Search results for the GEO ID: GSE29618  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM734022 | GPL3921 |
|
Bcells from influenza vaccinee (ID 25) at Day0 post-vaccination
|
Bcells of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Bcells
subject id: 25
time point: Day0
vaccine: FluMist, MedImmune
|
Flu-Bcells-25-Day0
|
| Sample_geo_accession | GSM734022
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734022/suppl/GSM734022.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734022/suppl/GSM734022.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734023 | GPL3921 |
|
Monocytes from influenza vaccinee (ID 25) at Day0 post-vaccination
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Monocytes of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Monocytes
subject id: 25
time point: Day0
vaccine: FluMist, MedImmune
|
Flu-Monocytes-25-Day0
|
| Sample_geo_accession | GSM734023
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734023/suppl/GSM734023.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734023/suppl/GSM734023.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734024 | GPL3921 |
|
pDC from influenza vaccinee (ID 25) at Day0 post-vaccination
|
pDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: pDC
subject id: 25
time point: Day0
vaccine: FluMist, MedImmune
|
Flu-pDC-25-Day0
|
| Sample_geo_accession | GSM734024
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734024/suppl/GSM734024.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734024/suppl/GSM734024.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734025 | GPL3921 |
|
Bcells from influenza vaccinee (ID 25) at Day7 post-vaccination
|
Bcells of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Bcells
subject id: 25
time point: Day7
vaccine: FluMist, MedImmune
|
Flu-Bcells-25-Day7
|
| Sample_geo_accession | GSM734025
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734025/suppl/GSM734025.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734025/suppl/GSM734025.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734026 | GPL3921 |
|
Monocytes from influenza vaccinee (ID 25) at Day7 post-vaccination
|
Monocytes of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Monocytes
subject id: 25
time point: Day7
vaccine: FluMist, MedImmune
|
Flu-Monocytes-25-Day7
|
| Sample_geo_accession | GSM734026
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734026/suppl/GSM734026.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734026/suppl/GSM734026.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734027 | GPL3921 |
|
pDC from influenza vaccinee (ID 25) at Day7 post-vaccination
|
pDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: pDC
subject id: 25
time point: Day7
vaccine: FluMist, MedImmune
|
Flu-pDC-25-Day7
|
| Sample_geo_accession | GSM734027
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734027/suppl/GSM734027.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734027/suppl/GSM734027.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734028 | GPL3921 |
|
Bcells from influenza vaccinee (ID 26) at Day0 post-vaccination
|
Bcells of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Bcells
subject id: 26
time point: Day0
vaccine: FluMist, MedImmune
|
Flu-Bcells-26-Day0
|
| Sample_geo_accession | GSM734028
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734028/suppl/GSM734028.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734028/suppl/GSM734028.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734029 | GPL3921 |
|
mDC from influenza vaccinee (ID 26) at Day0 post-vaccination
|
mDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: mDC
subject id: 26
time point: Day0
vaccine: FluMist, MedImmune
|
Flu-mDC-26-Day0
|
| Sample_geo_accession | GSM734029
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734029/suppl/GSM734029.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734029/suppl/GSM734029.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734030 | GPL3921 |
|
Monocytes from influenza vaccinee (ID 26) at Day0 post-vaccination
|
Monocytes of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Monocytes
subject id: 26
time point: Day0
vaccine: FluMist, MedImmune
|
Flu-Monocytes-26-Day0
|
| Sample_geo_accession | GSM734030
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734030/suppl/GSM734030.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734030/suppl/GSM734030.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734031 | GPL3921 |
|
pDC from influenza vaccinee (ID 26) at Day0 post-vaccination
|
pDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: pDC
subject id: 26
time point: Day0
vaccine: FluMist, MedImmune
|
Flu-pDC-26-Day0
|
| Sample_geo_accession | GSM734031
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734031/suppl/GSM734031.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734031/suppl/GSM734031.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734032 | GPL3921 |
|
Bcells from influenza vaccinee (ID 26) at Day7 post-vaccination
|
Bcells of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Bcells
subject id: 26
time point: Day7
vaccine: FluMist, MedImmune
|
Flu-Bcells-26-Day7
|
| Sample_geo_accession | GSM734032
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734032/suppl/GSM734032.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734032/suppl/GSM734032.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734033 | GPL3921 |
|
mDC from influenza vaccinee (ID 26) at Day7 post-vaccination
|
mDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: mDC
subject id: 26
time point: Day7
vaccine: FluMist, MedImmune
|
Flu-mDC-26-Day7
|
| Sample_geo_accession | GSM734033
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734033/suppl/GSM734033.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734033/suppl/GSM734033.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734034 | GPL3921 |
|
Monocytes from influenza vaccinee (ID 26) at Day7 post-vaccination
|
Monocytes of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Monocytes
subject id: 26
time point: Day7
vaccine: FluMist, MedImmune
|
Flu-Monocytes-26-Day7
|
| Sample_geo_accession | GSM734034
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734034/suppl/GSM734034.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734034/suppl/GSM734034.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734035 | GPL3921 |
|
pDC from influenza vaccinee (ID 26) at Day7 post-vaccination
|
pDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: pDC
subject id: 26
time point: Day7
vaccine: FluMist, MedImmune
|
Flu-pDC-26-Day7
|
| Sample_geo_accession | GSM734035
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734035/suppl/GSM734035.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734035/suppl/GSM734035.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734036 | GPL3921 |
|
mDC from influenza vaccinee (ID 33) at Day0 post-vaccination
|
mDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: mDC
subject id: 33
time point: Day0
vaccine: FluMist, MedImmune
|
Flu-mDC-33-Day0
|
| Sample_geo_accession | GSM734036
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734036/suppl/GSM734036.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734036/suppl/GSM734036.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734037 | GPL3921 |
|
Monocytes from influenza vaccinee (ID 33) at Day0 post-vaccination
|
Monocytes of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Monocytes
subject id: 33
time point: Day0
vaccine: FluMist, MedImmune
|
Flu-Monocytes-33-Day0
|
| Sample_geo_accession | GSM734037
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734037/suppl/GSM734037.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734037/suppl/GSM734037.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734038 | GPL3921 |
|
pDC from influenza vaccinee (ID 33) at Day0 post-vaccination
|
pDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: pDC
subject id: 33
time point: Day0
vaccine: FluMist, MedImmune
|
Flu-pDC-33-Day0
|
| Sample_geo_accession | GSM734038
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734038/suppl/GSM734038.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734038/suppl/GSM734038.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734039 | GPL3921 |
|
mDC from influenza vaccinee (ID 33) at Day7 post-vaccination
|
mDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: mDC
subject id: 33
time point: Day7
vaccine: FluMist, MedImmune
|
Flu-mDC-33-Day7
|
| Sample_geo_accession | GSM734039
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734039/suppl/GSM734039.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734039/suppl/GSM734039.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734040 | GPL3921 |
|
Monocytes from influenza vaccinee (ID 33) at Day7 post-vaccination
|
Monocytes of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Monocytes
subject id: 33
time point: Day7
vaccine: FluMist, MedImmune
|
Flu-Monocytes-33-Day7
|
| Sample_geo_accession | GSM734040
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734040/suppl/GSM734040.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734040/suppl/GSM734040.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734041 | GPL3921 |
|
pDC from influenza vaccinee (ID 33) at Day7 post-vaccination
|
pDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: pDC
subject id: 33
time point: Day7
vaccine: FluMist, MedImmune
|
Flu-pDC-33-Day7
|
| Sample_geo_accession | GSM734041
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734041/suppl/GSM734041.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734041/suppl/GSM734041.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734042 | GPL3921 |
|
Bcells from influenza vaccinee (ID 39) at Day0 post-vaccination
|
Bcells of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Bcells
subject id: 39
time point: Day0
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-Bcells-39-Day0
|
| Sample_geo_accession | GSM734042
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734042/suppl/GSM734042.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734042/suppl/GSM734042.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734043 | GPL3921 |
|
mDC from influenza vaccinee (ID 39) at Day0 post-vaccination
|
mDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: mDC
subject id: 39
time point: Day0
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-mDC-39-Day0
|
| Sample_geo_accession | GSM734043
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734043/suppl/GSM734043.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734043/suppl/GSM734043.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734044 | GPL3921 |
|
Monocytes from influenza vaccinee (ID 39) at Day0 post-vaccination
|
Monocytes of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Monocytes
subject id: 39
time point: Day0
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-Monocytes-39-Day0
|
| Sample_geo_accession | GSM734044
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734044/suppl/GSM734044.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734044/suppl/GSM734044.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734045 | GPL3921 |
|
pDC from influenza vaccinee (ID 39) at Day0 post-vaccination
|
pDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: pDC
subject id: 39
time point: Day0
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-pDC-39-Day0
|
| Sample_geo_accession | GSM734045
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734045/suppl/GSM734045.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734045/suppl/GSM734045.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734046 | GPL3921 |
|
Bcells from influenza vaccinee (ID 39) at Day7 post-vaccination
|
Bcells of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Bcells
subject id: 39
time point: Day7
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-Bcells-39-Day7
|
| Sample_geo_accession | GSM734046
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734046/suppl/GSM734046.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734046/suppl/GSM734046.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734047 | GPL3921 |
|
mDC from influenza vaccinee (ID 39) at Day7 post-vaccination
|
mDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: mDC
subject id: 39
time point: Day7
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-mDC-39-Day7
|
| Sample_geo_accession | GSM734047
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734047/suppl/GSM734047.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734047/suppl/GSM734047.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734048 | GPL3921 |
|
Monocytes from influenza vaccinee (ID 39) at Day7 post-vaccination
|
Monocytes of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Monocytes
subject id: 39
time point: Day7
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-Monocytes-39-Day7
|
| Sample_geo_accession | GSM734048
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734048/suppl/GSM734048.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734048/suppl/GSM734048.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734049 | GPL3921 |
|
pDC from influenza vaccinee (ID 39) at Day7 post-vaccination
|
pDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: pDC
subject id: 39
time point: Day7
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-pDC-39-Day7
|
| Sample_geo_accession | GSM734049
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734049/suppl/GSM734049.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734049/suppl/GSM734049.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734050 | GPL3921 |
|
Bcells from influenza vaccinee (ID 4) at Day0 post-vaccination
|
Bcells of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Bcells
subject id: 4
time point: Day0
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-Bcells-4-Day0
|
| Sample_geo_accession | GSM734050
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734050/suppl/GSM734050.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734050/suppl/GSM734050.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734051 | GPL3921 |
|
mDC from influenza vaccinee (ID 4) at Day0 post-vaccination
|
mDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: mDC
subject id: 4
time point: Day0
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-mDC-4-Day0
|
| Sample_geo_accession | GSM734051
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734051/suppl/GSM734051.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734051/suppl/GSM734051.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734052 | GPL3921 |
|
Monocytes from influenza vaccinee (ID 4) at Day0 post-vaccination
|
Monocytes of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Monocytes
subject id: 4
time point: Day0
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-Monocytes-4-Day0
|
| Sample_geo_accession | GSM734052
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734052/suppl/GSM734052.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734052/suppl/GSM734052.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734053 | GPL3921 |
|
pDC from influenza vaccinee (ID 4) at Day0 post-vaccination
|
pDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: pDC
subject id: 4
time point: Day0
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-pDC-4-Day0
|
| Sample_geo_accession | GSM734053
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734053/suppl/GSM734053.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734053/suppl/GSM734053.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734054 | GPL3921 |
|
Bcells from influenza vaccinee (ID 4) at Day7 post-vaccination
|
Bcells of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Bcells
subject id: 4
time point: Day7
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-Bcells-4-Day7
|
| Sample_geo_accession | GSM734054
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734054/suppl/GSM734054.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734054/suppl/GSM734054.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734055 | GPL3921 |
|
mDC from influenza vaccinee (ID 4) at Day7 post-vaccination
|
mDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: mDC
subject id: 4
time point: Day7
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-mDC-4-Day7
|
| Sample_geo_accession | GSM734055
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734055/suppl/GSM734055.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734055/suppl/GSM734055.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734056 | GPL3921 |
|
Monocytes from influenza vaccinee (ID 4) at Day7 post-vaccination
|
Monocytes of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Monocytes
subject id: 4
time point: Day7
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-Monocytes-4-Day7
|
| Sample_geo_accession | GSM734056
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734056/suppl/GSM734056.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734056/suppl/GSM734056.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734057 | GPL3921 |
|
pDC from influenza vaccinee (ID 4) at Day7 post-vaccination
|
pDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: pDC
subject id: 4
time point: Day7
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-pDC-4-Day7
|
| Sample_geo_accession | GSM734057
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734057/suppl/GSM734057.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734057/suppl/GSM734057.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734058 | GPL3921 |
|
Bcells from influenza vaccinee (ID 41) at Day0 post-vaccination
|
Bcells of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Bcells
subject id: 41
time point: Day0
vaccine: FluMist, MedImmune
|
Flu-Bcells-41-Day0
|
| Sample_geo_accession | GSM734058
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734058/suppl/GSM734058.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734058/suppl/GSM734058.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734059 | GPL3921 |
|
mDC from influenza vaccinee (ID 41) at Day0 post-vaccination
|
mDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: mDC
subject id: 41
time point: Day0
vaccine: FluMist, MedImmune
|
Flu-mDC-41-Day0
|
| Sample_geo_accession | GSM734059
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734059/suppl/GSM734059.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734059/suppl/GSM734059.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734060 | GPL3921 |
|
Monocytes from influenza vaccinee (ID 41) at Day0 post-vaccination
|
Monocytes of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Monocytes
subject id: 41
time point: Day0
vaccine: FluMist, MedImmune
|
Flu-Monocytes-41-Day0
|
| Sample_geo_accession | GSM734060
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734060/suppl/GSM734060.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734060/suppl/GSM734060.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734061 | GPL3921 |
|
pDC from influenza vaccinee (ID 41) at Day0 post-vaccination
|
pDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: pDC
subject id: 41
time point: Day0
vaccine: FluMist, MedImmune
|
Flu-pDC-41-Day0
|
| Sample_geo_accession | GSM734061
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734061/suppl/GSM734061.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734061/suppl/GSM734061.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734062 | GPL3921 |
|
Bcells from influenza vaccinee (ID 41) at Day7 post-vaccination
|
Bcells of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Bcells
subject id: 41
time point: Day7
vaccine: FluMist, MedImmune
|
Flu-Bcells-41-Day7
|
| Sample_geo_accession | GSM734062
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734062/suppl/GSM734062.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734062/suppl/GSM734062.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734063 | GPL3921 |
|
mDC from influenza vaccinee (ID 41) at Day7 post-vaccination
|
mDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: mDC
subject id: 41
time point: Day7
vaccine: FluMist, MedImmune
|
Flu-mDC-41-Day7
|
| Sample_geo_accession | GSM734063
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734063/suppl/GSM734063.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734063/suppl/GSM734063.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734064 | GPL3921 |
|
Monocytes from influenza vaccinee (ID 41) at Day7 post-vaccination
|
Monocytes of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Monocytes
subject id: 41
time point: Day7
vaccine: FluMist, MedImmune
|
Flu-Monocytes-41-Day7
|
| Sample_geo_accession | GSM734064
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734064/suppl/GSM734064.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734064/suppl/GSM734064.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734065 | GPL3921 |
|
pDC from influenza vaccinee (ID 41) at Day7 post-vaccination
|
pDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: pDC
subject id: 41
time point: Day7
vaccine: FluMist, MedImmune
|
Flu-pDC-41-Day7
|
| Sample_geo_accession | GSM734065
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734065/suppl/GSM734065.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734065/suppl/GSM734065.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734066 | GPL3921 |
|
Bcells from influenza vaccinee (ID 43) at Day0 post-vaccination
|
Bcells of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Bcells
subject id: 43
time point: Day0
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-Bcells-43-Day0
|
| Sample_geo_accession | GSM734066
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734066/suppl/GSM734066.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734066/suppl/GSM734066.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734067 | GPL3921 |
|
Bcells from influenza vaccinee (ID 43) at Day7 post-vaccination
|
Bcells of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Bcells
subject id: 43
time point: Day7
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-Bcells-43-Day7
|
| Sample_geo_accession | GSM734067
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734067/suppl/GSM734067.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734067/suppl/GSM734067.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734068 | GPL3921 |
|
mDC from influenza vaccinee (ID 47) at Day0 post-vaccination
|
mDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: mDC
subject id: 47
time point: Day0
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-mDC-47-Day0
|
| Sample_geo_accession | GSM734068
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734068/suppl/GSM734068.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734068/suppl/GSM734068.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734069 | GPL3921 |
|
Monocytes from influenza vaccinee (ID 47) at Day0 post-vaccination
|
Monocytes of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Monocytes
subject id: 47
time point: Day0
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-Monocytes-47-Day0
|
| Sample_geo_accession | GSM734069
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734069/suppl/GSM734069.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734069/suppl/GSM734069.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734070 | GPL3921 |
|
pDC from influenza vaccinee (ID 47) at Day0 post-vaccination
|
pDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: pDC
subject id: 47
time point: Day0
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-pDC-47-Day0
|
| Sample_geo_accession | GSM734070
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734070/suppl/GSM734070.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734070/suppl/GSM734070.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734071 | GPL3921 |
|
mDC from influenza vaccinee (ID 47) at Day7 post-vaccination
|
mDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: mDC
subject id: 47
time point: Day7
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-mDC-47-Day7
|
| Sample_geo_accession | GSM734071
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734071/suppl/GSM734071.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734071/suppl/GSM734071.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734072 | GPL3921 |
|
Monocytes from influenza vaccinee (ID 47) at Day7 post-vaccination
|
Monocytes of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Monocytes
subject id: 47
time point: Day7
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-Monocytes-47-Day7
|
| Sample_geo_accession | GSM734072
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734072/suppl/GSM734072.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734072/suppl/GSM734072.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734073 | GPL3921 |
|
pDC from influenza vaccinee (ID 47) at Day7 post-vaccination
|
pDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: pDC
subject id: 47
time point: Day7
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-pDC-47-Day7
|
| Sample_geo_accession | GSM734073
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734073/suppl/GSM734073.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734073/suppl/GSM734073.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734074 | GPL3921 |
|
Bcells from influenza vaccinee (ID 48) at Day0 post-vaccination
|
Bcells of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Bcells
subject id: 48
time point: Day0
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-Bcells-48-Day0
|
| Sample_geo_accession | GSM734074
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734074/suppl/GSM734074.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734074/suppl/GSM734074.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734075 | GPL3921 |
|
mDC from influenza vaccinee (ID 48) at Day0 post-vaccination
|
mDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: mDC
subject id: 48
time point: Day0
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-mDC-48-Day0
|
| Sample_geo_accession | GSM734075
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734075/suppl/GSM734075.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734075/suppl/GSM734075.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734076 | GPL3921 |
|
Monocytes from influenza vaccinee (ID 48) at Day0 post-vaccination
|
Monocytes of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Monocytes
subject id: 48
time point: Day0
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-Monocytes-48-Day0
|
| Sample_geo_accession | GSM734076
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734076/suppl/GSM734076.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734076/suppl/GSM734076.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734077 | GPL3921 |
|
pDC from influenza vaccinee (ID 48) at Day0 post-vaccination
|
pDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: pDC
subject id: 48
time point: Day0
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-pDC-48-Day0
|
| Sample_geo_accession | GSM734077
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734077/suppl/GSM734077.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734077/suppl/GSM734077.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734078 | GPL3921 |
|
Bcells from influenza vaccinee (ID 48) at Day7 post-vaccination
|
Bcells of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Bcells
subject id: 48
time point: Day7
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-Bcells-48-Day7
|
| Sample_geo_accession | GSM734078
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734078/suppl/GSM734078.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734078/suppl/GSM734078.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734079 | GPL3921 |
|
mDC from influenza vaccinee (ID 48) at Day7 post-vaccination
|
mDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: mDC
subject id: 48
time point: Day7
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-mDC-48-Day7
|
| Sample_geo_accession | GSM734079
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734079/suppl/GSM734079.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734079/suppl/GSM734079.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734080 | GPL3921 |
|
Monocytes from influenza vaccinee (ID 48) at Day7 post-vaccination
|
Monocytes of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Monocytes
subject id: 48
time point: Day7
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-Monocytes-48-Day7
|
| Sample_geo_accession | GSM734080
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734080/suppl/GSM734080.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734080/suppl/GSM734080.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734081 | GPL3921 |
|
pDC from influenza vaccinee (ID 48) at Day7 post-vaccination
|
pDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: pDC
subject id: 48
time point: Day7
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-pDC-48-Day7
|
| Sample_geo_accession | GSM734081
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734081/suppl/GSM734081.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734081/suppl/GSM734081.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734082 | GPL3921 |
|
Bcells from influenza vaccinee (ID 52) at Day0 post-vaccination
|
Bcells of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Bcells
subject id: 52
time point: Day0
vaccine: FluMist, MedImmune
|
Flu-Bcells-52-Day0
|
| Sample_geo_accession | GSM734082
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734082/suppl/GSM734082.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734082/suppl/GSM734082.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734083 | GPL3921 |
|
mDC from influenza vaccinee (ID 52) at Day0 post-vaccination
|
mDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: mDC
subject id: 52
time point: Day0
vaccine: FluMist, MedImmune
|
Flu-mDC-52-Day0
|
| Sample_geo_accession | GSM734083
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734083/suppl/GSM734083.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734083/suppl/GSM734083.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734084 | GPL3921 |
|
Monocytes from influenza vaccinee (ID 52) at Day0 post-vaccination
|
Monocytes of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Monocytes
subject id: 52
time point: Day0
vaccine: FluMist, MedImmune
|
Flu-Monocytes-52-Day0
|
| Sample_geo_accession | GSM734084
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734084/suppl/GSM734084.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734084/suppl/GSM734084.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734085 | GPL3921 |
|
pDC from influenza vaccinee (ID 52) at Day0 post-vaccination
|
pDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: pDC
subject id: 52
time point: Day0
vaccine: FluMist, MedImmune
|
Flu-pDC-52-Day0
|
| Sample_geo_accession | GSM734085
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734085/suppl/GSM734085.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734085/suppl/GSM734085.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734086 | GPL3921 |
|
Bcells from influenza vaccinee (ID 52) at Day7 post-vaccination
|
Bcells of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Bcells
subject id: 52
time point: Day7
vaccine: FluMist, MedImmune
|
Flu-Bcells-52-Day7
|
| Sample_geo_accession | GSM734086
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734086/suppl/GSM734086.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734086/suppl/GSM734086.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734087 | GPL3921 |
|
mDC from influenza vaccinee (ID 52) at Day7 post-vaccination
|
mDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: mDC
subject id: 52
time point: Day7
vaccine: FluMist, MedImmune
|
Flu-mDC-52-Day7
|
| Sample_geo_accession | GSM734087
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734087/suppl/GSM734087.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734087/suppl/GSM734087.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734088 | GPL3921 |
|
Monocytes from influenza vaccinee (ID 52) at Day7 post-vaccination
|
Monocytes of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Monocytes
subject id: 52
time point: Day7
vaccine: FluMist, MedImmune
|
Flu-Monocytes-52-Day7
|
| Sample_geo_accession | GSM734088
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734088/suppl/GSM734088.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734088/suppl/GSM734088.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734089 | GPL3921 |
|
pDC from influenza vaccinee (ID 52) at Day7 post-vaccination
|
pDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: pDC
subject id: 52
time point: Day7
vaccine: FluMist, MedImmune
|
Flu-pDC-52-Day7
|
| Sample_geo_accession | GSM734089
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734089/suppl/GSM734089.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734089/suppl/GSM734089.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734090 | GPL3921 |
|
Bcells from influenza vaccinee (ID 53) at Day0 post-vaccination
|
Bcells of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Bcells
subject id: 53
time point: Day0
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-Bcells-53-Day0
|
| Sample_geo_accession | GSM734090
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734090/suppl/GSM734090.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734090/suppl/GSM734090.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734091 | GPL3921 |
|
mDC from influenza vaccinee (ID 53) at Day0 post-vaccination
|
mDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: mDC
subject id: 53
time point: Day0
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-mDC-53-Day0
|
| Sample_geo_accession | GSM734091
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734091/suppl/GSM734091.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734091/suppl/GSM734091.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734092 | GPL3921 |
|
Monocytes from influenza vaccinee (ID 53) at Day0 post-vaccination
|
Monocytes of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Monocytes
subject id: 53
time point: Day0
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-Monocytes-53-Day0
|
| Sample_geo_accession | GSM734092
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734092/suppl/GSM734092.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734092/suppl/GSM734092.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734093 | GPL3921 |
|
pDC from influenza vaccinee (ID 53) at Day0 post-vaccination
|
pDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: pDC
subject id: 53
time point: Day0
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-pDC-53-Day0
|
| Sample_geo_accession | GSM734093
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734093/suppl/GSM734093.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734093/suppl/GSM734093.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734094 | GPL3921 |
|
Bcells from influenza vaccinee (ID 53) at Day7 post-vaccination
|
Bcells of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Bcells
subject id: 53
time point: Day7
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-Bcells-53-Day7
|
| Sample_geo_accession | GSM734094
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734094/suppl/GSM734094.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734094/suppl/GSM734094.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734095 | GPL3921 |
|
mDC from influenza vaccinee (ID 53) at Day7 post-vaccination
|
mDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: mDC
subject id: 53
time point: Day7
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-mDC-53-Day7
|
| Sample_geo_accession | GSM734095
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734095/suppl/GSM734095.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734095/suppl/GSM734095.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734096 | GPL3921 |
|
Monocytes from influenza vaccinee (ID 53) at Day7 post-vaccination
|
Monocytes of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Monocytes
subject id: 53
time point: Day7
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-Monocytes-53-Day7
|
| Sample_geo_accession | GSM734096
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734096/suppl/GSM734096.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734096/suppl/GSM734096.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734097 | GPL3921 |
|
pDC from influenza vaccinee (ID 53) at Day7 post-vaccination
|
pDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: pDC
subject id: 53
time point: Day7
vaccine: TIV (Fluarix, GlaxoSmithKline Biologicals)
|
Flu-pDC-53-Day7
|
| Sample_geo_accession | GSM734097
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734097/suppl/GSM734097.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734097/suppl/GSM734097.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734098 | GPL3921 |
|
Bcells from influenza vaccinee (ID 55) at Day0 post-vaccination
|
Bcells of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Bcells
subject id: 55
time point: Day0
vaccine: FluMist, MedImmune
|
Flu-Bcells-55-Day0
|
| Sample_geo_accession | GSM734098
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734098/suppl/GSM734098.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734098/suppl/GSM734098.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734099 | GPL3921 |
|
mDC from influenza vaccinee (ID 55) at Day0 post-vaccination
|
mDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: mDC
subject id: 55
time point: Day0
vaccine: FluMist, MedImmune
|
Flu-mDC-55-Day0
|
| Sample_geo_accession | GSM734099
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734099/suppl/GSM734099.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734099/suppl/GSM734099.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734100 | GPL3921 |
|
Monocytes from influenza vaccinee (ID 55) at Day0 post-vaccination
|
Monocytes of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Monocytes
subject id: 55
time point: Day0
vaccine: FluMist, MedImmune
|
Flu-Monocytes-55-Day0
|
| Sample_geo_accession | GSM734100
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734100/suppl/GSM734100.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734100/suppl/GSM734100.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734101 | GPL3921 |
|
pDC from influenza vaccinee (ID 55) at Day0 post-vaccination
|
pDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: pDC
subject id: 55
time point: Day0
vaccine: FluMist, MedImmune
|
Flu-pDC-55-Day0
|
| Sample_geo_accession | GSM734101
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734101/suppl/GSM734101.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734101/suppl/GSM734101.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734102 | GPL3921 |
|
Bcells from influenza vaccinee (ID 55) at Day7 post-vaccination
|
Bcells of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Bcells
subject id: 55
time point: Day7
vaccine: FluMist, MedImmune
|
Flu-Bcells-55-Day7
|
| Sample_geo_accession | GSM734102
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734102/suppl/GSM734102.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734102/suppl/GSM734102.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734103 | GPL3921 |
|
mDC from influenza vaccinee (ID 55) at Day7 post-vaccination
|
mDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: mDC
subject id: 55
time point: Day7
vaccine: FluMist, MedImmune
|
Flu-mDC-55-Day7
|
| Sample_geo_accession | GSM734103
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734103/suppl/GSM734103.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734103/suppl/GSM734103.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
| | |
|
GSM734104 | GPL3921 |
|
Monocytes from influenza vaccinee (ID 55) at Day7 post-vaccination
|
Monocytes of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
|
cell type: Monocytes
subject id: 55
time point: Day7
vaccine: FluMist, MedImmune
|
Flu-Monocytes-55-Day7
|
| Sample_geo_accession | GSM734104
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734104/suppl/GSM734104.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734104/suppl/GSM734104.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
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GSM734105 | GPL3921 |
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pDC from influenza vaccinee (ID 55) at Day7 post-vaccination
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pDC of subjects vaccinated with Influenza vaccine at day 0 (before vaccination) or at day 7 post-vaccination.
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cell type: pDC
subject id: 55
time point: Day7
vaccine: FluMist, MedImmune
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Flu-pDC-55-Day7
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| Sample_geo_accession | GSM734105
| | Sample_status | Public on Jul 10 2011
| | Sample_submission_date | May 29 2011
| | Sample_last_update_date | Aug 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Frozen PBMCs from 6 TIV and 6 LAIV vaccinees at day 0 and day 7 post-immunization (24 samples) were thaw, washed with FACS buffer (PBS with 5% FBS) and counted. First, the following antibodies were used to separate ~2 x 106 PBMCs into a “DC” fraction (cell enriched by negative selection) and a “B cell and Monocyte” fraction (cell enriched by positive selection), accordingly to manufacturer’s instructions (Miltenyi Biotech, Auburn, CA): biotin anti-CD56 (clone;B159, BD Biosciences), biotin anti-CD3 (clone;UCHT1, BD Biosciences), biotin anti-CD16 (clone;3G8, BD Biosciences), anti-CD19 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-CD14 MicroBeads (Miltenyi Biotech, Auburn, CA), anti-biotin MicroBeads (Miltenyi Biotech, Auburn, CA). Cells from “DC” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with FITC labeled lineage cocktail 1 (clones;SK7, 3G8, SJ25C1, L27, MφP9, NCAM16.2, BD Biosciences), PE labeled anti-CD123 (clone;9F5, BD Biosciences), PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences) and APC labeled anti-CD11c (clone;S-HCL-3, BD Biosciences). Cells from “B cell and Monocyte” fraction were washed 2x with FACS buffer (PBS with 5% FBS) and stained with PerCP labeled anti-HLA-DR (clone;L243(G46-6), BD Biosciences), FITC labeled anti-CD14 (clone; MφP9, BD Biosciences) and APC labeled anti-CD19 (clone;SJ25C1, BD Biosciences). Next, myeloid dendritic cells (lin-1- HLA-DR+ CD11Chigh CD123low) and plasmacytoid dendritic cells (lin-1- HLA-DR+ CD123high CD11Clow) were sorted from “DC” fraction, and B cells (HLA-DR+ CD19+) and monocytes (HLA-DR+ CD14+) sorted from “B cell and Monocyte” fraction using FACS Aria cell sorter (BD Biosciences). Following sorting, cells (~500 to ~50,000) were pelleted and resuspended in Trizol® reagent (Invitrogen, Carlsbad, CA).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was performed using the Trizol® (Invitrogen, Life Technologies Corporation) according to the manufacturer's instructions. Concentrations of total RNA were determined using a Nanodrop spectrophotometer or via the Ribogreen RNA quantitation kit (Molecular Probes/Invitrogen). RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN) according to the manufacturer’s instructions. Next, cDNA was labeled using the Nugen FL-Ovation cDNA Biotin Module V2 kit, following the manufacturer's protocol.
| | Sample_hyb_protocol | Hybridization to Affymetrix HT Human Genome U133A Array (Affymetrix, Inc) and washing was performed on the Affymetrix GeneChip Array Station (GCAS) automation platform.
| | Sample_scan_protocol | The arrays were scanned on the GeneChip HT Array Plate Scanner (Affymetrix 00-0332).
| | Sample_data_processing | RMA normalization was performed using Expression Console software (Affymetrix Inc, version 1.1).
| | Sample_platform_id | GPL3921
| | Sample_contact_name | Helder,I,Nakaya
| | Sample_contact_email | hnakaya@emory.edu
| | Sample_contact_phone | 1-404-712-2594
| | Sample_contact_laboratory | Bali Pulendran
| | Sample_contact_department | Emory Vaccine Center
| | Sample_contact_institute | Emory University
| | Sample_contact_address | 954 Gatewood Road, room 2040
| | Sample_contact_city | Atlanta
| | Sample_contact_state | GA
| | Sample_contact_zip/postal_code | 30329
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734105/suppl/GSM734105.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM734nnn/GSM734105/suppl/GSM734105.chp.gz
| | Sample_series_id | GSE29618
| | Sample_series_id | GSE29619
| | Sample_data_row_count | 22277
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