Search results for the GEO ID: GSE5547  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM128954 | GPL570 |
|
RR200_unifected_Skin_biopsy
|
Skin biopsy from healthy human subject
|
PBS treated skin (control) from resolver, id 200
|
Gene expression data from biopsy of PBS treated skin of subject with resolver phenotype. (control)
|
| Sample_geo_accession | GSM128954
| | Sample_status | Public on Sep 13 2007
| | Sample_submission_date | Aug 16 2006
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Control treated with sterile PBS only.
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Skin biopsy specimens were submerged in RNA Later (Qiagen, Valencia, CA) for 30 minutes immediately upon biopsy. Total RNA was isolated from the specimens using the RNeasy Fibrous Tissue mini kit (Qiagen) per manufacturer's instructions. Tissues were homogenized in lysis buffer using a Mini Bead Beater (Research Products International, Mt. Prospect, IL) with 1 µm silica beads. The homogenates were then digested with proteinase K and RNA was isolated using RNeasy spin columns per kit directions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stanley,M.,Spinola
| | Sample_contact_email | sspinola@iupui.edu
| | Sample_contact_department | Infectious Diseases
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 545 Barnhill Dr.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM128nnn/GSM128954/suppl/GSM128954.CEL.gz
| | Sample_series_id | GSE5547
| | Sample_data_row_count | 54675
| | |
|
GSM128955 | GPL570 |
|
RR203_unifected_Skin_biopsy
|
Skin biopsy from healthy human subject
|
PBS treated skin (control) from resolver, id 203
|
Gene expression data from biopsy of PBS treated skin of subject with resolver phenotype. (control)
|
| Sample_geo_accession | GSM128955
| | Sample_status | Public on Sep 13 2007
| | Sample_submission_date | Aug 16 2006
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Control treated with sterile PBS only.
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Skin biopsy specimens were submerged in RNA Later (Qiagen, Valencia, CA) for 30 minutes immediately upon biopsy. Total RNA was isolated from the specimens using the RNeasy Fibrous Tissue mini kit (Qiagen) per manufacturer's instructions. Tissues were homogenized in lysis buffer using a Mini Bead Beater (Research Products International, Mt. Prospect, IL) with 1 µm silica beads. The homogenates were then digested with proteinase K and RNA was isolated using RNeasy spin columns per kit directions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stanley,M.,Spinola
| | Sample_contact_email | sspinola@iupui.edu
| | Sample_contact_department | Infectious Diseases
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 545 Barnhill Dr.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM128nnn/GSM128955/suppl/GSM128955.CEL.gz
| | Sample_series_id | GSE5547
| | Sample_data_row_count | 54675
| | |
|
GSM128957 | GPL570 |
|
RR200_infected_skin_biopsy
|
Skin biopsy from healthy human subjects
|
H. ducreyi infected skin from resolver, id 200
|
Gene expression data from biopsy of infected skin of subject with resolver phenotype.
|
| Sample_geo_accession | GSM128957
| | Sample_status | Public on Sep 13 2007
| | Sample_submission_date | Aug 16 2006
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | skin innoculated with H.ducreyi
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Skin biopsy specimens were submerged in RNA Later (Qiagen, Valencia, CA) for 30 minutes immediately upon biopsy. Total RNA was isolated from the specimens using the RNeasy Fibrous Tissue mini kit (Qiagen) per manufacturer's instructions. Tissues were homogenized in lysis buffer using a Mini Bead Beater (Research Products International, Mt. Prospect, IL) with 1 µm silica beads. The homogenates were then digested with proteinase K and RNA was isolated using RNeasy spin columns per kit directions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stanley,M.,Spinola
| | Sample_contact_email | sspinola@iupui.edu
| | Sample_contact_department | Infectious Diseases
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 545 Barnhill Dr.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM128nnn/GSM128957/suppl/GSM128957.CEL.gz
| | Sample_series_id | GSE5547
| | Sample_data_row_count | 54675
| | |
|
GSM128958 | GPL570 |
|
RR203_infected_skin_biopsy
|
Skin biopsy from healthy human subjects
|
H. ducreyi infected skin from resolver, id 203
|
Gene expression data from biopsy of infected skin of subject with resolver phenotype.
|
| Sample_geo_accession | GSM128958
| | Sample_status | Public on Sep 13 2007
| | Sample_submission_date | Aug 16 2006
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | skin innoculated with H.ducreyi
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Skin biopsy specimens were submerged in RNA Later (Qiagen, Valencia, CA) for 30 minutes immediately upon biopsy. Total RNA was isolated from the specimens using the RNeasy Fibrous Tissue mini kit (Qiagen) per manufacturer's instructions. Tissues were homogenized in lysis buffer using a Mini Bead Beater (Research Products International, Mt. Prospect, IL) with 1 µm silica beads. The homogenates were then digested with proteinase K and RNA was isolated using RNeasy spin columns per kit directions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stanley,M.,Spinola
| | Sample_contact_email | sspinola@iupui.edu
| | Sample_contact_department | Infectious Diseases
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 545 Barnhill Dr.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM128nnn/GSM128958/suppl/GSM128958.CEL.gz
| | Sample_series_id | GSE5547
| | Sample_data_row_count | 54675
| | |
|
GSM128959 | GPL570 |
|
RR216_infected_skin_biopsy
|
Skin biopsy from healthy human subjects
|
H. ducreyi infected skin from resolver, id 216
|
Gene expression data from biopsy of infected skin of subject with resolver phenotype.
|
| Sample_geo_accession | GSM128959
| | Sample_status | Public on Sep 13 2007
| | Sample_submission_date | Aug 16 2006
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | skin innoculated with H.ducreyi
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Skin biopsy specimens were submerged in RNA Later (Qiagen, Valencia, CA) for 30 minutes immediately upon biopsy. Total RNA was isolated from the specimens using the RNeasy Fibrous Tissue mini kit (Qiagen) per manufacturer's instructions. Tissues were homogenized in lysis buffer using a Mini Bead Beater (Research Products International, Mt. Prospect, IL) with 1 µm silica beads. The homogenates were then digested with proteinase K and RNA was isolated using RNeasy spin columns per kit directions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stanley,M.,Spinola
| | Sample_contact_email | sspinola@iupui.edu
| | Sample_contact_department | Infectious Diseases
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 545 Barnhill Dr.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM128nnn/GSM128959/suppl/GSM128959.CEL.gz
| | Sample_series_id | GSE5547
| | Sample_data_row_count | 54675
| | |
|
GSM128960 | GPL570 |
|
PP149_unifected_Skin biopsy
|
Skin biopsy from healthy human subjects
|
PBS treated skin (control) from pustule former, id 149
|
Gene expression data from biopsy of PBS treated skin of subject with pustule-former phenotype. (control)
|
| Sample_geo_accession | GSM128960
| | Sample_status | Public on Sep 13 2007
| | Sample_submission_date | Aug 16 2006
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Control treated with sterile PBS only.
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Skin biopsy specimens were submerged in RNA Later (Qiagen, Valencia, CA) for 30 minutes immediately upon biopsy. Total RNA was isolated from the specimens using the RNeasy Fibrous Tissue mini kit (Qiagen) per manufacturer's instructions. Tissues were homogenized in lysis buffer using a Mini Bead Beater (Research Products International, Mt. Prospect, IL) with 1 µm silica beads. The homogenates were then digested with proteinase K and RNA was isolated using RNeasy spin columns per kit directions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stanley,M.,Spinola
| | Sample_contact_email | sspinola@iupui.edu
| | Sample_contact_department | Infectious Diseases
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 545 Barnhill Dr.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM128nnn/GSM128960/suppl/GSM128960.CEL.gz
| | Sample_series_id | GSE5547
| | Sample_data_row_count | 54675
| | |
|
GSM128961 | GPL570 |
|
PP164_unifected_Skin biopsy
|
Skin biopsy from healthy human subjects
|
PBS treated skin (control) from pustule former, id 164
|
Gene expression data from biopsy of PBS treated skin of subject with pustule-former phenotype. (control)
|
| Sample_geo_accession | GSM128961
| | Sample_status | Public on Sep 13 2007
| | Sample_submission_date | Aug 16 2006
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Control treated with sterile PBS only.
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Skin biopsy specimens were submerged in RNA Later (Qiagen, Valencia, CA) for 30 minutes immediately upon biopsy. Total RNA was isolated from the specimens using the RNeasy Fibrous Tissue mini kit (Qiagen) per manufacturer's instructions. Tissues were homogenized in lysis buffer using a Mini Bead Beater (Research Products International, Mt. Prospect, IL) with 1 µm silica beads. The homogenates were then digested with proteinase K and RNA was isolated using RNeasy spin columns per kit directions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stanley,M.,Spinola
| | Sample_contact_email | sspinola@iupui.edu
| | Sample_contact_department | Infectious Diseases
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 545 Barnhill Dr.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM128nnn/GSM128961/suppl/GSM128961.CEL.gz
| | Sample_series_id | GSE5547
| | Sample_data_row_count | 54675
| | |
|
GSM128962 | GPL570 |
|
PP243_unifected_Skin biopsy
|
Skin biopsy from healthy human subjects
|
PBS treated skin (control) from pustule former, id 243
|
Gene expression data from biopsy of PBS treated skin of subject with pustule-former phenotype. (control)
|
| Sample_geo_accession | GSM128962
| | Sample_status | Public on Sep 13 2007
| | Sample_submission_date | Aug 16 2006
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Control treated with sterile PBS only.
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Skin biopsy specimens were submerged in RNA Later (Qiagen, Valencia, CA) for 30 minutes immediately upon biopsy. Total RNA was isolated from the specimens using the RNeasy Fibrous Tissue mini kit (Qiagen) per manufacturer's instructions. Tissues were homogenized in lysis buffer using a Mini Bead Beater (Research Products International, Mt. Prospect, IL) with 1 µm silica beads. The homogenates were then digested with proteinase K and RNA was isolated using RNeasy spin columns per kit directions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stanley,M.,Spinola
| | Sample_contact_email | sspinola@iupui.edu
| | Sample_contact_department | Infectious Diseases
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 545 Barnhill Dr.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM128nnn/GSM128962/suppl/GSM128962.CEL.gz
| | Sample_series_id | GSE5547
| | Sample_data_row_count | 54675
| | |
|
GSM128963 | GPL570 |
|
PP149_infected_Skin biopsy
|
Skin biopsy from healthy human subjects
|
H. ducreyi infected skin from pustule former, id 149
|
Gene expression data from biopsy of infected skin of subject with pustule former phenotype.
|
| Sample_geo_accession | GSM128963
| | Sample_status | Public on Sep 13 2007
| | Sample_submission_date | Aug 16 2006
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | skin innoculated with H.ducreyi
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Skin biopsy specimens were submerged in RNA Later (Qiagen, Valencia, CA) for 30 minutes immediately upon biopsy. Total RNA was isolated from the specimens using the RNeasy Fibrous Tissue mini kit (Qiagen) per manufacturer's instructions. Tissues were homogenized in lysis buffer using a Mini Bead Beater (Research Products International, Mt. Prospect, IL) with 1 µm silica beads. The homogenates were then digested with proteinase K and RNA was isolated using RNeasy spin columns per kit directions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip? Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stanley,M.,Spinola
| | Sample_contact_email | sspinola@iupui.edu
| | Sample_contact_department | Infectious Diseases
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 545 Barnhill Dr.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM128nnn/GSM128963/suppl/GSM128963.CEL.gz
| | Sample_series_id | GSE5547
| | Sample_data_row_count | 54675
| | |
|
GSM128964 | GPL570 |
|
PP164_infected_Skin biopsy
|
Skin biopsy from healthy human subjects
|
H. ducreyi infected skin from pustule former, id 164
|
Gene expression data from biopsy of infected skin of subject with pustule former phenotype.
|
| Sample_geo_accession | GSM128964
| | Sample_status | Public on Sep 13 2007
| | Sample_submission_date | Aug 16 2006
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | skin innoculated with H.ducreyi
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Skin biopsy specimens were submerged in RNA Later (Qiagen, Valencia, CA) for 30 minutes immediately upon biopsy. Total RNA was isolated from the specimens using the RNeasy Fibrous Tissue mini kit (Qiagen) per manufacturer's instructions. Tissues were homogenized in lysis buffer using a Mini Bead Beater (Research Products International, Mt. Prospect, IL) with 1 µm silica beads. The homogenates were then digested with proteinase K and RNA was isolated using RNeasy spin columns per kit directions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip? Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stanley,M.,Spinola
| | Sample_contact_email | sspinola@iupui.edu
| | Sample_contact_department | Infectious Diseases
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 545 Barnhill Dr.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM128nnn/GSM128964/suppl/GSM128964.CEL.gz
| | Sample_series_id | GSE5547
| | Sample_data_row_count | 54675
| | |
|
GSM128965 | GPL570 |
|
PP243_infected_Skin biopsy
|
Skin biopsy from healthy human subjects
|
H. ducreyi infected skin from pustule former, id 243
|
Gene expression data from biopsy of infected skin of subject with pustule former phenotype.
|
| Sample_geo_accession | GSM128965
| | Sample_status | Public on Sep 13 2007
| | Sample_submission_date | Aug 16 2006
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | skin innoculated with H.ducreyi
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Skin biopsy specimens were submerged in RNA Later (Qiagen, Valencia, CA) for 30 minutes immediately upon biopsy. Total RNA was isolated from the specimens using the RNeasy Fibrous Tissue mini kit (Qiagen) per manufacturer's instructions. Tissues were homogenized in lysis buffer using a Mini Bead Beater (Research Products International, Mt. Prospect, IL) with 1 µm silica beads. The homogenates were then digested with proteinase K and RNA was isolated using RNeasy spin columns per kit directions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip? Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stanley,M.,Spinola
| | Sample_contact_email | sspinola@iupui.edu
| | Sample_contact_department | Infectious Diseases
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 545 Barnhill Dr.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM128nnn/GSM128965/suppl/GSM128965.CEL.gz
| | Sample_series_id | GSE5547
| | Sample_data_row_count | 54675
| | |
|
GSM128966 | GPL570 |
|
RR200_uninfected_DC
|
Monocyte derived Dendritic Cells from healthy human subjects
|
Dendritic Cells uninfected (control) from resolver, id 200
|
Gene expression from dendritic cells from human subject with resolver phenotype uninfected.
|
| Sample_geo_accession | GSM128966
| | Sample_status | Public on Sep 13 2007
| | Sample_submission_date | Aug 16 2006
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Untreated Dendritic cells (Control)
| | Sample_growth_protocol_ch1 | Peripheral blood was obtained from the 3 PP and 3RR subjects several mo after they were infected a third time. CD14+ peripheral blood monocytes were isolated from PBMC by positive selection magnetic beads (Miltenyi Biotec, Auburn, CA) and grown in the presence of recombinant human (rh) IL-4 (1 ng/ml) and rhGM-CSF (0.2 ng/ml) (R&D Systems, Minneapolis, MN). After 7 d of culture, the cells were HLA-DR+, CD86+ CD40+, CD3-, CD14-, and CD19- by flow cytometry. For controls, DC were untreated for 24 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy® Mini Kit, according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stanley,M.,Spinola
| | Sample_contact_email | sspinola@iupui.edu
| | Sample_contact_department | Infectious Diseases
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 545 Barnhill Dr.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM128nnn/GSM128966/suppl/GSM128966.CEL.gz
| | Sample_series_id | GSE5547
| | Sample_data_row_count | 54675
| | |
|
GSM128967 | GPL570 |
|
RR203_uninfected_DC
|
Monocyte derived dendritic cells from healthy human subjects
|
Dendritic cells uninfected (control) from resolver, id 203
|
Gene expression from Dendritic cells from human subject with resolver phenotype uninfected.
|
| Sample_geo_accession | GSM128967
| | Sample_status | Public on Sep 13 2007
| | Sample_submission_date | Aug 16 2006
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Untreated Dendritic cells (Control)
| | Sample_growth_protocol_ch1 | Peripheral blood was obtained from the 3 PP and 3RR subjects several mo after they were infected a third time. CD14+ peripheral blood monocytes were isolated from PBMC by positive selection magnetic beads (Miltenyi Biotec, Auburn, CA) and grown in the presence of recombinant human (rh) IL-4 (1 ng/ml) and rhGM-CSF (0.2 ng/ml) (R&D Systems, Minneapolis, MN). After 7 d of culture, the cells were HLA-DR+, CD86+ CD40+, CD3-, CD14-, and CD19- by flow cytometry. For controls, DC were untreated for 24 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy® Mini Kit, according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stanley,M.,Spinola
| | Sample_contact_email | sspinola@iupui.edu
| | Sample_contact_department | Infectious Diseases
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 545 Barnhill Dr.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM128nnn/GSM128967/suppl/GSM128967.CEL.gz
| | Sample_series_id | GSE5547
| | Sample_data_row_count | 54675
| | |
|
GSM128968 | GPL570 |
|
RR216_uninfected_DC
|
Monocyte derived Dendritic Cells from healthy human subjects
|
Dendritic Cells uninfected (control) from resolver, id 216
|
Gene expression from Dendritic cells from human subject with resolver phenotype uninfected.
|
| Sample_geo_accession | GSM128968
| | Sample_status | Public on Sep 13 2007
| | Sample_submission_date | Aug 16 2006
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Untreated Dendritic cells (Control)
| | Sample_growth_protocol_ch1 | Peripheral blood was obtained from the 3 PP and 3RR subjects several mo after they were infected a third time. CD14+ peripheral blood monocytes were isolated from PBMC by positive selection magnetic beads (Miltenyi Biotec, Auburn, CA) and grown in the presence of recombinant human (rh) IL-4 (1 ng/ml) and rhGM-CSF (0.2 ng/ml) (R&D Systems, Minneapolis, MN). After 7 d of culture, the cells were HLA-DR+, CD86+ CD40+, CD3-, CD14-, and CD19- by flow cytometry. For controls, DC were untreated for 24 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy® Mini Kit, according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stanley,M.,Spinola
| | Sample_contact_email | sspinola@iupui.edu
| | Sample_contact_department | Infectious Diseases
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 545 Barnhill Dr.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM128nnn/GSM128968/suppl/GSM128968.CEL.gz
| | Sample_series_id | GSE5547
| | Sample_data_row_count | 54675
| | |
|
GSM128969 | GPL570 |
|
RR200_infected_DC
|
Monocyte derived Dendritic Cells from healthy human subjects
|
Dendritic Cells infected with H. ducreyi from resolver, id 200
|
Gene expression from Dendritic cells from human subject with resolver phenotype infected with H. ducreyi.
|
| Sample_geo_accession | GSM128969
| | Sample_status | Public on Sep 13 2007
| | Sample_submission_date | Aug 16 2006
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Dendritic Cells incubated with H.ducreyi
| | Sample_growth_protocol_ch1 | Peripheral blood was obtained from the 3 PP and 3RR subjects several mo after they were infected a third time. CD14+ peripheral blood monocytes were isolated from PBMC by positive selection magnetic beads (Miltenyi Biotec, Auburn, CA) and grown in the presence of recombinant human (rh) IL-4 (1 ng/ml) and rhGM-CSF (0.2 ng/ml) (R&D Systems, Minneapolis, MN). After 7 d of culture, the cells were HLA-DR+, CD86+ CD40+, CD3-, CD14-, and CD19- by flow cytometry. DC were incubated with nonopsonized H. ducreyi for 90 min at an MOI of 30:1, washed to remove non-associated bacteria and incubated an additional 22.5 h.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy® Mini Kit, according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stanley,M.,Spinola
| | Sample_contact_email | sspinola@iupui.edu
| | Sample_contact_department | Infectious Diseases
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 545 Barnhill Dr.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM128nnn/GSM128969/suppl/GSM128969.CEL.gz
| | Sample_series_id | GSE5547
| | Sample_data_row_count | 54675
| | |
|
GSM128970 | GPL570 |
|
RR203_infected_DC
|
Monocyte derived dendritic cells from healthy human subjects
|
Dendritic Cells infected with H. ducreyi from resolver, id 203
|
Gene expression from Dendritic cells from human subject with resolver phenotype infected with H. ducreyi.
|
| Sample_geo_accession | GSM128970
| | Sample_status | Public on Sep 13 2007
| | Sample_submission_date | Aug 16 2006
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Dendritic cells incubated with H.ducreyi
| | Sample_growth_protocol_ch1 | Peripheral blood was obtained from the 3 PP and 3RR subjects several mo after they were infected a third time. CD14+ peripheral blood monocytes were isolated from PBMC by positive selection magnetic beads (Miltenyi Biotec, Auburn, CA) and grown in the presence of recombinant human (rh) IL-4 (1 ng/ml) and rhGM-CSF (0.2 ng/ml) (R&D Systems, Minneapolis, MN). After 7 d of culture, the cells were HLA-DR+, CD86+ CD40+, CD3-, CD14-, and CD19- by flow cytometry. DC were incubated with nonopsonized H. ducreyi for 90 min at an MOI of 30:1, washed to remove non-associated bacteria and incubated an additional 22.5 h.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy® Mini Kit, according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stanley,M.,Spinola
| | Sample_contact_email | sspinola@iupui.edu
| | Sample_contact_department | Infectious Diseases
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 545 Barnhill Dr.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM128nnn/GSM128970/suppl/GSM128970.CEL.gz
| | Sample_series_id | GSE5547
| | Sample_data_row_count | 54675
| | |
|
GSM128971 | GPL570 |
|
RR216_infected_DC
|
Monocyte derived Dendritic Cells from healthy human subjects
|
Dendritic cells infected with H. ducreyi from resolver, id 216
|
Gene expression from Dendritic cells from human subject with resolver phenotype infected with H. ducreyi.
|
| Sample_geo_accession | GSM128971
| | Sample_status | Public on Sep 13 2007
| | Sample_submission_date | Aug 16 2006
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Dendritic cells incubated with H.ducreyi
| | Sample_growth_protocol_ch1 | Peripheral blood was obtained from the 3 PP and 3RR subjects several mo after they were infected a third time. CD14+ peripheral blood monocytes were isolated from PBMC by positive selection magnetic beads (Miltenyi Biotec, Auburn, CA) and grown in the presence of recombinant human (rh) IL-4 (1 ng/ml) and rhGM-CSF (0.2 ng/ml) (R&D Systems, Minneapolis, MN). After 7 d of culture, the cells were HLA-DR+, CD86+ CD40+, CD3-, CD14-, and CD19- by flow cytometry. DC were incubated with nonopsonized H. ducreyi for 90 min at an MOI of 30:1, washed to remove non-associated bacteria and incubated an additional 22.5 h.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy® Mini Kit, according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stanley,M.,Spinola
| | Sample_contact_email | sspinola@iupui.edu
| | Sample_contact_department | Infectious Diseases
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 545 Barnhill Dr.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM128nnn/GSM128971/suppl/GSM128971.CEL.gz
| | Sample_series_id | GSE5547
| | Sample_data_row_count | 54675
| | |
|
GSM128972 | GPL570 |
|
PP149_uninfected_DC
|
Monocyte derived Dendritic Cells from healthy human subjects
|
Dendritic Cells uninfected (control) from pustule former, id 149
|
Gene expression from Dendritic cells from human subject with pustule former phenotype uninfected.
|
| Sample_geo_accession | GSM128972
| | Sample_status | Public on Sep 13 2007
| | Sample_submission_date | Aug 16 2006
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Untreated Dendritic Cells (Control)
| | Sample_growth_protocol_ch1 | Peripheral blood was obtained from the 3 PP and 3RR subjects several mo after they were infected a third time. CD14+ peripheral blood monocytes were isolated from PBMC by positive selection magnetic beads (Miltenyi Biotec, Auburn, CA) and grown in the presence of recombinant human (rh) IL-4 (1 ng/ml) and rhGM-CSF (0.2 ng/ml) (R&D Systems, Minneapolis, MN). After 7 d of culture, the cells were HLA-DR+, CD86+ CD40+, CD3-, CD14-, and CD19- by flow cytometry. For controls, DC were untreated for 24 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy® Mini Kit, according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stanley,M.,Spinola
| | Sample_contact_email | sspinola@iupui.edu
| | Sample_contact_department | Infectious Diseases
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 545 Barnhill Dr.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM128nnn/GSM128972/suppl/GSM128972.CEL.gz
| | Sample_series_id | GSE5547
| | Sample_data_row_count | 54675
| | |
|
GSM128973 | GPL570 |
|
PP164_uninfected_DC
|
Monocyte derived Dendritic Cells from healthy human subjects
|
Dendritic Cells uninfected (control) from pustule former, id 164
|
Gene expression from Dendritic cells from human subject with pustule former phenotype uninfected.
|
| Sample_geo_accession | GSM128973
| | Sample_status | Public on Sep 13 2007
| | Sample_submission_date | Aug 16 2006
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Untreated Dendritic Cells (Control)
| | Sample_growth_protocol_ch1 | Peripheral blood was obtained from the 3 PP and 3RR subjects several mo after they were infected a third time. CD14+ peripheral blood monocytes were isolated from PBMC by positive selection magnetic beads (Miltenyi Biotec, Auburn, CA) and grown in the presence of recombinant human (rh) IL-4 (1 ng/ml) and rhGM-CSF (0.2 ng/ml) (R&D Systems, Minneapolis, MN). After 7 d of culture, the cells were HLA-DR+, CD86+ CD40+, CD3-, CD14-, and CD19- by flow cytometry. For controls, DC were untreated for 24 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy® Mini Kit, according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stanley,M.,Spinola
| | Sample_contact_email | sspinola@iupui.edu
| | Sample_contact_department | Infectious Diseases
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 545 Barnhill Dr.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM128nnn/GSM128973/suppl/GSM128973.CEL.gz
| | Sample_series_id | GSE5547
| | Sample_data_row_count | 54675
| | |
|
GSM128974 | GPL570 |
|
PP243_uninfected_DC
|
Monocyte derived Dendritic Cells from healthy human subjects
|
Dendritic Cells uninfected (control) from pustule former, id 243
|
Gene expression from Dendritic cells from human subject with pustule former phenotype uninfected.
|
| Sample_geo_accession | GSM128974
| | Sample_status | Public on Sep 13 2007
| | Sample_submission_date | Aug 16 2006
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Untreated Dendritic Cells(Control)
| | Sample_growth_protocol_ch1 | Peripheral blood was obtained from the 3 PP and 3RR subjects several mo after they were infected a third time. CD14+ peripheral blood monocytes were isolated from PBMC by positive selection magnetic beads (Miltenyi Biotec, Auburn, CA) and grown in the presence of recombinant human (rh) IL-4 (1 ng/ml) and rhGM-CSF (0.2 ng/ml) (R&D Systems, Minneapolis, MN). After 7 d of culture, the cells were HLA-DR+, CD86+ CD40+, CD3-, CD14-, and CD19- by flow cytometry. For controls, DC were untreated for 24 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy® Mini Kit, according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stanley,M.,Spinola
| | Sample_contact_email | sspinola@iupui.edu
| | Sample_contact_department | Infectious Diseases
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 545 Barnhill Dr.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM128nnn/GSM128974/suppl/GSM128974.CEL.gz
| | Sample_series_id | GSE5547
| | Sample_data_row_count | 54675
| | |
|
GSM128975 | GPL570 |
|
PP149_infected_DC
|
Monocyte derived Dendritic Cells from healthy human subjects
|
Dendritic Cells infected with H. ducreyi from pustule former, id 149
|
Gene expression from Dendritic cells from human subject with pustule former phenotype infected with H. ducreyi.
|
| Sample_geo_accession | GSM128975
| | Sample_status | Public on Sep 13 2007
| | Sample_submission_date | Aug 16 2006
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Dendritic Cells incubated with H.ducreyi
| | Sample_growth_protocol_ch1 | Peripheral blood was obtained from the 3 PP and 3RR subjects several mo after they were infected a third time. CD14+ peripheral blood monocytes were isolated from PBMC by positive selection magnetic beads (Miltenyi Biotec, Auburn, CA) and grown in the presence of recombinant human (rh) IL-4 (1 ng/ml) and rhGM-CSF (0.2 ng/ml) (R&D Systems, Minneapolis, MN). After 7 d of culture, the cells were HLA-DR+, CD86+ CD40+, CD3-, CD14-, and CD19- by flow cytometry. DC were incubated with nonopsonized H. ducreyi for 90 min at an MOI of 30:1, washed to remove non-associated bacteria and incubated an additional 22.5 h.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy® Mini Kit, according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stanley,M.,Spinola
| | Sample_contact_email | sspinola@iupui.edu
| | Sample_contact_department | Infectious Diseases
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 545 Barnhill Dr.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM128nnn/GSM128975/suppl/GSM128975.CEL.gz
| | Sample_series_id | GSE5547
| | Sample_data_row_count | 54675
| | |
|
GSM128976 | GPL570 |
|
PP164_infected_DC
|
Monocyte derived Dendritic Cells from healthy human subjects
|
Dendritic Cells infected with H. ducreyi from pustule former, id 164
|
Gene expression from Dendritic cells from human subject with pustule former phenotype infected with H. ducreyi.
|
| Sample_geo_accession | GSM128976
| | Sample_status | Public on Sep 13 2007
| | Sample_submission_date | Aug 16 2006
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Dendritic Cells incubated with H.ducreyi
| | Sample_growth_protocol_ch1 | Peripheral blood was obtained from the 3 PP and 3RR subjects several mo after they were infected a third time. CD14+ peripheral blood monocytes were isolated from PBMC by positive selection magnetic beads (Miltenyi Biotec, Auburn, CA) and grown in the presence of recombinant human (rh) IL-4 (1 ng/ml) and rhGM-CSF (0.2 ng/ml) (R&D Systems, Minneapolis, MN). After 7 d of culture, the cells were HLA-DR+, CD86+ CD40+, CD3-, CD14-, and CD19- by flow cytometry. DC were incubated with nonopsonized H. ducreyi for 90 min at an MOI of 30:1, washed to remove non-associated bacteria and incubated an additional 22.5 h.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy® Mini Kit, according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stanley,M.,Spinola
| | Sample_contact_email | sspinola@iupui.edu
| | Sample_contact_department | Infectious Diseases
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 545 Barnhill Dr.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM128nnn/GSM128976/suppl/GSM128976.CEL.gz
| | Sample_series_id | GSE5547
| | Sample_data_row_count | 54675
| | |
|
GSM128977 | GPL570 |
|
PP243_infected_DC
|
Monocyte derived Dendritic Cells from healthy human subjects
|
Dendritic Cells infected with H. ducreyi from pustule former, id 243
|
Gene expression from Dendritic cells from human subject with pustule former phenotype infected with H. ducreyi.
|
| Sample_geo_accession | GSM128977
| | Sample_status | Public on Sep 13 2007
| | Sample_submission_date | Aug 16 2006
| | Sample_last_update_date | Sep 13 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Dendritic Cells incubated with H.ducreyi
| | Sample_growth_protocol_ch1 | Peripheral blood was obtained from the 3 PP and 3RR subjects several mo after they were infected a third time. CD14+ peripheral blood monocytes were isolated from PBMC by positive selection magnetic beads (Miltenyi Biotec, Auburn, CA) and grown in the presence of recombinant human (rh) IL-4 (1 ng/ml) and rhGM-CSF (0.2 ng/ml) (R&D Systems, Minneapolis, MN). After 7 d of culture, the cells were HLA-DR+, CD86+ CD40+, CD3-, CD14-, and CD19- by flow cytometry. DC were incubated with nonopsonized H. ducreyi for 90 min at an MOI of 30:1, washed to remove non-associated bacteria and incubated an additional 22.5 h.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNeasy® Mini Kit, according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Stanley,M.,Spinola
| | Sample_contact_email | sspinola@iupui.edu
| | Sample_contact_department | Infectious Diseases
| | Sample_contact_institute | Indiana University School of Medicine
| | Sample_contact_address | 545 Barnhill Dr.
| | Sample_contact_city | Indianapolis
| | Sample_contact_state | IN
| | Sample_contact_zip/postal_code | 46202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM128nnn/GSM128977/suppl/GSM128977.CEL.gz
| | Sample_series_id | GSE5547
| | Sample_data_row_count | 54675
| | |
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