Search results for the GEO ID: GSE37416  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM918524 | GPL570 |
|
PMN_0hr_ctrl_1
|
polymorphonuclear leukocytes, 0hr, control, replicate 1
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 0 hr
|
control PMNs
|
| Sample_geo_accession | GSM918524
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918524/suppl/GSM918524.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918524/suppl/GSM918524.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918525 | GPL570 |
|
PMN_0hr_ctrl_2
|
polymorphonuclear leukocytes, 0hr, control, replicate 2
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 0 hr
|
control PMNs
|
| Sample_geo_accession | GSM918525
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918525/suppl/GSM918525.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918525/suppl/GSM918525.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918526 | GPL570 |
|
PMN_0hr_ctrl_3
|
polymorphonuclear leukocytes, 0hr, control, replicate 3
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 0 hr
|
control PMNs
|
| Sample_geo_accession | GSM918526
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918526/suppl/GSM918526.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918526/suppl/GSM918526.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918527 | GPL570 |
|
PMN_0hr_ctrl_4
|
polymorphonuclear leukocytes, 0hr, control, replicate 4
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 0 hr
|
control PMNs
|
| Sample_geo_accession | GSM918527
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918527/suppl/GSM918527.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918527/suppl/GSM918527.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918528 | GPL570 |
|
PMN_0hr_LVS_1
|
polymorphonuclear leukocytes, 0hr, LVS-treated, replicate 1
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 0 hr
|
test PMNs
|
| Sample_geo_accession | GSM918528
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918528/suppl/GSM918528.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918528/suppl/GSM918528.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918529 | GPL570 |
|
PMN_0hr_LVS_2
|
polymorphonuclear leukocytes, 0hr, LVS-treated, replicate 2
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 0 hr
|
test PMNs
|
| Sample_geo_accession | GSM918529
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918529/suppl/GSM918529.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918529/suppl/GSM918529.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918530 | GPL570 |
|
PMN_0hr_LVS_3
|
polymorphonuclear leukocytes, 0hr, LVS-treated, replicate 3
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 0 hr
|
test PMNs
|
| Sample_geo_accession | GSM918530
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918530/suppl/GSM918530.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918530/suppl/GSM918530.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918531 | GPL570 |
|
PMN_0hr_LVS_4
|
polymorphonuclear leukocytes, 0hr, LVS-treated, replicate 4
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 0 hr
|
test PMNs
|
| Sample_geo_accession | GSM918531
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918531/suppl/GSM918531.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918531/suppl/GSM918531.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918532 | GPL570 |
|
PMN_3hr_ctrl_1
|
polymorphonuclear leukocytes, 3hr, control, replicate 1
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 3 hr
|
control PMNs
|
| Sample_geo_accession | GSM918532
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918532/suppl/GSM918532.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918532/suppl/GSM918532.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918533 | GPL570 |
|
PMN_3hr_ctrl_2
|
polymorphonuclear leukocytes, 3hr, control, replicate 2
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 3 hr
|
control PMNs
|
| Sample_geo_accession | GSM918533
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918533/suppl/GSM918533.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918533/suppl/GSM918533.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918534 | GPL570 |
|
PMN_3hr_ctrl_3
|
polymorphonuclear leukocytes, 3hr, control, replicate 3
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 3 hr
|
control PMNs
|
| Sample_geo_accession | GSM918534
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918534/suppl/GSM918534.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918534/suppl/GSM918534.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918535 | GPL570 |
|
PMN_3hr_ctrl_4
|
polymorphonuclear leukocytes, 3hr, control, replicate 4
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 3 hr
|
control PMNs
|
| Sample_geo_accession | GSM918535
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918535/suppl/GSM918535.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918535/suppl/GSM918535.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918536 | GPL570 |
|
PMN_3hr_LVS_1
|
polymorphonuclear leukocytes, 3hr, LVS-treated, replicate 1
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 3 hr
|
test PMNs
|
| Sample_geo_accession | GSM918536
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918536/suppl/GSM918536.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918536/suppl/GSM918536.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918537 | GPL570 |
|
PMN_3hr_LVS_2
|
polymorphonuclear leukocytes, 3hr, LVS-treated, replicate 2
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 3 hr
|
test PMNs
|
| Sample_geo_accession | GSM918537
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918537/suppl/GSM918537.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918537/suppl/GSM918537.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918538 | GPL570 |
|
PMN_3hr_LVS_3
|
polymorphonuclear leukocytes, 3hr, LVS-treated, replicate 3
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 3 hr
|
test PMNs
|
| Sample_geo_accession | GSM918538
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918538/suppl/GSM918538.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918538/suppl/GSM918538.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918539 | GPL570 |
|
PMN_3hr_LVS_4
|
polymorphonuclear leukocytes, 3hr, LVS-treated, replicate 4
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 3 hr
|
test PMNs
|
| Sample_geo_accession | GSM918539
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918539/suppl/GSM918539.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918539/suppl/GSM918539.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918540 | GPL570 |
|
PMN_6hr_ctrl_1
|
polymorphonuclear leukocytes, 6hr, control, replicate 1
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 6 hr
|
control PMNs
|
| Sample_geo_accession | GSM918540
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918540/suppl/GSM918540.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918540/suppl/GSM918540.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918541 | GPL570 |
|
PMN_6hr_ctrl_2
|
polymorphonuclear leukocytes, 6hr, control, replicate 2
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 6 hr
|
control PMNs
|
| Sample_geo_accession | GSM918541
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918541/suppl/GSM918541.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918541/suppl/GSM918541.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918542 | GPL570 |
|
PMN_6hr_ctrl_3
|
polymorphonuclear leukocytes, 6hr, control, replicate 3
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 6 hr
|
control PMNs
|
| Sample_geo_accession | GSM918542
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918542/suppl/GSM918542.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918542/suppl/GSM918542.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918543 | GPL570 |
|
PMN_6hr_ctrl_4
|
polymorphonuclear leukocytes, 6hr, control, replicate 4
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 6 hr
|
control PMNs
|
| Sample_geo_accession | GSM918543
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918543/suppl/GSM918543.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918543/suppl/GSM918543.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918544 | GPL570 |
|
PMN_6hr_LVS_1
|
polymorphonuclear leukocytes, 6hr, LVS-treated, replicate 1
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 6 hr
|
test PMNs
|
| Sample_geo_accession | GSM918544
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918544/suppl/GSM918544.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918544/suppl/GSM918544.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918545 | GPL570 |
|
PMN_6hr_LVS_2
|
polymorphonuclear leukocytes, 6hr, LVS-treated, replicate 2
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 6 hr
|
test PMNs
|
| Sample_geo_accession | GSM918545
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918545/suppl/GSM918545.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918545/suppl/GSM918545.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918546 | GPL570 |
|
PMN_6hr_LVS_3
|
polymorphonuclear leukocytes, 6hr, LVS-treated, replicate 3
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 6 hr
|
test PMNs
|
| Sample_geo_accession | GSM918546
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918546/suppl/GSM918546.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918546/suppl/GSM918546.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918547 | GPL570 |
|
PMN_6hr_LVS_4
|
polymorphonuclear leukocytes, 6hr, LVS-treated, replicate 4
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 6 hr
|
test PMNs
|
| Sample_geo_accession | GSM918547
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918547/suppl/GSM918547.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918547/suppl/GSM918547.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918548 | GPL570 |
|
PMN_12hr_ctrl_1
|
polymorphonuclear leukocytes, 12hr, control, replicate 1
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 12 hr
|
control PMNs
|
| Sample_geo_accession | GSM918548
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918548/suppl/GSM918548.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918548/suppl/GSM918548.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918549 | GPL570 |
|
PMN_12hr_ctrl_2
|
polymorphonuclear leukocytes, 12hr, control, replicate 2
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 12 hr
|
control PMNs
|
| Sample_geo_accession | GSM918549
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918549/suppl/GSM918549.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918549/suppl/GSM918549.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918550 | GPL570 |
|
PMN_12hr_ctrl_3
|
polymorphonuclear leukocytes, 12hr, control, replicate 3
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 12 hr
|
control PMNs
|
| Sample_geo_accession | GSM918550
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918550/suppl/GSM918550.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918550/suppl/GSM918550.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918551 | GPL570 |
|
PMN_12hr_ctrl_4
|
polymorphonuclear leukocytes, 12hr, control, replicate 4
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 12 hr
|
control PMNs
|
| Sample_geo_accession | GSM918551
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918551/suppl/GSM918551.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918551/suppl/GSM918551.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918552 | GPL570 |
|
PMN_12hr_LVS_1
|
polymorphonuclear leukocytes, 12hr, LVS-treated, replicate 1
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 12 hr
|
test PMNs
|
| Sample_geo_accession | GSM918552
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918552/suppl/GSM918552.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918552/suppl/GSM918552.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918553 | GPL570 |
|
PMN_12hr_LVS_2
|
polymorphonuclear leukocytes, 12hr, LVS-treated, replicate 2
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 12 hr
|
test PMNs
|
| Sample_geo_accession | GSM918553
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918553/suppl/GSM918553.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918553/suppl/GSM918553.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918554 | GPL570 |
|
PMN_12hr_LVS_3
|
polymorphonuclear leukocytes, 12hr, LVS-treated, replicate 3
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 12 hr
|
test PMNs
|
| Sample_geo_accession | GSM918554
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918554/suppl/GSM918554.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918554/suppl/GSM918554.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918555 | GPL570 |
|
PMN_12hr_LVS_4
|
polymorphonuclear leukocytes, 12hr, LVS-treated, replicate 4
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 12 hr
|
test PMNs
|
| Sample_geo_accession | GSM918555
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918555/suppl/GSM918555.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918555/suppl/GSM918555.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918556 | GPL570 |
|
PMN_24hr_ctrl_1
|
polymorphonuclear leukocytes, 24hr, control, replicate 1
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 24 hr
|
control PMNs
|
| Sample_geo_accession | GSM918556
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918556/suppl/GSM918556.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918556/suppl/GSM918556.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918557 | GPL570 |
|
PMN_24hr_ctrl_2
|
polymorphonuclear leukocytes, 24hr, control, replicate 2
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 24 hr
|
control PMNs
|
| Sample_geo_accession | GSM918557
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918557/suppl/GSM918557.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918557/suppl/GSM918557.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918558 | GPL570 |
|
PMN_24hr_ctrl_3
|
polymorphonuclear leukocytes, 24hr, control, replicate 3
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 24 hr
|
control PMNs
|
| Sample_geo_accession | GSM918558
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918558/suppl/GSM918558.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918558/suppl/GSM918558.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918559 | GPL570 |
|
PMN_24hr_ctrl_4
|
polymorphonuclear leukocytes, 24hr, control, replicate 4
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 24 hr
|
control PMNs
|
| Sample_geo_accession | GSM918559
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918559/suppl/GSM918559.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918559/suppl/GSM918559.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918560 | GPL570 |
|
PMN_24hr_LVS_1
|
polymorphonuclear leukocytes, 24hr, LVS-treated, replicate 1
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 24 hr
|
test PMNs
|
| Sample_geo_accession | GSM918560
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918560/suppl/GSM918560.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918560/suppl/GSM918560.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918561 | GPL570 |
|
PMN_24hr_LVS_2
|
polymorphonuclear leukocytes, 24hr, LVS-treated, replicate 2
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 24 hr
|
test PMNs
|
| Sample_geo_accession | GSM918561
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918561/suppl/GSM918561.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918561/suppl/GSM918561.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918562 | GPL570 |
|
PMN_24hr_LVS_3
|
polymorphonuclear leukocytes, 24hr, LVS-treated, replicate 3
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 24 hr
|
test PMNs
|
| Sample_geo_accession | GSM918562
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918562/suppl/GSM918562.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918562/suppl/GSM918562.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918563 | GPL570 |
|
PMN_24hr_LVS_4
|
polymorphonuclear leukocytes, 24hr, LVS-treated, replicate 4
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 24 hr
|
test PMNs
|
| Sample_geo_accession | GSM918563
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918563/suppl/GSM918563.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918563/suppl/GSM918563.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918564 | GPL570 |
|
PMN_48hr_ctrl_1
|
polymorphonuclear leukocytes, 48hr, control, replicate 1
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 48 hr
|
control PMNs
|
| Sample_geo_accession | GSM918564
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918564/suppl/GSM918564.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918564/suppl/GSM918564.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918565 | GPL570 |
|
PMN_48hr_ctrl_2
|
polymorphonuclear leukocytes, 48hr, control, replicate 2
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 48 hr
|
control PMNs
|
| Sample_geo_accession | GSM918565
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918565/suppl/GSM918565.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918565/suppl/GSM918565.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918566 | GPL570 |
|
PMN_48hr_ctrl_3
|
polymorphonuclear leukocytes, 48hr, control, replicate 3
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 48 hr
|
control PMNs
|
| Sample_geo_accession | GSM918566
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918566/suppl/GSM918566.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918566/suppl/GSM918566.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918567 | GPL570 |
|
PMN_48hr_ctrl_4
|
polymorphonuclear leukocytes, 48hr, control, replicate 4
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: control PMNs
time: 48 hr
|
control PMNs
|
| Sample_geo_accession | GSM918567
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918567/suppl/GSM918567.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918567/suppl/GSM918567.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918568 | GPL570 |
|
PMN_48hr_LVS_1
|
polymorphonuclear leukocytes, 48hr, LVS-treated, replicate 1
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 48 hr
|
test PMNs
|
| Sample_geo_accession | GSM918568
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918568/suppl/GSM918568.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918568/suppl/GSM918568.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918569 | GPL570 |
|
PMN_48hr_LVS_2
|
polymorphonuclear leukocytes, 48hr, LVS-treated, replicate 2
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 48 hr
|
test PMNs
|
| Sample_geo_accession | GSM918569
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918569/suppl/GSM918569.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918569/suppl/GSM918569.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918570 | GPL570 |
|
PMN_48hr_LVS_3
|
polymorphonuclear leukocytes, 48hr, LVS-treated, replicate 3
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 48 hr
|
test PMNs
|
| Sample_geo_accession | GSM918570
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918570/suppl/GSM918570.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918570/suppl/GSM918570.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
GSM918571 | GPL570 |
|
PMN_48hr_LVS_4
|
polymorphonuclear leukocytes, 48hr, LVS-treated, replicate 4
|
cell type: polymorphonuclear leukocytes
f. tularensis exposure status: test PMNs
time: 48 hr
|
test PMNs
|
| Sample_geo_accession | GSM918571
| | Sample_status | Public on Oct 22 2012
| | Sample_submission_date | Apr 19 2012
| | Sample_last_update_date | Oct 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors. PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C. Untreated PMNs serve as controls.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
| | Sample_hyb_protocol | cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using an Affymetrix scanner.
| | Sample_data_processing | Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table). All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 500 in at least one group. For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples. At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Addie,,Whitney
| | Sample_contact_email | awhitney@niaid.nih.gov
| | Sample_contact_laboratory | DeLeo
| | Sample_contact_department | LHBP
| | Sample_contact_institute | NIH/NIAID/RML
| | Sample_contact_address | 903 S 4th St
| | Sample_contact_city | Hamilton
| | Sample_contact_state | MT
| | Sample_contact_zip/postal_code | 59840
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918571/suppl/GSM918571.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM918nnn/GSM918571/suppl/GSM918571.CHP.gz
| | Sample_series_id | GSE37416
| | Sample_data_row_count | 54675
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
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