Search results for the GEO ID: GSE7138  |
(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 |
GSM170908 | GPL96 |
|
PBMC #1
|
peripheral blood PBMC #1
|
healthy blood donors
|
Gene expression in PBMC isolated from peripheral blood of healthy donors
|
| Sample_geo_accession | GSM170908
| | Sample_status | Public on Mar 28 2007
| | Sample_submission_date | Feb 22 2007
| | Sample_last_update_date | Mar 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Virginia Blood Services (Richmond, VA)
| | Sample_treatment_protocol_ch1 | Human blood was drawn from the antecubital veins of healthy blood donors and provided as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of samples was performed according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Hybridization of cRNA was performed according to standard Affymetrix protocols.
| | Sample_scan_protocol | Scanning was performed according to standard Affymetrix protocols.
| | Sample_data_processing | Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0). Of 22,283 probe sets on the HG-U133A chip, 78 internal control probes were removed and 22,215 probe sets representing 12,978 gene products were analyzed. Microarray gene expression intensities were normalized in order to ensure that all 22 array chips have the same inter-quartile ranges (IQR). In addition, they were log-transformed with base 2, which allows transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.rproject.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering & heatmap analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix website (www.affymetix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyzed. We eliminated non-expressed (within 2 SD from zero in all conditions) and housekeeping genes (not expressed).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,Albert,Gleissner
| | Sample_contact_fax | 434-924-2828
| | Sample_contact_laboratory | Ley
| | Sample_contact_department | Cardiovascular Research Center
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | MR5 Building, Rm. 1133
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM170nnn/GSM170908/suppl/GSM170908.cel.gz
| | Sample_series_id | GSE7138
| | Sample_data_row_count | 22283
| | |
|
GSM170910 | GPL96 |
|
PBMC #2
|
peripheral blood PBMC #2
|
healthy blood donors
|
Gene expression in PBMC isolated from peripheral blood of healthy donors
|
| Sample_geo_accession | GSM170910
| | Sample_status | Public on Mar 28 2007
| | Sample_submission_date | Feb 22 2007
| | Sample_last_update_date | Mar 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Virginia Blood Services (Richmond, VA)
| | Sample_treatment_protocol_ch1 | Human blood was drawn from the antecubital veins of healthy blood donors and provided as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of samples was performed according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Hybridization of cRNA was performed according to standard Affymetrix protocols.
| | Sample_scan_protocol | Scanning was performed according to standard Affymetrix protocols.
| | Sample_data_processing | Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0). Of 22,283 probe sets on the HG-U133A chip, 78 internal control probes were removed and 22,215 probe sets representing 12,978 gene products were analyzed. Microarray gene expression intensities were normalized in order to ensure that all 22 array chips have the same inter-quartile ranges (IQR). In addition, they were log-transformed with base 2, which allows transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.rproject.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering & heatmap analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix website (www.affymetix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyzed. We eliminated non-expressed (within 2 SD from zero in all conditions) and housekeeping genes (not expressed).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,Albert,Gleissner
| | Sample_contact_fax | 434-924-2828
| | Sample_contact_laboratory | Ley
| | Sample_contact_department | Cardiovascular Research Center
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | MR5 Building, Rm. 1133
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM170nnn/GSM170910/suppl/GSM170910.cel.gz
| | Sample_series_id | GSE7138
| | Sample_data_row_count | 22283
| | |
|
GSM170913 | GPL96 |
|
Monocytes #1
|
peripheral blood Monocytes #1
|
healthy blood donors
|
Gene expression in monocytes isolated from peripheral blood of healthy donors
|
| Sample_geo_accession | GSM170913
| | Sample_status | Public on Mar 28 2007
| | Sample_submission_date | Feb 22 2007
| | Sample_last_update_date | Mar 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Virginia Blood Services (Richmond, VA)
| | Sample_treatment_protocol_ch1 | Human blood was drawn from the antecubital veins of healthy blood donors and provided as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the
| | Sample_treatment_protocol_ch1 | mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer. From these PBMCs, monocytes were isolated using a negative selection monocyte isolation kit and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of the isolated fraction was > 97% as estimated by flow cytometry using anti-CD14.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of samples was performed according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Hybridization of cRNA was performed according to standard Affymetrix protocols.
| | Sample_scan_protocol | Scanning was performed according to standard Affymetrix protocols.
| | Sample_data_processing | Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0). Of 22,283 probe sets on the HG-U133A chip, 78 internal control probes were removed and 22,215 probe sets representing 12,978 gene products were analyzed. Microarray gene expression intensities were normalized in order to ensure that all 22 array chips have the same inter-quartile ranges (IQR). In addition, they were log-transformed with base 2, which allows transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.rproject.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering & heatmap analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix website (www.affymetix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyzed. We eliminated non-expressed (within 2 SD from zero in all conditions) and housekeeping genes (not expressed).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,Albert,Gleissner
| | Sample_contact_fax | 434-924-2828
| | Sample_contact_laboratory | Ley
| | Sample_contact_department | Cardiovascular Research Center
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | MR5 Building, Rm. 1133
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM170nnn/GSM170913/suppl/GSM170913.cel.gz
| | Sample_series_id | GSE7138
| | Sample_data_row_count | 22283
| | |
|
GSM170915 | GPL96 |
|
Monocytes #2
|
peripheral blood Monocytes #2
|
healthy blood donors
|
Gene expression in monocytes isolated from peripheral blood of healthy donors
|
| Sample_geo_accession | GSM170915
| | Sample_status | Public on Mar 28 2007
| | Sample_submission_date | Feb 22 2007
| | Sample_last_update_date | Mar 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Virginia Blood Services (Richmond, VA)
| | Sample_treatment_protocol_ch1 | Human blood was drawn from the antecubital veins of healthy blood donors and provided as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the
| | Sample_treatment_protocol_ch1 | mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer. From these PBMCs, monocytes were isolated using a negative selection monocyte isolation kit and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of the isolated fraction was > 97% as estimated by flow cytometry using anti-CD14.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of samples was performed according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Hybridization of cRNA was performed according to standard Affymetrix protocols.
| | Sample_scan_protocol | Scanning was performed according to standard Affymetrix protocols.
| | Sample_data_processing | Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0). Of 22,283 probe sets on the HG-U133A chip, 78 internal control probes were removed and 22,215 probe sets representing 12,978 gene products were analyzed. Microarray gene expression intensities were normalized in order to ensure that all 22 array chips have the same inter-quartile ranges (IQR). In addition, they were log-transformed with base 2, which allows transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.rproject.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering & heatmap analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix website (www.affymetix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyzed. We eliminated non-expressed (within 2 SD from zero in all conditions) and housekeeping genes (not expressed).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,Albert,Gleissner
| | Sample_contact_fax | 434-924-2828
| | Sample_contact_laboratory | Ley
| | Sample_contact_department | Cardiovascular Research Center
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | MR5 Building, Rm. 1133
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM170nnn/GSM170915/suppl/GSM170915.cel.gz
| | Sample_series_id | GSE7138
| | Sample_data_row_count | 22283
| | |
|
GSM170916 | GPL96 |
|
Macrophages 6d #1
|
peripheral blood Macrophages 6d #1
|
healthy blood donors
|
Gene expression in monocyte-derived macrophages from healthy donors
|
| Sample_geo_accession | GSM170916
| | Sample_status | Public on Mar 28 2007
| | Sample_submission_date | Feb 22 2007
| | Sample_last_update_date | Mar 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Virginia Blood Services (Richmond, VA)
| | Sample_treatment_protocol_ch1 | Human blood was drawn from the antecubital veins of healthy blood donors and provided as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the
| | Sample_treatment_protocol_ch1 | mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer. From these PBMCs, monocytes were isolated using a negative selection monocyte isolation kit and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of the isolated fraction was > 97% as estimated by flow cytometry using anti-CD14.
| | Sample_growth_protocol_ch1 | Monocytes were cultured in Macrophage Serum-Free Medium (MSFM, Invitrogen, Carlsbad, CA) in the presence of 1% media supplement nutridoma-HU (Roche Molecular Biochemicals, Indianapolis, IN) and 100 nM M-CSF for 6 days, after which the cells showed the expected morphological signs of macrophage differentiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of samples was performed according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Hybridization of cRNA was performed according to standard Affymetrix protocols.
| | Sample_scan_protocol | Scanning was performed according to standard Affymetrix protocols.
| | Sample_data_processing | Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0). Of 22,283 probe sets on the HG-U133A chip, 78 internal control probes were removed and 22,215 probe sets representing 12,978 gene products were analyzed. Microarray gene expression intensities were normalized in order to ensure that all 22 array chips have the same inter-quartile ranges (IQR). In addition, they were log-transformed with base 2, which allows transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.rproject.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering & heatmap analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix website (www.affymetix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyzed. We eliminated non-expressed (within 2 SD from zero in all conditions) and housekeeping genes (not expressed).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,Albert,Gleissner
| | Sample_contact_fax | 434-924-2828
| | Sample_contact_laboratory | Ley
| | Sample_contact_department | Cardiovascular Research Center
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | MR5 Building, Rm. 1133
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM170nnn/GSM170916/suppl/GSM170916.cel.gz
| | Sample_series_id | GSE7138
| | Sample_data_row_count | 22283
| | |
|
GSM170918 | GPL96 |
|
Macrophages 6d #2
|
peripheral blood Macrophages 6d #2
|
healthy blood donors
|
Gene expression in monocyte-derived macrophages from healthy donors
|
| Sample_geo_accession | GSM170918
| | Sample_status | Public on Mar 28 2007
| | Sample_submission_date | Feb 22 2007
| | Sample_last_update_date | Mar 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Virginia Blood Services (Richmond, VA)
| | Sample_treatment_protocol_ch1 | Human blood was drawn from the antecubital veins of healthy blood donors and provided as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the
| | Sample_treatment_protocol_ch1 | mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer. From these PBMCs, monocytes were isolated using a negative selection monocyte isolation kit and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of the isolated fraction was > 97% as estimated by flow cytometry using anti-CD14.
| | Sample_growth_protocol_ch1 | Monocytes were cultured in Macrophage Serum-Free Medium (MSFM, Invitrogen, Carlsbad, CA) in the presence of 1% media supplement nutridoma-HU (Roche Molecular Biochemicals, Indianapolis, IN) and 100 nM M-CSF for 6 days, after which the cells showed the expected morphological signs of macrophage differentiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of samples was performed according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Hybridization of cRNA was performed according to standard Affymetrix protocols.
| | Sample_scan_protocol | Scanning was performed according to standard Affymetrix protocols.
| | Sample_data_processing | Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0). Of 22,283 probe sets on the HG-U133A chip, 78 internal control probes were removed and 22,215 probe sets representing 12,978 gene products were analyzed. Microarray gene expression intensities were normalized in order to ensure that all 22 array chips have the same inter-quartile ranges (IQR). In addition, they were log-transformed with base 2, which allows transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.rproject.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering & heatmap analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix website (www.affymetix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyzed. We eliminated non-expressed (within 2 SD from zero in all conditions) and housekeeping genes (not expressed).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,Albert,Gleissner
| | Sample_contact_fax | 434-924-2828
| | Sample_contact_laboratory | Ley
| | Sample_contact_department | Cardiovascular Research Center
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | MR5 Building, Rm. 1133
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM170nnn/GSM170918/suppl/GSM170918.cel.gz
| | Sample_series_id | GSE7138
| | Sample_data_row_count | 22283
| | |
|
GSM170920 | GPL96 |
|
CCL2 #1
|
peripheral blood CCL2 #1
|
healthy blood donors
|
Gene expression in monocyte-derived macrophages from healthy donors stimulated with CCL2 for 5 hours
|
| Sample_geo_accession | GSM170920
| | Sample_status | Public on Mar 28 2007
| | Sample_submission_date | Feb 22 2007
| | Sample_last_update_date | Mar 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Virginia Blood Services (Richmond, VA)
| | Sample_treatment_protocol_ch1 | Human blood was drawn from the antecubital veins of healthy blood donors and provided as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the
| | Sample_treatment_protocol_ch1 | mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer. From these PBMCs, monocytes were isolated using a negative selection monocyte isolation kit and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of the isolated fraction was > 97% as estimated by flow cytometry using anti-CD14.
| | Sample_growth_protocol_ch1 | Monocytes were cultured in Macrophage Serum-Free Medium (MSFM, Invitrogen, Carlsbad, CA) in the presence of 1% media supplement nutridoma-HU (Roche Molecular Biochemicals, Indianapolis, IN) and 100 nM M-CSF for 6 days, after which the cells showed the expected morphological signs of macrophage differentiation. These macrophages were incubated with 100 nM CCL2 for 5 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of samples was performed according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Hybridization of cRNA was performed according to standard Affymetrix protocols.
| | Sample_scan_protocol | Scanning was performed according to standard Affymetrix protocols.
| | Sample_data_processing | Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0). Of 22,283 probe sets on the HG-U133A chip, 78 internal control probes were removed and 22,215 probe sets representing 12,978 gene products were analyzed. Microarray gene expression intensities were normalized in order to ensure that all 22 array chips have the same inter-quartile ranges (IQR). In addition, they were log-transformed with base 2, which allows transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.rproject.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering & heatmap analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix website (www.affymetix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyzed. We eliminated non-expressed (within 2 SD from zero in all conditions) and housekeeping genes (not expressed).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,Albert,Gleissner
| | Sample_contact_fax | 434-924-2828
| | Sample_contact_laboratory | Ley
| | Sample_contact_department | Cardiovascular Research Center
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | MR5 Building, Rm. 1133
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM170nnn/GSM170920/suppl/GSM170920.cel.gz
| | Sample_series_id | GSE7138
| | Sample_data_row_count | 22283
| | |
|
GSM170922 | GPL96 |
|
CCL2 #2
|
peripheral blood CCL2 #2
|
healthy blood donors
|
Gene expression in monocyte-derived macrophages from healthy donors stimulated with CCL2 for 5 hours
|
| Sample_geo_accession | GSM170922
| | Sample_status | Public on Mar 28 2007
| | Sample_submission_date | Feb 22 2007
| | Sample_last_update_date | Mar 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Virginia Blood Services (Richmond, VA)
| | Sample_treatment_protocol_ch1 | Human blood was drawn from the antecubital veins of healthy blood donors and provided as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the
| | Sample_treatment_protocol_ch1 | mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer. From these PBMCs, monocytes were isolated using a negative selection monocyte isolation kit and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of the isolated fraction was > 97% as estimated by flow cytometry using anti-CD14.
| | Sample_growth_protocol_ch1 | Monocytes were cultured in Macrophage Serum-Free Medium (MSFM, Invitrogen, Carlsbad, CA) in the presence of 1% media supplement nutridoma-HU (Roche Molecular Biochemicals, Indianapolis, IN) and 100 nM M-CSF for 6 days, after which the cells showed the expected morphological signs of macrophage differentiation. These macrophages were incubated with 100 nM CCL2 for 5 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of samples was performed according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Hybridization of cRNA was performed according to standard Affymetrix protocols.
| | Sample_scan_protocol | Scanning was performed according to standard Affymetrix protocols.
| | Sample_data_processing | Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0). Of 22,283 probe sets on the HG-U133A chip, 78 internal control probes were removed and 22,215 probe sets representing 12,978 gene products were analyzed. Microarray gene expression intensities were normalized in order to ensure that all 22 array chips have the same inter-quartile ranges (IQR). In addition, they were log-transformed with base 2, which allows transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.rproject.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering & heatmap analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix website (www.affymetix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyzed. We eliminated non-expressed (within 2 SD from zero in all conditions) and housekeeping genes (not expressed).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,Albert,Gleissner
| | Sample_contact_fax | 434-924-2828
| | Sample_contact_laboratory | Ley
| | Sample_contact_department | Cardiovascular Research Center
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | MR5 Building, Rm. 1133
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM170nnn/GSM170922/suppl/GSM170922.cel.gz
| | Sample_series_id | GSE7138
| | Sample_data_row_count | 22283
| | |
|
GSM170932 | GPL96 |
|
CXCL1 #1
|
peripheral blood CXCL1 #1
|
healthy blood donors
|
Gene expression in monocyte-derived macrophages from healthy donors stimulated with CXCL1 for 5 hours
|
| Sample_geo_accession | GSM170932
| | Sample_status | Public on Mar 28 2007
| | Sample_submission_date | Feb 22 2007
| | Sample_last_update_date | Mar 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Virginia Blood Services (Richmond, VA)
| | Sample_treatment_protocol_ch1 | Human blood was drawn from the antecubital veins of healthy blood donors and provided as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the
| | Sample_treatment_protocol_ch1 | mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer. From these PBMCs, monocytes were isolated using a negative selection monocyte isolation kit and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of the isolated fraction was > 97% as estimated by flow cytometry using anti-CD14.
| | Sample_growth_protocol_ch1 | Monocytes were cultured in Macrophage Serum-Free Medium (MSFM, Invitrogen, Carlsbad, CA) in the presence of 1% media supplement nutridoma-HU (Roche Molecular Biochemicals, Indianapolis, IN) and 100 nM M-CSF for 6 days, after which the cells showed the expected morphological signs of macrophage differentiation. These macrophages were incubated with 100 nM CXCL1 for 5 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of samples was performed according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Hybridization of cRNA was performed according to standard Affymetrix protocols.
| | Sample_scan_protocol | Scanning was performed according to standard Affymetrix protocols.
| | Sample_data_processing | Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0). Of 22,283 probe sets on the HG-U133A chip, 78 internal control probes were removed and 22,215 probe sets representing 12,978 gene products were analyzed. Microarray gene expression intensities were normalized in order to ensure that all 22 array chips have the same inter-quartile ranges (IQR). In addition, they were log-transformed with base 2, which allows transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.rproject.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering & heatmap analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix website (www.affymetix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyzed. We eliminated non-expressed (within 2 SD from zero in all conditions) and housekeeping genes (not expressed).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,Albert,Gleissner
| | Sample_contact_fax | 434-924-2828
| | Sample_contact_laboratory | Ley
| | Sample_contact_department | Cardiovascular Research Center
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | MR5 Building, Rm. 1133
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM170nnn/GSM170932/suppl/GSM170932.cel.gz
| | Sample_series_id | GSE7138
| | Sample_data_row_count | 22283
| | |
|
GSM170933 | GPL96 |
|
CXCL1 #2
|
peripheral blood CXCL1 #2
|
healthy blood donors
|
Gene expression in monocyte-derived macrophages from healthy donors stimulated with CXCL1 for 5 hours
|
| Sample_geo_accession | GSM170933
| | Sample_status | Public on Mar 28 2007
| | Sample_submission_date | Feb 22 2007
| | Sample_last_update_date | Mar 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Virginia Blood Services (Richmond, VA)
| | Sample_treatment_protocol_ch1 | Human blood was drawn from the antecubital veins of healthy blood donors and provided as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the
| | Sample_treatment_protocol_ch1 | mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer. From these PBMCs, monocytes were isolated using a negative selection monocyte isolation kit and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of the isolated fraction was > 97% as estimated by flow cytometry using anti-CD14.
| | Sample_growth_protocol_ch1 | Monocytes were cultured in Macrophage Serum-Free Medium (MSFM, Invitrogen, Carlsbad, CA) in the presence of 1% media supplement nutridoma-HU (Roche Molecular Biochemicals, Indianapolis, IN) and 100 nM M-CSF for 6 days, after which the cells showed the expected morphological signs of macrophage differentiation. These macrophages were incubated with 100 nM CXCL1 for 5 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of samples was performed according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Hybridization of cRNA was performed according to standard Affymetrix protocols.
| | Sample_scan_protocol | Scanning was performed according to standard Affymetrix protocols.
| | Sample_data_processing | Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0). Of 22,283 probe sets on the HG-U133A chip, 78 internal control probes were removed and 22,215 probe sets representing 12,978 gene products were analyzed. Microarray gene expression intensities were normalized in order to ensure that all 22 array chips have the same inter-quartile ranges (IQR). In addition, they were log-transformed with base 2, which allows transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.rproject.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering & heatmap analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix website (www.affymetix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyzed. We eliminated non-expressed (within 2 SD from zero in all conditions) and housekeeping genes (not expressed).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,Albert,Gleissner
| | Sample_contact_fax | 434-924-2828
| | Sample_contact_laboratory | Ley
| | Sample_contact_department | Cardiovascular Research Center
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | MR5 Building, Rm. 1133
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM170nnn/GSM170933/suppl/GSM170933.cel.gz
| | Sample_series_id | GSE7138
| | Sample_data_row_count | 22283
| | |
|
GSM170935 | GPL96 |
|
Macrophages 8d #1
|
peripheral blood Macrophages 8d #1
|
healthy blood donors
|
Gene expression in monocyte-derived macrophages from healthy donors
|
| Sample_geo_accession | GSM170935
| | Sample_status | Public on Mar 28 2007
| | Sample_submission_date | Feb 22 2007
| | Sample_last_update_date | Mar 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Virginia Blood Services (Richmond, VA)
| | Sample_treatment_protocol_ch1 | Human blood was drawn from the antecubital veins of healthy blood donors and provided as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the
| | Sample_treatment_protocol_ch1 | mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer. From these PBMCs, monocytes were isolated using a negative selection monocyte isolation kit and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of the isolated fraction was > 97% as estimated by flow cytometry using anti-CD14.
| | Sample_growth_protocol_ch1 | Monocytes were cultured in Macrophage Serum-Free Medium (MSFM, Invitrogen, Carlsbad, CA) in the presence of 1% media supplement nutridoma-HU (Roche Molecular Biochemicals, Indianapolis, IN) and 100 nM M-CSF for 8 days, after which the cells showed the expected morphological signs of macrophage differentiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of samples was performed according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Hybridization of cRNA was performed according to standard Affymetrix protocols.
| | Sample_scan_protocol | Scanning was performed according to standard Affymetrix protocols.
| | Sample_data_processing | Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0). Of 22,283 probe sets on the HG-U133A chip, 78 internal control probes were removed and 22,215 probe sets representing 12,978 gene products were analyzed. Microarray gene expression intensities were normalized in order to ensure that all 22 array chips have the same inter-quartile ranges (IQR). In addition, they were log-transformed with base 2, which allows transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.rproject.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering & heatmap analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix website (www.affymetix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyzed. We eliminated non-expressed (within 2 SD from zero in all conditions) and housekeeping genes (not expressed).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,Albert,Gleissner
| | Sample_contact_fax | 434-924-2828
| | Sample_contact_laboratory | Ley
| | Sample_contact_department | Cardiovascular Research Center
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | MR5 Building, Rm. 1133
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM170nnn/GSM170935/suppl/GSM170935.cel.gz
| | Sample_series_id | GSE7138
| | Sample_data_row_count | 22283
| | |
|
GSM170936 | GPL96 |
|
Macrophages 8d #2
|
peripheral blood Macrophages 8d #2
|
healthy blood donors
|
Gene expression in monocyte-derived macrophages from healthy donors
|
| Sample_geo_accession | GSM170936
| | Sample_status | Public on Mar 28 2007
| | Sample_submission_date | Feb 22 2007
| | Sample_last_update_date | Mar 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Virginia Blood Services (Richmond, VA)
| | Sample_treatment_protocol_ch1 | Human blood was drawn from the antecubital veins of healthy blood donors and provided as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the
| | Sample_treatment_protocol_ch1 | mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer. From these PBMCs, monocytes were isolated using a negative selection monocyte isolation kit and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of the isolated fraction was > 97% as estimated by flow cytometry using anti-CD14.
| | Sample_growth_protocol_ch1 | Monocytes were cultured in Macrophage Serum-Free Medium (MSFM, Invitrogen, Carlsbad, CA) in the presence of 1% media supplement nutridoma-HU (Roche Molecular Biochemicals, Indianapolis, IN) and 100 nM M-CSF for 8 days, after which the cells showed the expected morphological signs of macrophage differentiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of samples was performed according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Hybridization of cRNA was performed according to standard Affymetrix protocols.
| | Sample_scan_protocol | Scanning was performed according to standard Affymetrix protocols.
| | Sample_data_processing | Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0). Of 22,283 probe sets on the HG-U133A chip, 78 internal control probes were removed and 22,215 probe sets representing 12,978 gene products were analyzed. Microarray gene expression intensities were normalized in order to ensure that all 22 array chips have the same inter-quartile ranges (IQR). In addition, they were log-transformed with base 2, which allows transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.rproject.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering & heatmap analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix website (www.affymetix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyzed. We eliminated non-expressed (within 2 SD from zero in all conditions) and housekeeping genes (not expressed).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,Albert,Gleissner
| | Sample_contact_fax | 434-924-2828
| | Sample_contact_laboratory | Ley
| | Sample_contact_department | Cardiovascular Research Center
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | MR5 Building, Rm. 1133
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM170nnn/GSM170936/suppl/GSM170936.cel.gz
| | Sample_series_id | GSE7138
| | Sample_data_row_count | 22283
| | |
|
GSM170937 | GPL96 |
|
LDL #1
|
peripheral blood LDL #1
|
healthy blood donors
|
Gene expression in monocyte-derived macrophages from healthy donors stimulated with LDL for 2 days
|
| Sample_geo_accession | GSM170937
| | Sample_status | Public on Mar 28 2007
| | Sample_submission_date | Feb 22 2007
| | Sample_last_update_date | Mar 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Virginia Blood Services (Richmond, VA)
| | Sample_treatment_protocol_ch1 | Human blood was drawn from the antecubital veins of healthy blood donors and provided as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the
| | Sample_treatment_protocol_ch1 | mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer. From these PBMCs, monocytes were isolated using a negative selection monocyte isolation kit and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of the isolated fraction was > 97% as estimated by flow cytometry using anti-CD14.
| | Sample_growth_protocol_ch1 | Monocytes were cultured in Macrophage Serum-Free Medium (MSFM, Invitrogen, Carlsbad, CA) in the presence of 1% media supplement nutridoma-HU (Roche Molecular Biochemicals, Indianapolis, IN) and 100 nM M-CSF for 6 days, after which the cells showed the expected morphological signs of macrophage differentiation. Human monocyte-derived macrophages (MDM) were incubated with native LDL (100 µg/ml) for 2 days to induce foam cell formation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of samples was performed according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Hybridization of cRNA was performed according to standard Affymetrix protocols.
| | Sample_scan_protocol | Scanning was performed according to standard Affymetrix protocols.
| | Sample_data_processing | Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0). Of 22,283 probe sets on the HG-U133A chip, 78 internal control probes were removed and 22,215 probe sets representing 12,978 gene products were analyzed. Microarray gene expression intensities were normalized in order to ensure that all 22 array chips have the same inter-quartile ranges (IQR). In addition, they were log-transformed with base 2, which allows transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.rproject.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering & heatmap analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix website (www.affymetix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyzed. We eliminated non-expressed (within 2 SD from zero in all conditions) and housekeeping genes (not expressed).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,Albert,Gleissner
| | Sample_contact_fax | 434-924-2828
| | Sample_contact_laboratory | Ley
| | Sample_contact_department | Cardiovascular Research Center
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | MR5 Building, Rm. 1133
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM170nnn/GSM170937/suppl/GSM170937.cel.gz
| | Sample_series_id | GSE7138
| | Sample_data_row_count | 22283
| | |
|
GSM170938 | GPL96 |
|
LDL #2
|
peripheral blood LDL #2
|
healthy blood donors
|
Gene expression in monocyte-derived macrophages from healthy donors stimulated with LDL for 2 days
|
| Sample_geo_accession | GSM170938
| | Sample_status | Public on Mar 28 2007
| | Sample_submission_date | Feb 22 2007
| | Sample_last_update_date | Mar 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Virginia Blood Services (Richmond, VA)
| | Sample_treatment_protocol_ch1 | Human blood was drawn from the antecubital veins of healthy blood donors and provided as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the
| | Sample_treatment_protocol_ch1 | mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer. From these PBMCs, monocytes were isolated using a negative selection monocyte isolation kit and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of the isolated fraction was > 97% as estimated by flow cytometry using anti-CD14.
| | Sample_growth_protocol_ch1 | Monocytes were cultured in Macrophage Serum-Free Medium (MSFM, Invitrogen, Carlsbad, CA) in the presence of 1% media supplement nutridoma-HU (Roche Molecular Biochemicals, Indianapolis, IN) and 100 nM M-CSF for 6 days, after which the cells showed the expected morphological signs of macrophage differentiation. Human monocyte-derived macrophages (MDM) were incubated with native LDL (100 µg/ml) for 2 days to induce foam cell formation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of samples was performed according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Hybridization of cRNA was performed according to standard Affymetrix protocols.
| | Sample_scan_protocol | Scanning was performed according to standard Affymetrix protocols.
| | Sample_data_processing | Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0). Of 22,283 probe sets on the HG-U133A chip, 78 internal control probes were removed and 22,215 probe sets representing 12,978 gene products were analyzed. Microarray gene expression intensities were normalized in order to ensure that all 22 array chips have the same inter-quartile ranges (IQR). In addition, they were log-transformed with base 2, which allows transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.rproject.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering & heatmap analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix website (www.affymetix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyzed. We eliminated non-expressed (within 2 SD from zero in all conditions) and housekeeping genes (not expressed).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,Albert,Gleissner
| | Sample_contact_fax | 434-924-2828
| | Sample_contact_laboratory | Ley
| | Sample_contact_department | Cardiovascular Research Center
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | MR5 Building, Rm. 1133
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM170nnn/GSM170938/suppl/GSM170938.cel.gz
| | Sample_series_id | GSE7138
| | Sample_data_row_count | 22283
| | |
|
GSM170941 | GPL96 |
|
mmLDL #1
|
peripheral blood mmLDL #1
|
healthy blood donors
|
Gene expression in monocyte-derived macophages stimulated with mmLDL for two days.
|
| Sample_geo_accession | GSM170941
| | Sample_status | Public on Mar 28 2007
| | Sample_submission_date | Feb 22 2007
| | Sample_last_update_date | Mar 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Virginia Blood Services (Richmond, VA)
| | Sample_treatment_protocol_ch1 | Human blood was drawn from the antecubital veins of healthy blood donors and provided as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the
| | Sample_treatment_protocol_ch1 | mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer. From these PBMCs, monocytes were isolated using a negative selection monocyte isolation kit and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of the isolated fraction was > 97% as estimated by flow cytometry using anti-CD14.
| | Sample_growth_protocol_ch1 | Monocytes were cultured in Macrophage Serum-Free Medium (MSFM, Invitrogen, Carlsbad, CA) in the presence of 1% media supplement nutridoma-HU (Roche Molecular Biochemicals, Indianapolis, IN) and 100 nM M-CSF for 6 days, after which the cells showed the expected morphological signs of macrophage differentiation. Human monocyte-derived macrophages (MDM) were incubated with minimally modified LDL (mmLDL) (100 µg/ml) for 2 days to induce foam cell formation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of samples was performed according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Hybridization of cRNA was performed according to standard Affymetrix protocols.
| | Sample_scan_protocol | Scanning was performed according to standard Affymetrix protocols.
| | Sample_data_processing | Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0). Of 22,283 probe sets on the HG-U133A chip, 78 internal control probes were removed and 22,215 probe sets representing 12,978 gene products were analyzed. Microarray gene expression intensities were normalized in order to ensure that all 22 array chips have the same inter-quartile ranges (IQR). In addition, they were log-transformed with base 2, which allows transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.rproject.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering & heatmap analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix website (www.affymetix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyzed. We eliminated non-expressed (within 2 SD from zero in all conditions) and housekeeping genes (not expressed).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,Albert,Gleissner
| | Sample_contact_fax | 434-924-2828
| | Sample_contact_laboratory | Ley
| | Sample_contact_department | Cardiovascular Research Center
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | MR5 Building, Rm. 1133
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM170nnn/GSM170941/suppl/GSM170941.cel.gz
| | Sample_series_id | GSE7138
| | Sample_data_row_count | 22283
| | |
|
GSM170942 | GPL96 |
|
mmLDL #2
|
peripheral blood mmLDL #2
|
healthy blood donors
|
Gene expression in monocyte-derived macophages stimulated with mmLDL for two days.
|
| Sample_geo_accession | GSM170942
| | Sample_status | Public on Mar 28 2007
| | Sample_submission_date | Feb 22 2007
| | Sample_last_update_date | Mar 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Virginia Blood Services (Richmond, VA)
| | Sample_treatment_protocol_ch1 | Human blood was drawn from the antecubital veins of healthy blood donors and provided as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the
| | Sample_treatment_protocol_ch1 | mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer. From these PBMCs, monocytes were isolated using a negative selection monocyte isolation kit and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of the isolated fraction was > 97% as estimated by flow cytometry using anti-CD14.
| | Sample_growth_protocol_ch1 | Monocytes were cultured in Macrophage Serum-Free Medium (MSFM, Invitrogen, Carlsbad, CA) in the presence of 1% media supplement nutridoma-HU (Roche Molecular Biochemicals, Indianapolis, IN) and 100 nM M-CSF for 6 days, after which the cells showed the expected morphological signs of macrophage differentiation. Human monocyte-derived macrophages (MDM) were incubated with minimally modified LDL (mmLDL) (100 µg/ml) for 2 days to induce foam cell formation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of samples was performed according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Hybridization of cRNA was performed according to standard Affymetrix protocols.
| | Sample_scan_protocol | Scanning was performed according to standard Affymetrix protocols.
| | Sample_data_processing | Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0). Of 22,283 probe sets on the HG-U133A chip, 78 internal control probes were removed and 22,215 probe sets representing 12,978 gene products were analyzed. Microarray gene expression intensities were normalized in order to ensure that all 22 array chips have the same inter-quartile ranges (IQR). In addition, they were log-transformed with base 2, which allows transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.rproject.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering & heatmap analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix website (www.affymetix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyzed. We eliminated non-expressed (within 2 SD from zero in all conditions) and housekeeping genes (not expressed).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,Albert,Gleissner
| | Sample_contact_fax | 434-924-2828
| | Sample_contact_laboratory | Ley
| | Sample_contact_department | Cardiovascular Research Center
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | MR5 Building, Rm. 1133
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM170nnn/GSM170942/suppl/GSM170942.cel.gz
| | Sample_series_id | GSE7138
| | Sample_data_row_count | 22283
| | |
|
GSM170943 | GPL96 |
|
oxLDL #1
|
peripheral blood oxLDL #1
|
healthy blood donors
|
Gene expression in monocyte-derived macophages stimulated with oxLDL for two days.
|
| Sample_geo_accession | GSM170943
| | Sample_status | Public on Mar 28 2007
| | Sample_submission_date | Feb 22 2007
| | Sample_last_update_date | Mar 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Virginia Blood Services (Richmond, VA)
| | Sample_treatment_protocol_ch1 | Human blood was drawn from the antecubital veins of healthy blood donors and provided as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the
| | Sample_treatment_protocol_ch1 | mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer. From these PBMCs, monocytes were isolated using a negative selection monocyte isolation kit and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of the isolated fraction was > 97% as estimated by flow cytometry using anti-CD14.
| | Sample_growth_protocol_ch1 | Monocytes were cultured in Macrophage Serum-Free Medium (MSFM, Invitrogen, Carlsbad, CA) in the presence of 1% media supplement nutridoma-HU (Roche Molecular Biochemicals, Indianapolis, IN) and 100 nM M-CSF for 6 days, after which the cells showed the expected morphological signs of macrophage differentiation. Human monocyte-derived macrophages (MDM) were incubated with minimally oxidized LDL (oxLDL) (100 µg/ml) for 2 days to induce foam cell formation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of samples was performed according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Hybridization of cRNA was performed according to standard Affymetrix protocols.
| | Sample_scan_protocol | Scanning was performed according to standard Affymetrix protocols.
| | Sample_data_processing | Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0). Of 22,283 probe sets on the HG-U133A chip, 78 internal control probes were removed and 22,215 probe sets representing 12,978 gene products were analyzed. Microarray gene expression intensities were normalized in order to ensure that all 22 array chips have the same inter-quartile ranges (IQR). In addition, they were log-transformed with base 2, which allows transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.rproject.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering & heatmap analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix website (www.affymetix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyzed. We eliminated non-expressed (within 2 SD from zero in all conditions) and housekeeping genes (not expressed).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,Albert,Gleissner
| | Sample_contact_fax | 434-924-2828
| | Sample_contact_laboratory | Ley
| | Sample_contact_department | Cardiovascular Research Center
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | MR5 Building, Rm. 1133
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM170nnn/GSM170943/suppl/GSM170943.cel.gz
| | Sample_series_id | GSE7138
| | Sample_data_row_count | 22283
| | |
|
GSM170944 | GPL96 |
|
oxLDL #2
|
peripheral blood oxLDL #2
|
healthy blood donors
|
Gene expression in monocyte-derived macophages stimulated with oxLDL for two days.
|
| Sample_geo_accession | GSM170944
| | Sample_status | Public on Mar 28 2007
| | Sample_submission_date | Feb 22 2007
| | Sample_last_update_date | Mar 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Virginia Blood Services (Richmond, VA)
| | Sample_treatment_protocol_ch1 | Human blood was drawn from the antecubital veins of healthy blood donors and provided as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the
| | Sample_treatment_protocol_ch1 | mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer. From these PBMCs, monocytes were isolated using a negative selection monocyte isolation kit and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of the isolated fraction was > 97% as estimated by flow cytometry using anti-CD14.
| | Sample_growth_protocol_ch1 | Monocytes were cultured in Macrophage Serum-Free Medium (MSFM, Invitrogen, Carlsbad, CA) in the presence of 1% media supplement nutridoma-HU (Roche Molecular Biochemicals, Indianapolis, IN) and 100 nM M-CSF for 6 days, after which the cells showed the expected morphological signs of macrophage differentiation. Human monocyte-derived macrophages (MDM) were incubated with minimally oxidized LDL (oxLDL) (100 µg/ml) for 2 days to induce foam cell formation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of samples was performed according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Hybridization of cRNA was performed according to standard Affymetrix protocols.
| | Sample_scan_protocol | Scanning was performed according to standard Affymetrix protocols.
| | Sample_data_processing | Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0). Of 22,283 probe sets on the HG-U133A chip, 78 internal control probes were removed and 22,215 probe sets representing 12,978 gene products were analyzed. Microarray gene expression intensities were normalized in order to ensure that all 22 array chips have the same inter-quartile ranges (IQR). In addition, they were log-transformed with base 2, which allows transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.rproject.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering & heatmap analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix website (www.affymetix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyzed. We eliminated non-expressed (within 2 SD from zero in all conditions) and housekeeping genes (not expressed).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,Albert,Gleissner
| | Sample_contact_fax | 434-924-2828
| | Sample_contact_laboratory | Ley
| | Sample_contact_department | Cardiovascular Research Center
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | MR5 Building, Rm. 1133
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM170nnn/GSM170944/suppl/GSM170944.cel.gz
| | Sample_series_id | GSE7138
| | Sample_data_row_count | 22283
| | |
|
GSM170969 | GPL96 |
|
CXCL4 #1
|
peripheral blood CXCL4 #1
|
healthy blood donors
|
Gene expression in monocyte derived macrophages from healthy donors
|
| Sample_geo_accession | GSM170969
| | Sample_status | Public on Mar 28 2007
| | Sample_submission_date | Feb 22 2007
| | Sample_last_update_date | Mar 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Virginia Blood Services (Richmond, VA)
| | Sample_treatment_protocol_ch1 | Human blood was drawn from the antecubital veins of healthy blood donors and provided
| | Sample_treatment_protocol_ch1 | as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in
| | Sample_treatment_protocol_ch1 | monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the
| | Sample_treatment_protocol_ch1 | mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer. From these PBMCs, monocytes were isolated using a negative selection monocyte isolation kit and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of the isolated fraction was > 97% as estimated by flow cytometry using anti-CD14.
| | Sample_growth_protocol_ch1 | Monocytes were incubated with CXCL4 (100 nM) for 6 days to obtain macrophage differentiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Media was aspirated and cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of samples was performed according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Hybridization of cRNA was performed according to standard Affymetrix protocols.
| | Sample_scan_protocol | Scanning was performed according to standard Affymetrix protocols.
| | Sample_data_processing | Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0). Of 22,283 probe sets on the HG-U133A chip, 78 internal control probes were removed and 22,215 probe sets representing 12,978 gene products were analyzed. Microarray gene expression intensities were normalized in order to ensure that all 22 array chips have the same inter-quartile ranges (IQR). In addition, they were log-transformed with base 2, which allows transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.rproject.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering & heatmap analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix website (www.affymetix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyzed. We eliminated non-expressed (within 2 SD from zero in all conditions) and housekeeping genes (not expressed).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,Albert,Gleissner
| | Sample_contact_fax | 434-924-2828
| | Sample_contact_laboratory | Ley
| | Sample_contact_department | Cardiovascular Research Center
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | MR5 Building, Rm. 1133
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM170nnn/GSM170969/suppl/GSM170969.cel.gz
| | Sample_series_id | GSE7138
| | Sample_data_row_count | 22283
| | |
|
GSM170970 | GPL96 |
|
CXCL4 #2
|
peripheral blood CXCL4 #2
|
healthy blood donors
|
Gene expression in monocyte derived macrophages from healthy donors
|
| Sample_geo_accession | GSM170970
| | Sample_status | Public on Mar 28 2007
| | Sample_submission_date | Feb 22 2007
| | Sample_last_update_date | Mar 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Virginia Blood Services (Richmond, VA)
| | Sample_treatment_protocol_ch1 | Human blood was drawn from the antecubital veins of healthy blood donors and provided
| | Sample_treatment_protocol_ch1 | as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in
| | Sample_treatment_protocol_ch1 | monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the
| | Sample_treatment_protocol_ch1 | mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer. From these PBMCs, monocytes were isolated using a negative selection monocyte isolation kit and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of the isolated fraction was > 97% as estimated by flow cytometry using anti-CD14.
| | Sample_growth_protocol_ch1 | Monocytes were incubated with CXCL4 (100 nM) for 6 days to obtain macrophage differentiation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Media was aspirated and cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of samples was performed according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Hybridization of cRNA was performed according to standard Affymetrix protocols.
| | Sample_scan_protocol | Scanning was performed according to standard Affymetrix protocols.
| | Sample_data_processing | Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0). Of 22,283 probe sets on the HG-U133A chip, 78 internal control probes were removed and 22,215 probe sets representing 12,978 gene products were analyzed. Microarray gene expression intensities were normalized in order to ensure that all 22 array chips have the same inter-quartile ranges (IQR). In addition, they were log-transformed with base 2, which allows transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.rproject.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering & heatmap analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix website (www.affymetix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyzed. We eliminated non-expressed (within 2 SD from zero in all conditions) and housekeeping genes (not expressed).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,Albert,Gleissner
| | Sample_contact_fax | 434-924-2828
| | Sample_contact_laboratory | Ley
| | Sample_contact_department | Cardiovascular Research Center
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | MR5 Building, Rm. 1133
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM170nnn/GSM170970/suppl/GSM170970.cel.gz
| | Sample_series_id | GSE7138
| | Sample_data_row_count | 22283
| | |
|
GSM170971 | GPL96 |
|
CXCL4+oxLDL #1
|
peripheral blood CXCL4+oxLDL #1
|
healthy blood donors
|
Gene expression in monocyte derived macrophages from healthy donors treated with oxLDL for 2 days
|
| Sample_geo_accession | GSM170971
| | Sample_status | Public on Mar 28 2007
| | Sample_submission_date | Feb 22 2007
| | Sample_last_update_date | Mar 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Virginia Blood Services (Richmond, VA)
| | Sample_treatment_protocol_ch1 | Human blood was drawn from the antecubital veins of healthy blood donors and provided
| | Sample_treatment_protocol_ch1 | as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in
| | Sample_treatment_protocol_ch1 | monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the
| | Sample_treatment_protocol_ch1 | mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer. From these PBMCs, monocytes were isolated using a negative selection monocyte isolation kit and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of the isolated fraction was > 97% as estimated by flow cytometry using anti-CD14.
| | Sample_growth_protocol_ch1 | Monocytes were incubated with CXCL4 (100 nM) for 6 days to obtain macrophage differentiation. Macrophages were treated with oxidized LDL (oxLDL) (100 µg/ml) for 2 days to induce foam cell formation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Media was aspirated and cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of samples was performed according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Hybridization of cRNA was performed according to standard Affymetrix protocols.
| | Sample_scan_protocol | Scanning was performed according to standard Affymetrix protocols.
| | Sample_data_processing | Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0). Of 22,283 probe sets on the HG-U133A chip, 78 internal control probes were removed and 22,215 probe sets representing 12,978 gene products were analyzed. Microarray gene expression intensities were normalized in order to ensure that all 22 array chips have the same inter-quartile ranges (IQR). In addition, they were log-transformed with base 2, which allows transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.rproject.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering & heatmap analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix website (www.affymetix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyzed. We eliminated non-expressed (within 2 SD from zero in all conditions) and housekeeping genes (not expressed).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,Albert,Gleissner
| | Sample_contact_fax | 434-924-2828
| | Sample_contact_laboratory | Ley
| | Sample_contact_department | Cardiovascular Research Center
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | MR5 Building, Rm. 1133
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM170nnn/GSM170971/suppl/GSM170971.cel.gz
| | Sample_series_id | GSE7138
| | Sample_data_row_count | 22283
| | |
|
GSM170972 | GPL96 |
|
CXCL4+oxLDL #2
|
peripheral blood CXCL4+oxLDL #2
|
healthy blood donors
|
Gene expression in monocyte derived macrophages from healthy donors treated with oxLDL for 2 days
|
| Sample_geo_accession | GSM170972
| | Sample_status | Public on Mar 28 2007
| | Sample_submission_date | Feb 22 2007
| | Sample_last_update_date | Mar 27 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Virginia Blood Services (Richmond, VA)
| | Sample_treatment_protocol_ch1 | Human blood was drawn from the antecubital veins of healthy blood donors and provided
| | Sample_treatment_protocol_ch1 | as buffy coats by the Virginia Blood Services (Richmond, VA). The mononuclear fractions were pooled from four unidentified donors to decrease individual variations in
| | Sample_treatment_protocol_ch1 | monocytes. Mixed peripheral blood mononuclear cells (PBMCs) were isolated by Histopaque 1.077 (Sigma Diagnostics, Inc., St. Louis, MO). Following centrifugation, the
| | Sample_treatment_protocol_ch1 | mononuclear layer was removed and washed with PBS containing 0.02% ethylenediaminetetraacetate (EDTA). The pellet was resuspended in 1X H-lyse Buffer (R&D Systems Inc., Minneapolis, MN), and washed with wash buffer. From these PBMCs, monocytes were isolated using a negative selection monocyte isolation kit and LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of the isolated fraction was > 97% as estimated by flow cytometry using anti-CD14.
| | Sample_growth_protocol_ch1 | Monocytes were incubated with CXCL4 (100 nM) for 6 days to obtain macrophage differentiation. Macrophages were treated with oxidized LDL (oxLDL) (100 µg/ml) for 2 days to induce foam cell formation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Media was aspirated and cells were washed with PBS twice. mRNA was isolated using RNEasy Kits (Qiagen, Valencia, CA) according to manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling of samples was performed according to standard Affymetrix protocols.
| | Sample_hyb_protocol | Hybridization of cRNA was performed according to standard Affymetrix protocols.
| | Sample_scan_protocol | Scanning was performed according to standard Affymetrix protocols.
| | Sample_data_processing | Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0). Of 22,283 probe sets on the HG-U133A chip, 78 internal control probes were removed and 22,215 probe sets representing 12,978 gene products were analyzed. Microarray gene expression intensities were normalized in order to ensure that all 22 array chips have the same inter-quartile ranges (IQR). In addition, they were log-transformed with base 2, which allows transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.rproject.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering & heatmap analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix website (www.affymetix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyzed. We eliminated non-expressed (within 2 SD from zero in all conditions) and housekeeping genes (not expressed).
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,Albert,Gleissner
| | Sample_contact_fax | 434-924-2828
| | Sample_contact_laboratory | Ley
| | Sample_contact_department | Cardiovascular Research Center
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | MR5 Building, Rm. 1133
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22903
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM170nnn/GSM170972/suppl/GSM170972.cel.gz
| | Sample_series_id | GSE7138
| | 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: |
|
|
|
