacytoid and conventional DCs were enriched using Miltenyi blood dendritic cell isolation kit II (cat. 130-091-379) and a VarioMACS magnet, as directed by the manufacturer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mock- or RSV-infected DCs were pelleted 24 hours post-infection, washed once with PBS, and then RNA was extracted organically with Trizol and chloroform and further purified with RNeasy (Qiagen), as directed by the manufacturer. RNA was DNase treated (Qiagen), as directed by the manufacturer. RNA concentration was measured with a Nanodrop spectrophotometer and was sent to Vanderbilt Microarray Shared Resources (VMSR) core facility. RNA integrity was analyzed by the VMSR core on an Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs with RNA integrity numbers equal to or greater than 7.0 were used for further analysis, amplified with Nugen amplification kit as directed by the manufacturer, and hybridized to Affymetrix human U1.33 plus 2.0 3¢ UTR transcriptional profile array.
| | Sample_hyb_protocol | 15 μg of biotin-labeled aRNA was fragmented and hybridized on to the Affymetrix Human Genome U133 plus 2.0 GeneChip. After hybridization, the GeneChip was washed, stained with strepavidin/phycoerythrin conjugate and biotinylated antibody.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G with AutoLoader.
| | Sample_data_processing | Data from all 12 arrays were batch normalized with the RMA quantile algorithm using Expression Console software (Affymetrix)
| | Sample_platform_id | GPL570
| | Sample_contact_name | James,,Crowe
| | Sample_contact_email | james.crowe@vanderbilt.edu, natalie.thornburg@vanderbilt.edu, frances.house@vanderbilt.edu
| | Sample_contact_phone | 615-343-8064
| | Sample_contact_fax | 615-343-4456
| | Sample_contact_laboratory | Crowe laboratory
| | Sample_contact_department | Vanderbilt Vaccine Center
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | T2219 21st Avenue South,
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232-2905
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594168/suppl/GSM594168.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594168/suppl/GSM594168.chp.gz
| | Sample_series_id | GSE24132
| | Sample_data_row_count | 54675
| | |
|
GSM594169 | GPL570 |
|
Cord donor 052808 DCs RSV infected
|
Umbillical cord blood dendritic cells, respiratory syncytial virus infected
|
age: neonatal
tissue: blood
cell types: isolated conventional and plasmacytoid dendritic cells
infection: respiratory syncytial virus infected
|
|
| Sample_geo_accession | GSM594169
| | Sample_status | Public on Nov 01 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells from each donor were divided in half, and were either infected at an MOI of 3.0 with RSV wild-type strain A2 grown in HEp-2 cells or mock infected with a supernatant from a parallel uninfected HEp-2 cell-culture monolayer.
| | Sample_growth_protocol_ch1 | Human peripheral blood was collected with the approval of the Vanderbilt University Institutional Review Board. Sixty mL of peripheral blood was collected from healthy adult donors or 10 – 25 mL blood was collected from umbilical cords. PBMCs and cord blood mononuclear cells (CBMCs) were isolated using Ficoll (Sigma Histopaque 1077). Mixed cultures of primary plasmacytoid and conventional DCs were enriched using Miltenyi blood dendritic cell isolation kit II (cat. 130-091-379) and a VarioMACS magnet, as directed by the manufacturer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mock- or RSV-infected DCs were pelleted 24 hours post-infection, washed once with PBS, and then RNA was extracted organically with Trizol and chloroform and further purified with RNeasy (Qiagen), as directed by the manufacturer. RNA was DNase treated (Qiagen), as directed by the manufacturer. RNA concentration was measured with a Nanodrop spectrophotometer and was sent to Vanderbilt Microarray Shared Resources (VMSR) core facility. RNA integrity was analyzed by the VMSR core on an Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs with RNA integrity numbers equal to or greater than 7.0 were used for further analysis, amplified with Nugen amplification kit as directed by the manufacturer, and hybridized to Affymetrix human U1.33 plus 2.0 3¢ UTR transcriptional profile array.
| | Sample_hyb_protocol | 15 μg of biotin-labeled aRNA was fragmented and hybridized on to the Affymetrix Human Genome U133 plus 2.0 GeneChip. After hybridization, the GeneChip was washed, stained with strepavidin/phycoerythrin conjugate and biotinylated antibody.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G with AutoLoader.
| | Sample_data_processing | Data from all 12 arrays were batch normalized with the RMA quantile algorithm using Expression Console software (Affymetrix)
| | Sample_platform_id | GPL570
| | Sample_contact_name | James,,Crowe
| | Sample_contact_email | james.crowe@vanderbilt.edu, natalie.thornburg@vanderbilt.edu, frances.house@vanderbilt.edu
| | Sample_contact_phone | 615-343-8064
| | Sample_contact_fax | 615-343-4456
| | Sample_contact_laboratory | Crowe laboratory
| | Sample_contact_department | Vanderbilt Vaccine Center
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | T2219 21st Avenue South,
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232-2905
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594169/suppl/GSM594169.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594169/suppl/GSM594169.chp.gz
| | Sample_series_id | GSE24132
| | Sample_data_row_count | 54675
| | |
|
GSM594170 | GPL570 |
|
Cord donor 060408A DCs mock infected
|
Umbillical cord blood dendritic cells, mock infected
|
age: neonatal
tissue: blood
cell types: isolated conventional and plasmacytoid dendritic cells
infection: mock infected
|
|
| Sample_geo_accession | GSM594170
| | Sample_status | Public on Nov 01 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells from each donor were divided in half, and were either infected at an MOI of 3.0 with RSV wild-type strain A2 grown in HEp-2 cells or mock infected with a supernatant from a parallel uninfected HEp-2 cell-culture monolayer.
| | Sample_growth_protocol_ch1 | Human peripheral blood was collected with the approval of the Vanderbilt University Institutional Review Board. Sixty mL of peripheral blood was collected from healthy adult donors or 10 – 25 mL blood was collected from umbilical cords. PBMCs and cord blood mononuclear cells (CBMCs) were isolated using Ficoll (Sigma Histopaque 1077). Mixed cultures of primary plasmacytoid and conventional DCs were enriched using Miltenyi blood dendritic cell isolation kit II (cat. 130-091-379) and a VarioMACS magnet, as directed by the manufacturer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mock- or RSV-infected DCs were pelleted 24 hours post-infection, washed once with PBS, and then RNA was extracted organically with Trizol and chloroform and further purified with RNeasy (Qiagen), as directed by the manufacturer. RNA was DNase treated (Qiagen), as directed by the manufacturer. RNA concentration was measured with a Nanodrop spectrophotometer and was sent to Vanderbilt Microarray Shared Resources (VMSR) core facility. RNA integrity was analyzed by the VMSR core on an Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs with RNA integrity numbers equal to or greater than 7.0 were used for further analysis, amplified with Nugen amplification kit as directed by the manufacturer, and hybridized to Affymetrix human U1.33 plus 2.0 3¢ UTR transcriptional profile array.
| | Sample_hyb_protocol | 15 μg of biotin-labeled aRNA was fragmented and hybridized on to the Affymetrix Human Genome U133 plus 2.0 GeneChip. After hybridization, the GeneChip was washed, stained with strepavidin/phycoerythrin conjugate and biotinylated antibody.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G with AutoLoader.
| | Sample_data_processing | Data from all 12 arrays were batch normalized with the RMA quantile algorithm using Expression Console software (Affymetrix)
| | Sample_platform_id | GPL570
| | Sample_contact_name | James,,Crowe
| | Sample_contact_email | james.crowe@vanderbilt.edu, natalie.thornburg@vanderbilt.edu, frances.house@vanderbilt.edu
| | Sample_contact_phone | 615-343-8064
| | Sample_contact_fax | 615-343-4456
| | Sample_contact_laboratory | Crowe laboratory
| | Sample_contact_department | Vanderbilt Vaccine Center
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | T2219 21st Avenue South,
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232-2905
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594170/suppl/GSM594170.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594170/suppl/GSM594170.chp.gz
| | Sample_series_id | GSE24132
| | Sample_data_row_count | 54675
| | |
|
GSM594171 | GPL570 |
|
Cord donor 060408A DCs RSV infected
|
Umbillical cord blood dendritic cells, respiratory syncytial virus infected
|
age: neonatal
tissue: blood
cell types: isolated conventional and plasmacytoid dendritic cells
infection: respiratory syncytial virus infected
|
|
| Sample_geo_accession | GSM594171
| | Sample_status | Public on Nov 01 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells from each donor were divided in half, and were either infected at an MOI of 3.0 with RSV wild-type strain A2 grown in HEp-2 cells or mock infected with a supernatant from a parallel uninfected HEp-2 cell-culture monolayer.
| | Sample_growth_protocol_ch1 | Human peripheral blood was collected with the approval of the Vanderbilt University Institutional Review Board. Sixty mL of peripheral blood was collected from healthy adult donors or 10 – 25 mL blood was collected from umbilical cords. PBMCs and cord blood mononuclear cells (CBMCs) were isolated using Ficoll (Sigma Histopaque 1077). Mixed cultures of primary plasmacytoid and conventional DCs were enriched using Miltenyi blood dendritic cell isolation kit II (cat. 130-091-379) and a VarioMACS magnet, as directed by the manufacturer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mock- or RSV-infected DCs were pelleted 24 hours post-infection, washed once with PBS, and then RNA was extracted organically with Trizol and chloroform and further purified with RNeasy (Qiagen), as directed by the manufacturer. RNA was DNase treated (Qiagen), as directed by the manufacturer. RNA concentration was measured with a Nanodrop spectrophotometer and was sent to Vanderbilt Microarray Shared Resources (VMSR) core facility. RNA integrity was analyzed by the VMSR core on an Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs with RNA integrity numbers equal to or greater than 7.0 were used for further analysis, amplified with Nugen amplification kit as directed by the manufacturer, and hybridized to Affymetrix human U1.33 plus 2.0 3¢ UTR transcriptional profile array.
| | Sample_hyb_protocol | 15 μg of biotin-labeled aRNA was fragmented and hybridized on to the Affymetrix Human Genome U133 plus 2.0 GeneChip. After hybridization, the GeneChip was washed, stained with strepavidin/phycoerythrin conjugate and biotinylated antibody.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G with AutoLoader.
| | Sample_data_processing | Data from all 12 arrays were batch normalized with the RMA quantile algorithm using Expression Console software (Affymetrix)
| | Sample_platform_id | GPL570
| | Sample_contact_name | James,,Crowe
| | Sample_contact_email | james.crowe@vanderbilt.edu, natalie.thornburg@vanderbilt.edu, frances.house@vanderbilt.edu
| | Sample_contact_phone | 615-343-8064
| | Sample_contact_fax | 615-343-4456
| | Sample_contact_laboratory | Crowe laboratory
| | Sample_contact_department | Vanderbilt Vaccine Center
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | T2219 21st Avenue South,
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232-2905
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594171/suppl/GSM594171.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594171/suppl/GSM594171.chp.gz
| | Sample_series_id | GSE24132
| | Sample_data_row_count | 54675
| | |
|
GSM594172 | GPL570 |
|
Cord donor 060408B DCs mock infected
|
Umbillical cord blood dendritic cells, mock infected
|
age: neonatal
tissue: blood
cell types: isolated conventional and plasmacytoid dendritic cells
infection: mock infected
|
|
| Sample_geo_accession | GSM594172
| | Sample_status | Public on Nov 01 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells from each donor were divided in half, and were either infected at an MOI of 3.0 with RSV wild-type strain A2 grown in HEp-2 cells or mock infected with a supernatant from a parallel uninfected HEp-2 cell-culture monolayer.
| | Sample_growth_protocol_ch1 | Human peripheral blood was collected with the approval of the Vanderbilt University Institutional Review Board. Sixty mL of peripheral blood was collected from healthy adult donors or 10 – 25 mL blood was collected from umbilical cords. PBMCs and cord blood mononuclear cells (CBMCs) were isolated using Ficoll (Sigma Histopaque 1077). Mixed cultures of primary plasmacytoid and conventional DCs were enriched using Miltenyi blood dendritic cell isolation kit II (cat. 130-091-379) and a VarioMACS magnet, as directed by the manufacturer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mock- or RSV-infected DCs were pelleted 24 hours post-infection, washed once with PBS, and then RNA was extracted organically with Trizol and chloroform and further purified with RNeasy (Qiagen), as directed by the manufacturer. RNA was DNase treated (Qiagen), as directed by the manufacturer. RNA concentration was measured with a Nanodrop spectrophotometer and was sent to Vanderbilt Microarray Shared Resources (VMSR) core facility. RNA integrity was analyzed by the VMSR core on an Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs with RNA integrity numbers equal to or greater than 7.0 were used for further analysis, amplified with Nugen amplification kit as directed by the manufacturer, and hybridized to Affymetrix human U1.33 plus 2.0 3¢ UTR transcriptional profile array.
| | Sample_hyb_protocol | 15 μg of biotin-labeled aRNA was fragmented and hybridized on to the Affymetrix Human Genome U133 plus 2.0 GeneChip. After hybridization, the GeneChip was washed, stained with strepavidin/phycoerythrin conjugate and biotinylated antibody.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G with AutoLoader.
| | Sample_data_processing | Data from all 12 arrays were batch normalized with the RMA quantile algorithm using Expression Console software (Affymetrix)
| | Sample_platform_id | GPL570
| | Sample_contact_name | James,,Crowe
| | Sample_contact_email | james.crowe@vanderbilt.edu, natalie.thornburg@vanderbilt.edu, frances.house@vanderbilt.edu
| | Sample_contact_phone | 615-343-8064
| | Sample_contact_fax | 615-343-4456
| | Sample_contact_laboratory | Crowe laboratory
| | Sample_contact_department | Vanderbilt Vaccine Center
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | T2219 21st Avenue South,
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232-2905
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594172/suppl/GSM594172.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594172/suppl/GSM594172.chp.gz
| | Sample_series_id | GSE24132
| | Sample_data_row_count | 54675
| | |
|
GSM594173 | GPL570 |
|
Cord donor 060408B DCs RSV infected
|
Umbillical cord blood dendritic cells, respiratory syncytial virus infected
|
age: neonatal
tissue: blood
cell types: isolated conventional and plasmacytoid dendritic cells
infection: respiratory syncytial virus infected
|
|
| Sample_geo_accession | GSM594173
| | Sample_status | Public on Nov 01 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells from each donor were divided in half, and were either infected at an MOI of 3.0 with RSV wild-type strain A2 grown in HEp-2 cells or mock infected with a supernatant from a parallel uninfected HEp-2 cell-culture monolayer.
| | Sample_growth_protocol_ch1 | Human peripheral blood was collected with the approval of the Vanderbilt University Institutional Review Board. Sixty mL of peripheral blood was collected from healthy adult donors or 10 – 25 mL blood was collected from umbilical cords. PBMCs and cord blood mononuclear cells (CBMCs) were isolated using Ficoll (Sigma Histopaque 1077). Mixed cultures of primary plasmacytoid and conventional DCs were enriched using Miltenyi blood dendritic cell isolation kit II (cat. 130-091-379) and a VarioMACS magnet, as directed by the manufacturer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mock- or RSV-infected DCs were pelleted 24 hours post-infection, washed once with PBS, and then RNA was extracted organically with Trizol and chloroform and further purified with RNeasy (Qiagen), as directed by the manufacturer. RNA was DNase treated (Qiagen), as directed by the manufacturer. RNA concentration was measured with a Nanodrop spectrophotometer and was sent to Vanderbilt Microarray Shared Resources (VMSR) core facility. RNA integrity was analyzed by the VMSR core on an Agilent 2100 bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNAs with RNA integrity numbers equal to or greater than 7.0 were used for further analysis, amplified with Nugen amplification kit as directed by the manufacturer, and hybridized to Affymetrix human U1.33 plus 2.0 3¢ UTR transcriptional profile array.
| | Sample_hyb_protocol | 15 μg of biotin-labeled aRNA was fragmented and hybridized on to the Affymetrix Human Genome U133 plus 2.0 GeneChip. After hybridization, the GeneChip was washed, stained with strepavidin/phycoerythrin conjugate and biotinylated antibody.
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 7G with AutoLoader.
| | Sample_data_processing | Data from all 12 arrays were batch normalized with the RMA quantile algorithm using Expression Console software (Affymetrix)
| | Sample_platform_id | GPL570
| | Sample_contact_name | James,,Crowe
| | Sample_contact_email | james.crowe@vanderbilt.edu, natalie.thornburg@vanderbilt.edu, frances.house@vanderbilt.edu
| | Sample_contact_phone | 615-343-8064
| | Sample_contact_fax | 615-343-4456
| | Sample_contact_laboratory | Crowe laboratory
| | Sample_contact_department | Vanderbilt Vaccine Center
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | T2219 21st Avenue South,
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37232-2905
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594173/suppl/GSM594173.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594173/suppl/GSM594173.chp.gz
| | Sample_series_id | GSE24132
| | Sample_data_row_count | 54675
| | |
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
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