Search results for the GEO ID: GSE8515  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM211500 | GPL96 |
|
Control, Rep1
|
Control, biological replicate 1
|
Human monocyte-derived macrophages obtained from peripheral blood mononuclear cells
|
Control, biological replicate 1
|
| Sample_geo_accession | GSM211500
| | Sample_status | Public on Sep 15 2007
| | Sample_submission_date | Jul 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Just before the experiment with cytokines the medium was changed to DMEM containing 0.5% of pooled human serum and the cells were stimulated with IL-1 (15 ng/ml), or IL-6 (25 ng/ml) for the period of 4 h. These rather low concentrations of cytokines that may occur in vivo were selected in preliminary trials as sufficient to stimulate the expression of manganese superoxide dismutase (MnSOD).
| | Sample_growth_protocol_ch1 | Human monocyte-derived macrophages (hMDMs) were obtained from peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from human blood of 7 healthy donors using a Ficoll-Paque (Pharmacia, Uppsala, Sweden) density gradient. Cells from each donor were split into three aliquots to stimulate them later with a mock stimulant, IL-1 and IL-6 and plated at 4x107 in PrimariaTM 25cm2 cell culture flasks with vented caps (Becton Dickinson, Franklin Lakes, NJ, USA) in RPMI1640 (Invitrogen) supplemented with 2mM L-glutamine, 50 g/ml gentamycin (Sigma), and 10% pooled heat-inactivated human AB serum. After 24 h, non-adherent PBMCs were removed by washing with complete medium, and adherent cells were cultured in this medium for 7 days with fresh medium changed every 2 days. The MDMs phenotype was controlled, after non-enzymatic detachment of cells, by immunofluorescent staining of CD14 (clone: TÜK4, DakoCytomation Denmark A/S, Glostrup, Denmark), CD16 (clone: DJ130c, DakoCytomation), CD11b (clone: ICRF44, Becton Dickinson and Co., Franklin Lakes, USA), and CD209 (clone: DCN46, Becton Dickinson) and subsequent flow cytometry analysis. The routine procedure used in our laboratory yields cells positive in at least 90% for the first three markers and less than 1% for CD209. It should be added that the adherent cells acquire typical macrophage morphology and extensive phagocytic activity against live Staphylococcus aureus and apoptotic neutrophils. Resting (non-stimulated) cells do not produce proinflammatory cytokines: IL-1, TNF-a or IL-6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated from unstimulated (control) and cytokine-stimulated cells by Chomczynski and Sacchi procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following labeling, samples were hybridized to the GeneChip Test3 array (Affymetrix, Santa Clara, CA) for quality control. Fragmented cRNA (15 μg) was used for hybridization to the GeneChip Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA). Arrays were washed and stained with streptavidin-phycoerythrin (Merck, Darmstadt, Germany) in Fluidic Station 400 (Affymetrix, Santa Clara, CA) according to standard protocol of the manufacturer.
| | Sample_scan_protocol | The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was normalized by dChip 2006 (MBEI)
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marcin,,Piechota
| | Sample_contact_email | marpiech@if-pan.krakow.pl
| | Sample_contact_phone | (+4812) 6623328
| | Sample_contact_department | Molecular Neuropharmacology
| | Sample_contact_institute | Institute of Pharmacology PAS
| | Sample_contact_address | Smetna 12
| | Sample_contact_city | Krakow
| | Sample_contact_zip/postal_code | 31-343
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM211nnn/GSM211500/suppl/GSM211500.CEL.gz
| | Sample_series_id | GSE8515
| | Sample_data_row_count | 22283
| | |
|
GSM211501 | GPL96 |
|
Control, Rep2
|
Control, biological replicate 2
|
Human monocyte-derived macrophages obtained from peripheral blood mononuclear cells
|
Control, biological replicate 2
|
| Sample_geo_accession | GSM211501
| | Sample_status | Public on Sep 15 2007
| | Sample_submission_date | Jul 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Just before the experiment with cytokines the medium was changed to DMEM containing 0.5% of pooled human serum and the cells were stimulated with IL-1 (15 ng/ml), or IL-6 (25 ng/ml) for the period of 4 h. These rather low concentrations of cytokines that may occur in vivo were selected in preliminary trials as sufficient to stimulate the expression of manganese superoxide dismutase (MnSOD).
| | Sample_growth_protocol_ch1 | Human monocyte-derived macrophages (hMDMs) were obtained from peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from human blood of 7 healthy donors using a Ficoll-Paque (Pharmacia, Uppsala, Sweden) density gradient. Cells from each donor were split into three aliquots to stimulate them later with a mock stimulant, IL-1 and IL-6 and plated at 4x107 in PrimariaTM 25cm2 cell culture flasks with vented caps (Becton Dickinson, Franklin Lakes, NJ, USA) in RPMI1640 (Invitrogen) supplemented with 2mM L-glutamine, 50 g/ml gentamycin (Sigma), and 10% pooled heat-inactivated human AB serum. After 24 h, non-adherent PBMCs were removed by washing with complete medium, and adherent cells were cultured in this medium for 7 days with fresh medium changed every 2 days. The MDMs phenotype was controlled, after non-enzymatic detachment of cells, by immunofluorescent staining of CD14 (clone: TÜK4, DakoCytomation Denmark A/S, Glostrup, Denmark), CD16 (clone: DJ130c, DakoCytomation), CD11b (clone: ICRF44, Becton Dickinson and Co., Franklin Lakes, USA), and CD209 (clone: DCN46, Becton Dickinson) and subsequent flow cytometry analysis. The routine procedure used in our laboratory yields cells positive in at least 90% for the first three markers and less than 1% for CD209. It should be added that the adherent cells acquire typical macrophage morphology and extensive phagocytic activity against live Staphylococcus aureus and apoptotic neutrophils. Resting (non-stimulated) cells do not produce proinflammatory cytokines: IL-1, TNF-a or IL-6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated from unstimulated (control) and cytokine-stimulated cells by Chomczynski and Sacchi procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following labeling, samples were hybridized to the GeneChip Test3 array (Affymetrix, Santa Clara, CA) for quality control. Fragmented cRNA (15 μg) was used for hybridization to the GeneChip Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA). Arrays were washed and stained with streptavidin-phycoerythrin (Merck, Darmstadt, Germany) in Fluidic Station 400 (Affymetrix, Santa Clara, CA) according to standard protocol of the manufacturer.
| | Sample_scan_protocol | The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was normalized by dChip 2006 (MBEI)
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marcin,,Piechota
| | Sample_contact_email | marpiech@if-pan.krakow.pl
| | Sample_contact_phone | (+4812) 6623328
| | Sample_contact_department | Molecular Neuropharmacology
| | Sample_contact_institute | Institute of Pharmacology PAS
| | Sample_contact_address | Smetna 12
| | Sample_contact_city | Krakow
| | Sample_contact_zip/postal_code | 31-343
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM211nnn/GSM211501/suppl/GSM211501.CEL.gz
| | Sample_series_id | GSE8515
| | Sample_data_row_count | 22283
| | |
|
GSM211502 | GPL96 |
|
Control, Rep3
|
Control, biological replicate 3
|
Human monocyte-derived macrophages obtained from peripheral blood mononuclear cells
|
Control, biological replicate 3
|
| Sample_geo_accession | GSM211502
| | Sample_status | Public on Sep 15 2007
| | Sample_submission_date | Jul 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Just before the experiment with cytokines the medium was changed to DMEM containing 0.5% of pooled human serum and the cells were stimulated with IL-1 (15 ng/ml), or IL-6 (25 ng/ml) for the period of 4 h. These rather low concentrations of cytokines that may occur in vivo were selected in preliminary trials as sufficient to stimulate the expression of manganese superoxide dismutase (MnSOD).
| | Sample_growth_protocol_ch1 | Human monocyte-derived macrophages (hMDMs) were obtained from peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from human blood of 7 healthy donors using a Ficoll-Paque (Pharmacia, Uppsala, Sweden) density gradient. Cells from each donor were split into three aliquots to stimulate them later with a mock stimulant, IL-1 and IL-6 and plated at 4x107 in PrimariaTM 25cm2 cell culture flasks with vented caps (Becton Dickinson, Franklin Lakes, NJ, USA) in RPMI1640 (Invitrogen) supplemented with 2mM L-glutamine, 50 g/ml gentamycin (Sigma), and 10% pooled heat-inactivated human AB serum. After 24 h, non-adherent PBMCs were removed by washing with complete medium, and adherent cells were cultured in this medium for 7 days with fresh medium changed every 2 days. The MDMs phenotype was controlled, after non-enzymatic detachment of cells, by immunofluorescent staining of CD14 (clone: TÜK4, DakoCytomation Denmark A/S, Glostrup, Denmark), CD16 (clone: DJ130c, DakoCytomation), CD11b (clone: ICRF44, Becton Dickinson and Co., Franklin Lakes, USA), and CD209 (clone: DCN46, Becton Dickinson) and subsequent flow cytometry analysis. The routine procedure used in our laboratory yields cells positive in at least 90% for the first three markers and less than 1% for CD209. It should be added that the adherent cells acquire typical macrophage morphology and extensive phagocytic activity against live Staphylococcus aureus and apoptotic neutrophils. Resting (non-stimulated) cells do not produce proinflammatory cytokines: IL-1, TNF-a or IL-6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated from unstimulated (control) and cytokine-stimulated cells by Chomczynski and Sacchi procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following labeling, samples were hybridized to the GeneChip Test3 array (Affymetrix, Santa Clara, CA) for quality control. Fragmented cRNA (15 μg) was used for hybridization to the GeneChip Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA). Arrays were washed and stained with streptavidin-phycoerythrin (Merck, Darmstadt, Germany) in Fluidic Station 400 (Affymetrix, Santa Clara, CA) according to standard protocol of the manufacturer.
| | Sample_scan_protocol | The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was normalized by dChip 2006 (MBEI)
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marcin,,Piechota
| | Sample_contact_email | marpiech@if-pan.krakow.pl
| | Sample_contact_phone | (+4812) 6623328
| | Sample_contact_department | Molecular Neuropharmacology
| | Sample_contact_institute | Institute of Pharmacology PAS
| | Sample_contact_address | Smetna 12
| | Sample_contact_city | Krakow
| | Sample_contact_zip/postal_code | 31-343
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM211nnn/GSM211502/suppl/GSM211502.CEL.gz
| | Sample_series_id | GSE8515
| | Sample_data_row_count | 22283
| | |
|
GSM211503 | GPL96 |
|
Control, Rep4
|
Control, biological replicate 4
|
Human monocyte-derived macrophages obtained from peripheral blood mononuclear cells
|
Control, biological replicate 4
|
| Sample_geo_accession | GSM211503
| | Sample_status | Public on Sep 15 2007
| | Sample_submission_date | Jul 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Just before the experiment with cytokines the medium was changed to DMEM containing 0.5% of pooled human serum and the cells were stimulated with IL-1 (15 ng/ml), or IL-6 (25 ng/ml) for the period of 4 h. These rather low concentrations of cytokines that may occur in vivo were selected in preliminary trials as sufficient to stimulate the expression of manganese superoxide dismutase (MnSOD).
| | Sample_growth_protocol_ch1 | Human monocyte-derived macrophages (hMDMs) were obtained from peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from human blood of 7 healthy donors using a Ficoll-Paque (Pharmacia, Uppsala, Sweden) density gradient. Cells from each donor were split into three aliquots to stimulate them later with a mock stimulant, IL-1 and IL-6 and plated at 4x107 in PrimariaTM 25cm2 cell culture flasks with vented caps (Becton Dickinson, Franklin Lakes, NJ, USA) in RPMI1640 (Invitrogen) supplemented with 2mM L-glutamine, 50 g/ml gentamycin (Sigma), and 10% pooled heat-inactivated human AB serum. After 24 h, non-adherent PBMCs were removed by washing with complete medium, and adherent cells were cultured in this medium for 7 days with fresh medium changed every 2 days. The MDMs phenotype was controlled, after non-enzymatic detachment of cells, by immunofluorescent staining of CD14 (clone: TÜK4, DakoCytomation Denmark A/S, Glostrup, Denmark), CD16 (clone: DJ130c, DakoCytomation), CD11b (clone: ICRF44, Becton Dickinson and Co., Franklin Lakes, USA), and CD209 (clone: DCN46, Becton Dickinson) and subsequent flow cytometry analysis. The routine procedure used in our laboratory yields cells positive in at least 90% for the first three markers and less than 1% for CD209. It should be added that the adherent cells acquire typical macrophage morphology and extensive phagocytic activity against live Staphylococcus aureus and apoptotic neutrophils. Resting (non-stimulated) cells do not produce proinflammatory cytokines: IL-1, TNF-a or IL-6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated from unstimulated (control) and cytokine-stimulated cells by Chomczynski and Sacchi procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following labeling, samples were hybridized to the GeneChip Test3 array (Affymetrix, Santa Clara, CA) for quality control. Fragmented cRNA (15 μg) was used for hybridization to the GeneChip Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA). Arrays were washed and stained with streptavidin-phycoerythrin (Merck, Darmstadt, Germany) in Fluidic Station 400 (Affymetrix, Santa Clara, CA) according to standard protocol of the manufacturer.
| | Sample_scan_protocol | The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was normalized by dChip 2006 (MBEI)
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marcin,,Piechota
| | Sample_contact_email | marpiech@if-pan.krakow.pl
| | Sample_contact_phone | (+4812) 6623328
| | Sample_contact_department | Molecular Neuropharmacology
| | Sample_contact_institute | Institute of Pharmacology PAS
| | Sample_contact_address | Smetna 12
| | Sample_contact_city | Krakow
| | Sample_contact_zip/postal_code | 31-343
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM211nnn/GSM211503/suppl/GSM211503.CEL.gz
| | Sample_series_id | GSE8515
| | Sample_data_row_count | 22283
| | |
|
GSM211504 | GPL96 |
|
Control, Rep5
|
Control, biological replicate 5
|
Human monocyte-derived macrophages obtained from peripheral blood mononuclear cells
|
Control, biological replicate 5
|
| Sample_geo_accession | GSM211504
| | Sample_status | Public on Sep 15 2007
| | Sample_submission_date | Jul 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Just before the experiment with cytokines the medium was changed to DMEM containing 0.5% of pooled human serum and the cells were stimulated with IL-1 (15 ng/ml), or IL-6 (25 ng/ml) for the period of 4 h. These rather low concentrations of cytokines that may occur in vivo were selected in preliminary trials as sufficient to stimulate the expression of manganese superoxide dismutase (MnSOD).
| | Sample_growth_protocol_ch1 | Human monocyte-derived macrophages (hMDMs) were obtained from peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from human blood of 7 healthy donors using a Ficoll-Paque (Pharmacia, Uppsala, Sweden) density gradient. Cells from each donor were split into three aliquots to stimulate them later with a mock stimulant, IL-1 and IL-6 and plated at 4x107 in PrimariaTM 25cm2 cell culture flasks with vented caps (Becton Dickinson, Franklin Lakes, NJ, USA) in RPMI1640 (Invitrogen) supplemented with 2mM L-glutamine, 50 g/ml gentamycin (Sigma), and 10% pooled heat-inactivated human AB serum. After 24 h, non-adherent PBMCs were removed by washing with complete medium, and adherent cells were cultured in this medium for 7 days with fresh medium changed every 2 days. The MDMs phenotype was controlled, after non-enzymatic detachment of cells, by immunofluorescent staining of CD14 (clone: TÜK4, DakoCytomation Denmark A/S, Glostrup, Denmark), CD16 (clone: DJ130c, DakoCytomation), CD11b (clone: ICRF44, Becton Dickinson and Co., Franklin Lakes, USA), and CD209 (clone: DCN46, Becton Dickinson) and subsequent flow cytometry analysis. The routine procedure used in our laboratory yields cells positive in at least 90% for the first three markers and less than 1% for CD209. It should be added that the adherent cells acquire typical macrophage morphology and extensive phagocytic activity against live Staphylococcus aureus and apoptotic neutrophils. Resting (non-stimulated) cells do not produce proinflammatory cytokines: IL-1, TNF-a or IL-6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated from unstimulated (control) and cytokine-stimulated cells by Chomczynski and Sacchi procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following labeling, samples were hybridized to the GeneChip Test3 array (Affymetrix, Santa Clara, CA) for quality control. Fragmented cRNA (15 μg) was used for hybridization to the GeneChip Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA). Arrays were washed and stained with streptavidin-phycoerythrin (Merck, Darmstadt, Germany) in Fluidic Station 400 (Affymetrix, Santa Clara, CA) according to standard protocol of the manufacturer.
| | Sample_scan_protocol | The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was normalized by dChip 2006 (MBEI)
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marcin,,Piechota
| | Sample_contact_email | marpiech@if-pan.krakow.pl
| | Sample_contact_phone | (+4812) 6623328
| | Sample_contact_department | Molecular Neuropharmacology
| | Sample_contact_institute | Institute of Pharmacology PAS
| | Sample_contact_address | Smetna 12
| | Sample_contact_city | Krakow
| | Sample_contact_zip/postal_code | 31-343
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM211nnn/GSM211504/suppl/GSM211504.CEL.gz
| | Sample_series_id | GSE8515
| | Sample_data_row_count | 22283
| | |
|
GSM211505 | GPL96 |
|
IL-1, Rep1
|
Interleukin 1 replicate 1
|
Human monocyte-derived macrophages obtained from peripheral blood mononuclear cells
|
Interleukin 1 replicate 1
|
| Sample_geo_accession | GSM211505
| | Sample_status | Public on Sep 15 2007
| | Sample_submission_date | Jul 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Just before the experiment with cytokines the medium was changed to DMEM containing 0.5% of pooled human serum and the cells were stimulated with IL-1 (15 ng/ml), or IL-6 (25 ng/ml) for the period of 4 h. These rather low concentrations of cytokines that may occur in vivo were selected in preliminary trials as sufficient to stimulate the expression of manganese superoxide dismutase (MnSOD).
| | Sample_growth_protocol_ch1 | Human monocyte-derived macrophages (hMDMs) were obtained from peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from human blood of 7 healthy donors using a Ficoll-Paque (Pharmacia, Uppsala, Sweden) density gradient. Cells from each donor were split into three aliquots to stimulate them later with a mock stimulant, IL-1 and IL-6 and plated at 4x107 in PrimariaTM 25cm2 cell culture flasks with vented caps (Becton Dickinson, Franklin Lakes, NJ, USA) in RPMI1640 (Invitrogen) supplemented with 2mM L-glutamine, 50 g/ml gentamycin (Sigma), and 10% pooled heat-inactivated human AB serum. After 24 h, non-adherent PBMCs were removed by washing with complete medium, and adherent cells were cultured in this medium for 7 days with fresh medium changed every 2 days. The MDMs phenotype was controlled, after non-enzymatic detachment of cells, by immunofluorescent staining of CD14 (clone: TÜK4, DakoCytomation Denmark A/S, Glostrup, Denmark), CD16 (clone: DJ130c, DakoCytomation), CD11b (clone: ICRF44, Becton Dickinson and Co., Franklin Lakes, USA), and CD209 (clone: DCN46, Becton Dickinson) and subsequent flow cytometry analysis. The routine procedure used in our laboratory yields cells positive in at least 90% for the first three markers and less than 1% for CD209. It should be added that the adherent cells acquire typical macrophage morphology and extensive phagocytic activity against live Staphylococcus aureus and apoptotic neutrophils. Resting (non-stimulated) cells do not produce proinflammatory cytokines: IL-1, TNF-a or IL-6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated from unstimulated (control) and cytokine-stimulated cells by Chomczynski and Sacchi procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following labeling, samples were hybridized to the GeneChip Test3 array (Affymetrix, Santa Clara, CA) for quality control. Fragmented cRNA (15 μg) was used for hybridization to the GeneChip Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA). Arrays were washed and stained with streptavidin-phycoerythrin (Merck, Darmstadt, Germany) in Fluidic Station 400 (Affymetrix, Santa Clara, CA) according to standard protocol of the manufacturer.
| | Sample_scan_protocol | The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was normalized by dChip 2006 (MBEI)
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marcin,,Piechota
| | Sample_contact_email | marpiech@if-pan.krakow.pl
| | Sample_contact_phone | (+4812) 6623328
| | Sample_contact_department | Molecular Neuropharmacology
| | Sample_contact_institute | Institute of Pharmacology PAS
| | Sample_contact_address | Smetna 12
| | Sample_contact_city | Krakow
| | Sample_contact_zip/postal_code | 31-343
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM211nnn/GSM211505/suppl/GSM211505.CEL.gz
| | Sample_series_id | GSE8515
| | Sample_data_row_count | 22283
| | |
|
GSM211506 | GPL96 |
|
IL-1, Rep2
|
Interleukin 1 replicate 2
|
Human monocyte-derived macrophages obtained from peripheral blood mononuclear cells
|
Interleukin 1 replicate 2
|
| Sample_geo_accession | GSM211506
| | Sample_status | Public on Sep 15 2007
| | Sample_submission_date | Jul 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Just before the experiment with cytokines the medium was changed to DMEM containing 0.5% of pooled human serum and the cells were stimulated with IL-1 (15 ng/ml), or IL-6 (25 ng/ml) for the period of 4 h. These rather low concentrations of cytokines that may occur in vivo were selected in preliminary trials as sufficient to stimulate the expression of manganese superoxide dismutase (MnSOD).
| | Sample_growth_protocol_ch1 | Human monocyte-derived macrophages (hMDMs) were obtained from peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from human blood of 7 healthy donors using a Ficoll-Paque (Pharmacia, Uppsala, Sweden) density gradient. Cells from each donor were split into three aliquots to stimulate them later with a mock stimulant, IL-1 and IL-6 and plated at 4x107 in PrimariaTM 25cm2 cell culture flasks with vented caps (Becton Dickinson, Franklin Lakes, NJ, USA) in RPMI1640 (Invitrogen) supplemented with 2mM L-glutamine, 50 g/ml gentamycin (Sigma), and 10% pooled heat-inactivated human AB serum. After 24 h, non-adherent PBMCs were removed by washing with complete medium, and adherent cells were cultured in this medium for 7 days with fresh medium changed every 2 days. The MDMs phenotype was controlled, after non-enzymatic detachment of cells, by immunofluorescent staining of CD14 (clone: TÜK4, DakoCytomation Denmark A/S, Glostrup, Denmark), CD16 (clone: DJ130c, DakoCytomation), CD11b (clone: ICRF44, Becton Dickinson and Co., Franklin Lakes, USA), and CD209 (clone: DCN46, Becton Dickinson) and subsequent flow cytometry analysis. The routine procedure used in our laboratory yields cells positive in at least 90% for the first three markers and less than 1% for CD209. It should be added that the adherent cells acquire typical macrophage morphology and extensive phagocytic activity against live Staphylococcus aureus and apoptotic neutrophils. Resting (non-stimulated) cells do not produce proinflammatory cytokines: IL-1, TNF-a or IL-6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated from unstimulated (control) and cytokine-stimulated cells by Chomczynski and Sacchi procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following labeling, samples were hybridized to the GeneChip Test3 array (Affymetrix, Santa Clara, CA) for quality control. Fragmented cRNA (15 μg) was used for hybridization to the GeneChip Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA). Arrays were washed and stained with streptavidin-phycoerythrin (Merck, Darmstadt, Germany) in Fluidic Station 400 (Affymetrix, Santa Clara, CA) according to standard protocol of the manufacturer.
| | Sample_scan_protocol | The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was normalized by dChip 2006 (MBEI)
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marcin,,Piechota
| | Sample_contact_email | marpiech@if-pan.krakow.pl
| | Sample_contact_phone | (+4812) 6623328
| | Sample_contact_department | Molecular Neuropharmacology
| | Sample_contact_institute | Institute of Pharmacology PAS
| | Sample_contact_address | Smetna 12
| | Sample_contact_city | Krakow
| | Sample_contact_zip/postal_code | 31-343
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM211nnn/GSM211506/suppl/GSM211506.CEL.gz
| | Sample_series_id | GSE8515
| | Sample_data_row_count | 22283
| | |
|
GSM211507 | GPL96 |
|
IL-1, Rep3
|
Interleukin 1 replicate 3
|
Human monocyte-derived macrophages obtained from peripheral blood mononuclear cells
|
Interleukin 1 replicate 3
|
| Sample_geo_accession | GSM211507
| | Sample_status | Public on Sep 15 2007
| | Sample_submission_date | Jul 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Just before the experiment with cytokines the medium was changed to DMEM containing 0.5% of pooled human serum and the cells were stimulated with IL-1 (15 ng/ml), or IL-6 (25 ng/ml) for the period of 4 h. These rather low concentrations of cytokines that may occur in vivo were selected in preliminary trials as sufficient to stimulate the expression of manganese superoxide dismutase (MnSOD).
| | Sample_growth_protocol_ch1 | Human monocyte-derived macrophages (hMDMs) were obtained from peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from human blood of 7 healthy donors using a Ficoll-Paque (Pharmacia, Uppsala, Sweden) density gradient. Cells from each donor were split into three aliquots to stimulate them later with a mock stimulant, IL-1 and IL-6 and plated at 4x107 in PrimariaTM 25cm2 cell culture flasks with vented caps (Becton Dickinson, Franklin Lakes, NJ, USA) in RPMI1640 (Invitrogen) supplemented with 2mM L-glutamine, 50 g/ml gentamycin (Sigma), and 10% pooled heat-inactivated human AB serum. After 24 h, non-adherent PBMCs were removed by washing with complete medium, and adherent cells were cultured in this medium for 7 days with fresh medium changed every 2 days. The MDMs phenotype was controlled, after non-enzymatic detachment of cells, by immunofluorescent staining of CD14 (clone: TÜK4, DakoCytomation Denmark A/S, Glostrup, Denmark), CD16 (clone: DJ130c, DakoCytomation), CD11b (clone: ICRF44, Becton Dickinson and Co., Franklin Lakes, USA), and CD209 (clone: DCN46, Becton Dickinson) and subsequent flow cytometry analysis. The routine procedure used in our laboratory yields cells positive in at least 90% for the first three markers and less than 1% for CD209. It should be added that the adherent cells acquire typical macrophage morphology and extensive phagocytic activity against live Staphylococcus aureus and apoptotic neutrophils. Resting (non-stimulated) cells do not produce proinflammatory cytokines: IL-1, TNF-a or IL-6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated from unstimulated (control) and cytokine-stimulated cells by Chomczynski and Sacchi procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following labeling, samples were hybridized to the GeneChip Test3 array (Affymetrix, Santa Clara, CA) for quality control. Fragmented cRNA (15 μg) was used for hybridization to the GeneChip Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA). Arrays were washed and stained with streptavidin-phycoerythrin (Merck, Darmstadt, Germany) in Fluidic Station 400 (Affymetrix, Santa Clara, CA) according to standard protocol of the manufacturer.
| | Sample_scan_protocol | The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was normalized by dChip 2006 (MBEI)
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marcin,,Piechota
| | Sample_contact_email | marpiech@if-pan.krakow.pl
| | Sample_contact_phone | (+4812) 6623328
| | Sample_contact_department | Molecular Neuropharmacology
| | Sample_contact_institute | Institute of Pharmacology PAS
| | Sample_contact_address | Smetna 12
| | Sample_contact_city | Krakow
| | Sample_contact_zip/postal_code | 31-343
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM211nnn/GSM211507/suppl/GSM211507.CEL.gz
| | Sample_series_id | GSE8515
| | Sample_data_row_count | 22283
| | |
|
GSM211508 | GPL96 |
|
IL-1, Rep4
|
Interleukin 1 replicate 4
|
Human monocyte-derived macrophages obtained from peripheral blood mononuclear cells
|
Interleukin 1 replicate 4
|
| Sample_geo_accession | GSM211508
| | Sample_status | Public on Sep 15 2007
| | Sample_submission_date | Jul 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Just before the experiment with cytokines the medium was changed to DMEM containing 0.5% of pooled human serum and the cells were stimulated with IL-1 (15 ng/ml), or IL-6 (25 ng/ml) for the period of 4 h. These rather low concentrations of cytokines that may occur in vivo were selected in preliminary trials as sufficient to stimulate the expression of manganese superoxide dismutase (MnSOD).
| | Sample_growth_protocol_ch1 | Human monocyte-derived macrophages (hMDMs) were obtained from peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from human blood of 7 healthy donors using a Ficoll-Paque (Pharmacia, Uppsala, Sweden) density gradient. Cells from each donor were split into three aliquots to stimulate them later with a mock stimulant, IL-1 and IL-6 and plated at 4x107 in PrimariaTM 25cm2 cell culture flasks with vented caps (Becton Dickinson, Franklin Lakes, NJ, USA) in RPMI1640 (Invitrogen) supplemented with 2mM L-glutamine, 50 g/ml gentamycin (Sigma), and 10% pooled heat-inactivated human AB serum. After 24 h, non-adherent PBMCs were removed by washing with complete medium, and adherent cells were cultured in this medium for 7 days with fresh medium changed every 2 days. The MDMs phenotype was controlled, after non-enzymatic detachment of cells, by immunofluorescent staining of CD14 (clone: TÜK4, DakoCytomation Denmark A/S, Glostrup, Denmark), CD16 (clone: DJ130c, DakoCytomation), CD11b (clone: ICRF44, Becton Dickinson and Co., Franklin Lakes, USA), and CD209 (clone: DCN46, Becton Dickinson) and subsequent flow cytometry analysis. The routine procedure used in our laboratory yields cells positive in at least 90% for the first three markers and less than 1% for CD209. It should be added that the adherent cells acquire typical macrophage morphology and extensive phagocytic activity against live Staphylococcus aureus and apoptotic neutrophils. Resting (non-stimulated) cells do not produce proinflammatory cytokines: IL-1, TNF-a or IL-6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated from unstimulated (control) and cytokine-stimulated cells by Chomczynski and Sacchi procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following labeling, samples were hybridized to the GeneChip Test3 array (Affymetrix, Santa Clara, CA) for quality control. Fragmented cRNA (15 μg) was used for hybridization to the GeneChip Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA). Arrays were washed and stained with streptavidin-phycoerythrin (Merck, Darmstadt, Germany) in Fluidic Station 400 (Affymetrix, Santa Clara, CA) according to standard protocol of the manufacturer.
| | Sample_scan_protocol | The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was normalized by dChip 2006 (MBEI)
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marcin,,Piechota
| | Sample_contact_email | marpiech@if-pan.krakow.pl
| | Sample_contact_phone | (+4812) 6623328
| | Sample_contact_department | Molecular Neuropharmacology
| | Sample_contact_institute | Institute of Pharmacology PAS
| | Sample_contact_address | Smetna 12
| | Sample_contact_city | Krakow
| | Sample_contact_zip/postal_code | 31-343
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM211nnn/GSM211508/suppl/GSM211508.CEL.gz
| | Sample_series_id | GSE8515
| | Sample_data_row_count | 22283
| | |
|
GSM211509 | GPL96 |
|
IL-1, Rep5
|
Interleukin 1 replicate 5
|
Human monocyte-derived macrophages obtained from peripheral blood mononuclear cells
|
Interleukin 1 replicate 5
|
| Sample_geo_accession | GSM211509
| | Sample_status | Public on Sep 15 2007
| | Sample_submission_date | Jul 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Just before the experiment with cytokines the medium was changed to DMEM containing 0.5% of pooled human serum and the cells were stimulated with IL-1 (15 ng/ml), or IL-6 (25 ng/ml) for the period of 4 h. These rather low concentrations of cytokines that may occur in vivo were selected in preliminary trials as sufficient to stimulate the expression of manganese superoxide dismutase (MnSOD).
| | Sample_growth_protocol_ch1 | Human monocyte-derived macrophages (hMDMs) were obtained from peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from human blood of 7 healthy donors using a Ficoll-Paque (Pharmacia, Uppsala, Sweden) density gradient. Cells from each donor were split into three aliquots to stimulate them later with a mock stimulant, IL-1 and IL-6 and plated at 4x107 in PrimariaTM 25cm2 cell culture flasks with vented caps (Becton Dickinson, Franklin Lakes, NJ, USA) in RPMI1640 (Invitrogen) supplemented with 2mM L-glutamine, 50 g/ml gentamycin (Sigma), and 10% pooled heat-inactivated human AB serum. After 24 h, non-adherent PBMCs were removed by washing with complete medium, and adherent cells were cultured in this medium for 7 days with fresh medium changed every 2 days. The MDMs phenotype was controlled, after non-enzymatic detachment of cells, by immunofluorescent staining of CD14 (clone: TÜK4, DakoCytomation Denmark A/S, Glostrup, Denmark), CD16 (clone: DJ130c, DakoCytomation), CD11b (clone: ICRF44, Becton Dickinson and Co., Franklin Lakes, USA), and CD209 (clone: DCN46, Becton Dickinson) and subsequent flow cytometry analysis. The routine procedure used in our laboratory yields cells positive in at least 90% for the first three markers and less than 1% for CD209. It should be added that the adherent cells acquire typical macrophage morphology and extensive phagocytic activity against live Staphylococcus aureus and apoptotic neutrophils. Resting (non-stimulated) cells do not produce proinflammatory cytokines: IL-1, TNF-a or IL-6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated from unstimulated (control) and cytokine-stimulated cells by Chomczynski and Sacchi procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following labeling, samples were hybridized to the GeneChip Test3 array (Affymetrix, Santa Clara, CA) for quality control. Fragmented cRNA (15 μg) was used for hybridization to the GeneChip Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA). Arrays were washed and stained with streptavidin-phycoerythrin (Merck, Darmstadt, Germany) in Fluidic Station 400 (Affymetrix, Santa Clara, CA) according to standard protocol of the manufacturer.
| | Sample_scan_protocol | The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was normalized by dChip 2006 (MBEI)
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marcin,,Piechota
| | Sample_contact_email | marpiech@if-pan.krakow.pl
| | Sample_contact_phone | (+4812) 6623328
| | Sample_contact_department | Molecular Neuropharmacology
| | Sample_contact_institute | Institute of Pharmacology PAS
| | Sample_contact_address | Smetna 12
| | Sample_contact_city | Krakow
| | Sample_contact_zip/postal_code | 31-343
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM211nnn/GSM211509/suppl/GSM211509.CEL.gz
| | Sample_series_id | GSE8515
| | Sample_data_row_count | 22283
| | |
|
GSM211510 | GPL96 |
|
IL-6, Rep1
|
Interleukin 6 replicate 1
|
Human monocyte-derived macrophages obtained from peripheral blood mononuclear cells
|
Interleukin 6 replicate 1
|
| Sample_geo_accession | GSM211510
| | Sample_status | Public on Sep 15 2007
| | Sample_submission_date | Jul 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Just before the experiment with cytokines the medium was changed to DMEM containing 0.5% of pooled human serum and the cells were stimulated with IL-1 (15 ng/ml), or IL-6 (25 ng/ml) for the period of 4 h. These rather low concentrations of cytokines that may occur in vivo were selected in preliminary trials as sufficient to stimulate the expression of manganese superoxide dismutase (MnSOD).
| | Sample_growth_protocol_ch1 | Human monocyte-derived macrophages (hMDMs) were obtained from peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from human blood of 7 healthy donors using a Ficoll-Paque (Pharmacia, Uppsala, Sweden) density gradient. Cells from each donor were split into three aliquots to stimulate them later with a mock stimulant, IL-1 and IL-6 and plated at 4x107 in PrimariaTM 25cm2 cell culture flasks with vented caps (Becton Dickinson, Franklin Lakes, NJ, USA) in RPMI1640 (Invitrogen) supplemented with 2mM L-glutamine, 50 g/ml gentamycin (Sigma), and 10% pooled heat-inactivated human AB serum. After 24 h, non-adherent PBMCs were removed by washing with complete medium, and adherent cells were cultured in this medium for 7 days with fresh medium changed every 2 days. The MDMs phenotype was controlled, after non-enzymatic detachment of cells, by immunofluorescent staining of CD14 (clone: TÜK4, DakoCytomation Denmark A/S, Glostrup, Denmark), CD16 (clone: DJ130c, DakoCytomation), CD11b (clone: ICRF44, Becton Dickinson and Co., Franklin Lakes, USA), and CD209 (clone: DCN46, Becton Dickinson) and subsequent flow cytometry analysis. The routine procedure used in our laboratory yields cells positive in at least 90% for the first three markers and less than 1% for CD209. It should be added that the adherent cells acquire typical macrophage morphology and extensive phagocytic activity against live Staphylococcus aureus and apoptotic neutrophils. Resting (non-stimulated) cells do not produce proinflammatory cytokines: IL-1, TNF-a or IL-6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated from unstimulated (control) and cytokine-stimulated cells by Chomczynski and Sacchi procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following labeling, samples were hybridized to the GeneChip Test3 array (Affymetrix, Santa Clara, CA) for quality control. Fragmented cRNA (15 μg) was used for hybridization to the GeneChip Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA). Arrays were washed and stained with streptavidin-phycoerythrin (Merck, Darmstadt, Germany) in Fluidic Station 400 (Affymetrix, Santa Clara, CA) according to standard protocol of the manufacturer.
| | Sample_scan_protocol | The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was normalized by dChip 2006 (MBEI)
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marcin,,Piechota
| | Sample_contact_email | marpiech@if-pan.krakow.pl
| | Sample_contact_phone | (+4812) 6623328
| | Sample_contact_department | Molecular Neuropharmacology
| | Sample_contact_institute | Institute of Pharmacology PAS
| | Sample_contact_address | Smetna 12
| | Sample_contact_city | Krakow
| | Sample_contact_zip/postal_code | 31-343
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM211nnn/GSM211510/suppl/GSM211510.CEL.gz
| | Sample_series_id | GSE8515
| | Sample_data_row_count | 22283
| | |
|
GSM211511 | GPL96 |
|
IL-6, Rep2
|
Interleukin 6 replicate 2
|
Human monocyte-derived macrophages obtained from peripheral blood mononuclear cells
|
Interleukin 6 replicate 2
|
| Sample_geo_accession | GSM211511
| | Sample_status | Public on Sep 15 2007
| | Sample_submission_date | Jul 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Just before the experiment with cytokines the medium was changed to DMEM containing 0.5% of pooled human serum and the cells were stimulated with IL-1 (15 ng/ml), or IL-6 (25 ng/ml) for the period of 4 h. These rather low concentrations of cytokines that may occur in vivo were selected in preliminary trials as sufficient to stimulate the expression of manganese superoxide dismutase (MnSOD).
| | Sample_growth_protocol_ch1 | Human monocyte-derived macrophages (hMDMs) were obtained from peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from human blood of 7 healthy donors using a Ficoll-Paque (Pharmacia, Uppsala, Sweden) density gradient. Cells from each donor were split into three aliquots to stimulate them later with a mock stimulant, IL-1 and IL-6 and plated at 4x107 in PrimariaTM 25cm2 cell culture flasks with vented caps (Becton Dickinson, Franklin Lakes, NJ, USA) in RPMI1640 (Invitrogen) supplemented with 2mM L-glutamine, 50 g/ml gentamycin (Sigma), and 10% pooled heat-inactivated human AB serum. After 24 h, non-adherent PBMCs were removed by washing with complete medium, and adherent cells were cultured in this medium for 7 days with fresh medium changed every 2 days. The MDMs phenotype was controlled, after non-enzymatic detachment of cells, by immunofluorescent staining of CD14 (clone: TÜK4, DakoCytomation Denmark A/S, Glostrup, Denmark), CD16 (clone: DJ130c, DakoCytomation), CD11b (clone: ICRF44, Becton Dickinson and Co., Franklin Lakes, USA), and CD209 (clone: DCN46, Becton Dickinson) and subsequent flow cytometry analysis. The routine procedure used in our laboratory yields cells positive in at least 90% for the first three markers and less than 1% for CD209. It should be added that the adherent cells acquire typical macrophage morphology and extensive phagocytic activity against live Staphylococcus aureus and apoptotic neutrophils. Resting (non-stimulated) cells do not produce proinflammatory cytokines: IL-1, TNF-a or IL-6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated from unstimulated (control) and cytokine-stimulated cells by Chomczynski and Sacchi procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following labeling, samples were hybridized to the GeneChip Test3 array (Affymetrix, Santa Clara, CA) for quality control. Fragmented cRNA (15 μg) was used for hybridization to the GeneChip Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA). Arrays were washed and stained with streptavidin-phycoerythrin (Merck, Darmstadt, Germany) in Fluidic Station 400 (Affymetrix, Santa Clara, CA) according to standard protocol of the manufacturer.
| | Sample_scan_protocol | The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was normalized by dChip 2006 (MBEI)
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marcin,,Piechota
| | Sample_contact_email | marpiech@if-pan.krakow.pl
| | Sample_contact_phone | (+4812) 6623328
| | Sample_contact_department | Molecular Neuropharmacology
| | Sample_contact_institute | Institute of Pharmacology PAS
| | Sample_contact_address | Smetna 12
| | Sample_contact_city | Krakow
| | Sample_contact_zip/postal_code | 31-343
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM211nnn/GSM211511/suppl/GSM211511.CEL.gz
| | Sample_series_id | GSE8515
| | Sample_data_row_count | 22283
| | |
|
GSM211512 | GPL96 |
|
IL-6, Rep3
|
Interleukin 6 replicate 3
|
Human monocyte-derived macrophages obtained from peripheral blood mononuclear cells
|
Interleukin 6 replicate 3
|
| Sample_geo_accession | GSM211512
| | Sample_status | Public on Sep 15 2007
| | Sample_submission_date | Jul 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Just before the experiment with cytokines the medium was changed to DMEM containing 0.5% of pooled human serum and the cells were stimulated with IL-1 (15 ng/ml), or IL-6 (25 ng/ml) for the period of 4 h. These rather low concentrations of cytokines that may occur in vivo were selected in preliminary trials as sufficient to stimulate the expression of manganese superoxide dismutase (MnSOD).
| | Sample_growth_protocol_ch1 | Human monocyte-derived macrophages (hMDMs) were obtained from peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from human blood of 7 healthy donors using a Ficoll-Paque (Pharmacia, Uppsala, Sweden) density gradient. Cells from each donor were split into three aliquots to stimulate them later with a mock stimulant, IL-1 and IL-6 and plated at 4x107 in PrimariaTM 25cm2 cell culture flasks with vented caps (Becton Dickinson, Franklin Lakes, NJ, USA) in RPMI1640 (Invitrogen) supplemented with 2mM L-glutamine, 50 g/ml gentamycin (Sigma), and 10% pooled heat-inactivated human AB serum. After 24 h, non-adherent PBMCs were removed by washing with complete medium, and adherent cells were cultured in this medium for 7 days with fresh medium changed every 2 days. The MDMs phenotype was controlled, after non-enzymatic detachment of cells, by immunofluorescent staining of CD14 (clone: TÜK4, DakoCytomation Denmark A/S, Glostrup, Denmark), CD16 (clone: DJ130c, DakoCytomation), CD11b (clone: ICRF44, Becton Dickinson and Co., Franklin Lakes, USA), and CD209 (clone: DCN46, Becton Dickinson) and subsequent flow cytometry analysis. The routine procedure used in our laboratory yields cells positive in at least 90% for the first three markers and less than 1% for CD209. It should be added that the adherent cells acquire typical macrophage morphology and extensive phagocytic activity against live Staphylococcus aureus and apoptotic neutrophils. Resting (non-stimulated) cells do not produce proinflammatory cytokines: IL-1, TNF-a or IL-6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated from unstimulated (control) and cytokine-stimulated cells by Chomczynski and Sacchi procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following labeling, samples were hybridized to the GeneChip Test3 array (Affymetrix, Santa Clara, CA) for quality control. Fragmented cRNA (15 μg) was used for hybridization to the GeneChip Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA). Arrays were washed and stained with streptavidin-phycoerythrin (Merck, Darmstadt, Germany) in Fluidic Station 400 (Affymetrix, Santa Clara, CA) according to standard protocol of the manufacturer.
| | Sample_scan_protocol | The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was normalized by dChip 2006 (MBEI)
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marcin,,Piechota
| | Sample_contact_email | marpiech@if-pan.krakow.pl
| | Sample_contact_phone | (+4812) 6623328
| | Sample_contact_department | Molecular Neuropharmacology
| | Sample_contact_institute | Institute of Pharmacology PAS
| | Sample_contact_address | Smetna 12
| | Sample_contact_city | Krakow
| | Sample_contact_zip/postal_code | 31-343
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM211nnn/GSM211512/suppl/GSM211512.CEL.gz
| | Sample_series_id | GSE8515
| | Sample_data_row_count | 22283
| | |
|
GSM211513 | GPL96 |
|
IL-6, Rep4
|
Interleukin 6 replicate 4
|
Human monocyte-derived macrophages obtained from peripheral blood mononuclear cells
|
Interleukin 6 replicate 4
|
| Sample_geo_accession | GSM211513
| | Sample_status | Public on Sep 15 2007
| | Sample_submission_date | Jul 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Just before the experiment with cytokines the medium was changed to DMEM containing 0.5% of pooled human serum and the cells were stimulated with IL-1 (15 ng/ml), or IL-6 (25 ng/ml) for the period of 4 h. These rather low concentrations of cytokines that may occur in vivo were selected in preliminary trials as sufficient to stimulate the expression of manganese superoxide dismutase (MnSOD).
| | Sample_growth_protocol_ch1 | Human monocyte-derived macrophages (hMDMs) were obtained from peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from human blood of 7 healthy donors using a Ficoll-Paque (Pharmacia, Uppsala, Sweden) density gradient. Cells from each donor were split into three aliquots to stimulate them later with a mock stimulant, IL-1 and IL-6 and plated at 4x107 in PrimariaTM 25cm2 cell culture flasks with vented caps (Becton Dickinson, Franklin Lakes, NJ, USA) in RPMI1640 (Invitrogen) supplemented with 2mM L-glutamine, 50 g/ml gentamycin (Sigma), and 10% pooled heat-inactivated human AB serum. After 24 h, non-adherent PBMCs were removed by washing with complete medium, and adherent cells were cultured in this medium for 7 days with fresh medium changed every 2 days. The MDMs phenotype was controlled, after non-enzymatic detachment of cells, by immunofluorescent staining of CD14 (clone: TÜK4, DakoCytomation Denmark A/S, Glostrup, Denmark), CD16 (clone: DJ130c, DakoCytomation), CD11b (clone: ICRF44, Becton Dickinson and Co., Franklin Lakes, USA), and CD209 (clone: DCN46, Becton Dickinson) and subsequent flow cytometry analysis. The routine procedure used in our laboratory yields cells positive in at least 90% for the first three markers and less than 1% for CD209. It should be added that the adherent cells acquire typical macrophage morphology and extensive phagocytic activity against live Staphylococcus aureus and apoptotic neutrophils. Resting (non-stimulated) cells do not produce proinflammatory cytokines: IL-1, TNF-a or IL-6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated from unstimulated (control) and cytokine-stimulated cells by Chomczynski and Sacchi procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following labeling, samples were hybridized to the GeneChip Test3 array (Affymetrix, Santa Clara, CA) for quality control. Fragmented cRNA (15 μg) was used for hybridization to the GeneChip Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA). Arrays were washed and stained with streptavidin-phycoerythrin (Merck, Darmstadt, Germany) in Fluidic Station 400 (Affymetrix, Santa Clara, CA) according to standard protocol of the manufacturer.
| | Sample_scan_protocol | The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was normalized by dChip 2006 (MBEI)
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marcin,,Piechota
| | Sample_contact_email | marpiech@if-pan.krakow.pl
| | Sample_contact_phone | (+4812) 6623328
| | Sample_contact_department | Molecular Neuropharmacology
| | Sample_contact_institute | Institute of Pharmacology PAS
| | Sample_contact_address | Smetna 12
| | Sample_contact_city | Krakow
| | Sample_contact_zip/postal_code | 31-343
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM211nnn/GSM211513/suppl/GSM211513.CEL.gz
| | Sample_series_id | GSE8515
| | Sample_data_row_count | 22283
| | |
|
GSM211514 | GPL96 |
|
IL-6, Rep5
|
Interleukin 6 replicate 5
|
Human monocyte-derived macrophages obtained from peripheral blood mononuclear cells
|
Interleukin 6 replicate 5
|
| Sample_geo_accession | GSM211514
| | Sample_status | Public on Sep 15 2007
| | Sample_submission_date | Jul 18 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Just before the experiment with cytokines the medium was changed to DMEM containing 0.5% of pooled human serum and the cells were stimulated with IL-1 (15 ng/ml), or IL-6 (25 ng/ml) for the period of 4 h. These rather low concentrations of cytokines that may occur in vivo were selected in preliminary trials as sufficient to stimulate the expression of manganese superoxide dismutase (MnSOD).
| | Sample_growth_protocol_ch1 | Human monocyte-derived macrophages (hMDMs) were obtained from peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from human blood of 7 healthy donors using a Ficoll-Paque (Pharmacia, Uppsala, Sweden) density gradient. Cells from each donor were split into three aliquots to stimulate them later with a mock stimulant, IL-1 and IL-6 and plated at 4x107 in PrimariaTM 25cm2 cell culture flasks with vented caps (Becton Dickinson, Franklin Lakes, NJ, USA) in RPMI1640 (Invitrogen) supplemented with 2mM L-glutamine, 50 g/ml gentamycin (Sigma), and 10% pooled heat-inactivated human AB serum. After 24 h, non-adherent PBMCs were removed by washing with complete medium, and adherent cells were cultured in this medium for 7 days with fresh medium changed every 2 days. The MDMs phenotype was controlled, after non-enzymatic detachment of cells, by immunofluorescent staining of CD14 (clone: TÜK4, DakoCytomation Denmark A/S, Glostrup, Denmark), CD16 (clone: DJ130c, DakoCytomation), CD11b (clone: ICRF44, Becton Dickinson and Co., Franklin Lakes, USA), and CD209 (clone: DCN46, Becton Dickinson) and subsequent flow cytometry analysis. The routine procedure used in our laboratory yields cells positive in at least 90% for the first three markers and less than 1% for CD209. It should be added that the adherent cells acquire typical macrophage morphology and extensive phagocytic activity against live Staphylococcus aureus and apoptotic neutrophils. Resting (non-stimulated) cells do not produce proinflammatory cytokines: IL-1, TNF-a or IL-6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated from unstimulated (control) and cytokine-stimulated cells by Chomczynski and Sacchi procedure.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following labeling, samples were hybridized to the GeneChip Test3 array (Affymetrix, Santa Clara, CA) for quality control. Fragmented cRNA (15 μg) was used for hybridization to the GeneChip Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA). Arrays were washed and stained with streptavidin-phycoerythrin (Merck, Darmstadt, Germany) in Fluidic Station 400 (Affymetrix, Santa Clara, CA) according to standard protocol of the manufacturer.
| | Sample_scan_protocol | The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Data was normalized by dChip 2006 (MBEI)
| | Sample_platform_id | GPL96
| | Sample_contact_name | Marcin,,Piechota
| | Sample_contact_email | marpiech@if-pan.krakow.pl
| | Sample_contact_phone | (+4812) 6623328
| | Sample_contact_department | Molecular Neuropharmacology
| | Sample_contact_institute | Institute of Pharmacology PAS
| | Sample_contact_address | Smetna 12
| | Sample_contact_city | Krakow
| | Sample_contact_zip/postal_code | 31-343
| | Sample_contact_country | Poland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM211nnn/GSM211514/suppl/GSM211514.CEL.gz
| | Sample_series_id | GSE8515
| | Sample_data_row_count | 22283
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
