Search results for the GEO ID: GSE39264  |
(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 |
GSM959062 | GPL8759 |
|
BL6_apoe_4 wk-3
|
MAECs isolated from 4 week ApoE -/- mice
|
strain: C57BL/6
genotype: ApoE -/-
cell type: aortic endothelial cells
treatment: no treatment
disease state: pre-lesioned hyperlipidemic
|
Gene expression data from amplified RNA isolated directly from the intima of mouse aortas.
|
| Sample_geo_accession | GSM959062
| | Sample_status | Public on Jul 11 2012
| | Sample_submission_date | Jul 11 2012
| | Sample_last_update_date | Jul 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | DMEM with 1% FBS was used as the cell culture medium; vessels were incubated for 4 hours in a cell culture incubator at 37 C, 5% CO2. 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) and oxLDL were prepared as previously described 28, 29 Lipopolysaccharide (LPS) was purchased from List Biological Laboratories. OxPAPC and oxLDL were added to DMEM for a final concentration of 50 ug/mL, LPS was formulated for a final concentration of 4 ng/mL. After aortas were opened en face, each was placed in one well of a 12-well cell culture plate along with 1 mL of the appropriate DMEM formulation pre-warmed to 37C. After the 4 hour treatment, aortas were removed from media and placed lumen side up on a glass slide; isolation continued as described above, beginning with hematoxylin treatment.
| | Sample_growth_protocol_ch1 | Mice were maintained in the UCLA barrier facility on chow diet prior to euthanization
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNAqueous®-Micro Kit by Ambion. The buffer and collagenase solution containing scraped endothelial cells was pipetted directly into 100 uL of Lysis buffer in a 200 uL PCR tube, vortexed, then incubated at 42 C for 30 minutes on a PCR thermalcycler. RNA isolation continued following the manufacturer’s protocol, including suggestions to pre-wet the filter assembly with 30 uL Lysis buffer prior to isolation and to preheat elution solution to 95 C. RNA was stored at -80 C after isolation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The products of RNA amplification were treated with the NuGEN Encore Biotin Module prior to hybridization according to manufacturer’s protocol
| | Sample_hyb_protocol | Entire sample was hybridized for 40 hr on a 96 well HTA plate according to manufacturer protocol.
| | Sample_scan_protocol | GeneChips were processed using GCOS.
| | Sample_data_processing | Microarray results were normalized using RMA in the “affy” package
| | Sample_platform_id | GPL8759
| | Sample_contact_name | Ayca,,Erbilgin
| | Sample_contact_email | ayca.erbilgin@gmail.com
| | Sample_contact_phone | 310 825 1595
| | Sample_contact_laboratory | Lusis
| | Sample_contact_department | Medicine/Cardiology
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 675 Charles E Young Dr South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM959nnn/GSM959062/suppl/GSM959062_BL6_apoe_4_wk-3.cel.gz
| | Sample_series_id | GSE39264
| | Sample_data_row_count | 22626
| | |
|
GSM959063 | GPL8759 |
|
BL6_apoe_4 wk-4
|
MAECs isolated from 4 week ApoE -/- mice
|
strain: C57BL/6
genotype: ApoE -/-
cell type: aortic endothelial cells
treatment: no treatment
disease state: pre-lesioned hyperlipidemic
|
Gene expression data from amplified RNA isolated directly from the intima of mouse aortas.
|
| Sample_geo_accession | GSM959063
| | Sample_status | Public on Jul 11 2012
| | Sample_submission_date | Jul 11 2012
| | Sample_last_update_date | Jul 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | DMEM with 1% FBS was used as the cell culture medium; vessels were incubated for 4 hours in a cell culture incubator at 37 C, 5% CO2. 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) and oxLDL were prepared as previously described 28, 29 Lipopolysaccharide (LPS) was purchased from List Biological Laboratories. OxPAPC and oxLDL were added to DMEM for a final concentration of 50 ug/mL, LPS was formulated for a final concentration of 4 ng/mL. After aortas were opened en face, each was placed in one well of a 12-well cell culture plate along with 1 mL of the appropriate DMEM formulation pre-warmed to 37C. After the 4 hour treatment, aortas were removed from media and placed lumen side up on a glass slide; isolation continued as described above, beginning with hematoxylin treatment.
| | Sample_growth_protocol_ch1 | Mice were maintained in the UCLA barrier facility on chow diet prior to euthanization
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNAqueous®-Micro Kit by Ambion. The buffer and collagenase solution containing scraped endothelial cells was pipetted directly into 100 uL of Lysis buffer in a 200 uL PCR tube, vortexed, then incubated at 42 C for 30 minutes on a PCR thermalcycler. RNA isolation continued following the manufacturer’s protocol, including suggestions to pre-wet the filter assembly with 30 uL Lysis buffer prior to isolation and to preheat elution solution to 95 C. RNA was stored at -80 C after isolation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The products of RNA amplification were treated with the NuGEN Encore Biotin Module prior to hybridization according to manufacturer’s protocol
| | Sample_hyb_protocol | Entire sample was hybridized for 40 hr on a 96 well HTA plate according to manufacturer protocol.
| | Sample_scan_protocol | GeneChips were processed using GCOS.
| | Sample_data_processing | Microarray results were normalized using RMA in the “affy” package
| | Sample_platform_id | GPL8759
| | Sample_contact_name | Ayca,,Erbilgin
| | Sample_contact_email | ayca.erbilgin@gmail.com
| | Sample_contact_phone | 310 825 1595
| | Sample_contact_laboratory | Lusis
| | Sample_contact_department | Medicine/Cardiology
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 675 Charles E Young Dr South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM959nnn/GSM959063/suppl/GSM959063_BL6_apoe_4_wk-4.cel.gz
| | Sample_series_id | GSE39264
| | Sample_data_row_count | 22626
| | |
|
GSM959064 | GPL8759 |
|
BL6_apoe_4 wk-5
|
MAECs isolated from 4 week ApoE -/- mice
|
strain: C57BL/6
genotype: ApoE -/-
cell type: aortic endothelial cells
treatment: no treatment
disease state: pre-lesioned hyperlipidemic
|
Gene expression data from amplified RNA isolated directly from the intima of mouse aortas.
|
| Sample_geo_accession | GSM959064
| | Sample_status | Public on Jul 11 2012
| | Sample_submission_date | Jul 11 2012
| | Sample_last_update_date | Jul 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | DMEM with 1% FBS was used as the cell culture medium; vessels were incubated for 4 hours in a cell culture incubator at 37 C, 5% CO2. 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) and oxLDL were prepared as previously described 28, 29 Lipopolysaccharide (LPS) was purchased from List Biological Laboratories. OxPAPC and oxLDL were added to DMEM for a final concentration of 50 ug/mL, LPS was formulated for a final concentration of 4 ng/mL. After aortas were opened en face, each was placed in one well of a 12-well cell culture plate along with 1 mL of the appropriate DMEM formulation pre-warmed to 37C. After the 4 hour treatment, aortas were removed from media and placed lumen side up on a glass slide; isolation continued as described above, beginning with hematoxylin treatment.
| | Sample_growth_protocol_ch1 | Mice were maintained in the UCLA barrier facility on chow diet prior to euthanization
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNAqueous®-Micro Kit by Ambion. The buffer and collagenase solution containing scraped endothelial cells was pipetted directly into 100 uL of Lysis buffer in a 200 uL PCR tube, vortexed, then incubated at 42 C for 30 minutes on a PCR thermalcycler. RNA isolation continued following the manufacturer’s protocol, including suggestions to pre-wet the filter assembly with 30 uL Lysis buffer prior to isolation and to preheat elution solution to 95 C. RNA was stored at -80 C after isolation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The products of RNA amplification were treated with the NuGEN Encore Biotin Module prior to hybridization according to manufacturer’s protocol
| | Sample_hyb_protocol | Entire sample was hybridized for 40 hr on a 96 well HTA plate according to manufacturer protocol.
| | Sample_scan_protocol | GeneChips were processed using GCOS.
| | Sample_data_processing | Microarray results were normalized using RMA in the “affy” package
| | Sample_platform_id | GPL8759
| | Sample_contact_name | Ayca,,Erbilgin
| | Sample_contact_email | ayca.erbilgin@gmail.com
| | Sample_contact_phone | 310 825 1595
| | Sample_contact_laboratory | Lusis
| | Sample_contact_department | Medicine/Cardiology
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 675 Charles E Young Dr South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM959nnn/GSM959064/suppl/GSM959064_BL6_apoe_4_wk-5.cel.gz
| | Sample_series_id | GSE39264
| | Sample_data_row_count | 22626
| | |
|
GSM959065 | GPL8759 |
|
BL6_apoe_4 wk-6
|
MAECs isolated from 4 week ApoE -/- mice
|
strain: C57BL/6
genotype: ApoE -/-
cell type: aortic endothelial cells
treatment: no treatment
disease state: pre-lesioned hyperlipidemic
|
Gene expression data from amplified RNA isolated directly from the intima of mouse aortas.
|
| Sample_geo_accession | GSM959065
| | Sample_status | Public on Jul 11 2012
| | Sample_submission_date | Jul 11 2012
| | Sample_last_update_date | Jul 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | DMEM with 1% FBS was used as the cell culture medium; vessels were incubated for 4 hours in a cell culture incubator at 37 C, 5% CO2. 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) and oxLDL were prepared as previously described 28, 29 Lipopolysaccharide (LPS) was purchased from List Biological Laboratories. OxPAPC and oxLDL were added to DMEM for a final concentration of 50 ug/mL, LPS was formulated for a final concentration of 4 ng/mL. After aortas were opened en face, each was placed in one well of a 12-well cell culture plate along with 1 mL of the appropriate DMEM formulation pre-warmed to 37C. After the 4 hour treatment, aortas were removed from media and placed lumen side up on a glass slide; isolation continued as described above, beginning with hematoxylin treatment.
| | Sample_growth_protocol_ch1 | Mice were maintained in the UCLA barrier facility on chow diet prior to euthanization
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNAqueous®-Micro Kit by Ambion. The buffer and collagenase solution containing scraped endothelial cells was pipetted directly into 100 uL of Lysis buffer in a 200 uL PCR tube, vortexed, then incubated at 42 C for 30 minutes on a PCR thermalcycler. RNA isolation continued following the manufacturer’s protocol, including suggestions to pre-wet the filter assembly with 30 uL Lysis buffer prior to isolation and to preheat elution solution to 95 C. RNA was stored at -80 C after isolation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The products of RNA amplification were treated with the NuGEN Encore Biotin Module prior to hybridization according to manufacturer’s protocol
| | Sample_hyb_protocol | Entire sample was hybridized for 40 hr on a 96 well HTA plate according to manufacturer protocol.
| | Sample_scan_protocol | GeneChips were processed using GCOS.
| | Sample_data_processing | Microarray results were normalized using RMA in the “affy” package
| | Sample_platform_id | GPL8759
| | Sample_contact_name | Ayca,,Erbilgin
| | Sample_contact_email | ayca.erbilgin@gmail.com
| | Sample_contact_phone | 310 825 1595
| | Sample_contact_laboratory | Lusis
| | Sample_contact_department | Medicine/Cardiology
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 675 Charles E Young Dr South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM959nnn/GSM959065/suppl/GSM959065_BL6_apoe_4_wk-6.cel.gz
| | Sample_series_id | GSE39264
| | Sample_data_row_count | 22626
| | |
|
GSM959066 | GPL8759 |
|
BL6_wt_4 wk-7
|
MAECs isolated from 4 week wild-type mice
|
strain: C57BL/6
genotype: wild-type
cell type: aortic endothelial cells
treatment: no treatment
disease state: control normal-lipidemic
|
Gene expression data from amplified RNA isolated directly from the intima of mouse aortas.
|
| Sample_geo_accession | GSM959066
| | Sample_status | Public on Jul 11 2012
| | Sample_submission_date | Jul 11 2012
| | Sample_last_update_date | Jul 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | DMEM with 1% FBS was used as the cell culture medium; vessels were incubated for 4 hours in a cell culture incubator at 37 C, 5% CO2. 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) and oxLDL were prepared as previously described 28, 29 Lipopolysaccharide (LPS) was purchased from List Biological Laboratories. OxPAPC and oxLDL were added to DMEM for a final concentration of 50 ug/mL, LPS was formulated for a final concentration of 4 ng/mL. After aortas were opened en face, each was placed in one well of a 12-well cell culture plate along with 1 mL of the appropriate DMEM formulation pre-warmed to 37C. After the 4 hour treatment, aortas were removed from media and placed lumen side up on a glass slide; isolation continued as described above, beginning with hematoxylin treatment.
| | Sample_growth_protocol_ch1 | Mice were maintained in the UCLA barrier facility on chow diet prior to euthanization
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNAqueous®-Micro Kit by Ambion. The buffer and collagenase solution containing scraped endothelial cells was pipetted directly into 100 uL of Lysis buffer in a 200 uL PCR tube, vortexed, then incubated at 42 C for 30 minutes on a PCR thermalcycler. RNA isolation continued following the manufacturer’s protocol, including suggestions to pre-wet the filter assembly with 30 uL Lysis buffer prior to isolation and to preheat elution solution to 95 C. RNA was stored at -80 C after isolation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The products of RNA amplification were treated with the NuGEN Encore Biotin Module prior to hybridization according to manufacturer’s protocol
| | Sample_hyb_protocol | Entire sample was hybridized for 40 hr on a 96 well HTA plate according to manufacturer protocol.
| | Sample_scan_protocol | GeneChips were processed using GCOS.
| | Sample_data_processing | Microarray results were normalized using RMA in the “affy” package
| | Sample_platform_id | GPL8759
| | Sample_contact_name | Ayca,,Erbilgin
| | Sample_contact_email | ayca.erbilgin@gmail.com
| | Sample_contact_phone | 310 825 1595
| | Sample_contact_laboratory | Lusis
| | Sample_contact_department | Medicine/Cardiology
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 675 Charles E Young Dr South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM959nnn/GSM959066/suppl/GSM959066_BL6_wt_4_wk-7.cel.gz
| | Sample_series_id | GSE39264
| | Sample_data_row_count | 22626
| | |
|
GSM959067 | GPL8759 |
|
BL6_wt_4 wk-8
|
MAECs isolated from 4 week wild-type mice
|
strain: C57BL/6
genotype: wild-type
cell type: aortic endothelial cells
treatment: no treatment
disease state: control normal-lipidemic
|
Gene expression data from amplified RNA isolated directly from the intima of mouse aortas.
|
| Sample_geo_accession | GSM959067
| | Sample_status | Public on Jul 11 2012
| | Sample_submission_date | Jul 11 2012
| | Sample_last_update_date | Jul 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | DMEM with 1% FBS was used as the cell culture medium; vessels were incubated for 4 hours in a cell culture incubator at 37 C, 5% CO2. 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) and oxLDL were prepared as previously described 28, 29 Lipopolysaccharide (LPS) was purchased from List Biological Laboratories. OxPAPC and oxLDL were added to DMEM for a final concentration of 50 ug/mL, LPS was formulated for a final concentration of 4 ng/mL. After aortas were opened en face, each was placed in one well of a 12-well cell culture plate along with 1 mL of the appropriate DMEM formulation pre-warmed to 37C. After the 4 hour treatment, aortas were removed from media and placed lumen side up on a glass slide; isolation continued as described above, beginning with hematoxylin treatment.
| | Sample_growth_protocol_ch1 | Mice were maintained in the UCLA barrier facility on chow diet prior to euthanization
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNAqueous®-Micro Kit by Ambion. The buffer and collagenase solution containing scraped endothelial cells was pipetted directly into 100 uL of Lysis buffer in a 200 uL PCR tube, vortexed, then incubated at 42 C for 30 minutes on a PCR thermalcycler. RNA isolation continued following the manufacturer’s protocol, including suggestions to pre-wet the filter assembly with 30 uL Lysis buffer prior to isolation and to preheat elution solution to 95 C. RNA was stored at -80 C after isolation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The products of RNA amplification were treated with the NuGEN Encore Biotin Module prior to hybridization according to manufacturer’s protocol
| | Sample_hyb_protocol | Entire sample was hybridized for 40 hr on a 96 well HTA plate according to manufacturer protocol.
| | Sample_scan_protocol | GeneChips were processed using GCOS.
| | Sample_data_processing | Microarray results were normalized using RMA in the “affy” package
| | Sample_platform_id | GPL8759
| | Sample_contact_name | Ayca,,Erbilgin
| | Sample_contact_email | ayca.erbilgin@gmail.com
| | Sample_contact_phone | 310 825 1595
| | Sample_contact_laboratory | Lusis
| | Sample_contact_department | Medicine/Cardiology
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 675 Charles E Young Dr South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM959nnn/GSM959067/suppl/GSM959067_BL6_wt_4_wk-8.cel.gz
| | Sample_series_id | GSE39264
| | Sample_data_row_count | 22626
| | |
|
GSM959068 | GPL8759 |
|
BL6_wt_4 wk-12
|
MAECs isolated from 4 week wild-type mice
|
strain: C57BL/6
genotype: wild-type
cell type: aortic endothelial cells
treatment: no treatment
disease state: control normal-lipidemic
|
Gene expression data from amplified RNA isolated directly from the intima of mouse aortas.
|
| Sample_geo_accession | GSM959068
| | Sample_status | Public on Jul 11 2012
| | Sample_submission_date | Jul 11 2012
| | Sample_last_update_date | Jul 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | DMEM with 1% FBS was used as the cell culture medium; vessels were incubated for 4 hours in a cell culture incubator at 37 C, 5% CO2. 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) and oxLDL were prepared as previously described 28, 29 Lipopolysaccharide (LPS) was purchased from List Biological Laboratories. OxPAPC and oxLDL were added to DMEM for a final concentration of 50 ug/mL, LPS was formulated for a final concentration of 4 ng/mL. After aortas were opened en face, each was placed in one well of a 12-well cell culture plate along with 1 mL of the appropriate DMEM formulation pre-warmed to 37C. After the 4 hour treatment, aortas were removed from media and placed lumen side up on a glass slide; isolation continued as described above, beginning with hematoxylin treatment.
| | Sample_growth_protocol_ch1 | Mice were maintained in the UCLA barrier facility on chow diet prior to euthanization
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNAqueous®-Micro Kit by Ambion. The buffer and collagenase solution containing scraped endothelial cells was pipetted directly into 100 uL of Lysis buffer in a 200 uL PCR tube, vortexed, then incubated at 42 C for 30 minutes on a PCR thermalcycler. RNA isolation continued following the manufacturer’s protocol, including suggestions to pre-wet the filter assembly with 30 uL Lysis buffer prior to isolation and to preheat elution solution to 95 C. RNA was stored at -80 C after isolation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The products of RNA amplification were treated with the NuGEN Encore Biotin Module prior to hybridization according to manufacturer’s protocol
| | Sample_hyb_protocol | Entire sample was hybridized for 40 hr on a 96 well HTA plate according to manufacturer protocol.
| | Sample_scan_protocol | GeneChips were processed using GCOS.
| | Sample_data_processing | Microarray results were normalized using RMA in the “affy” package
| | Sample_platform_id | GPL8759
| | Sample_contact_name | Ayca,,Erbilgin
| | Sample_contact_email | ayca.erbilgin@gmail.com
| | Sample_contact_phone | 310 825 1595
| | Sample_contact_laboratory | Lusis
| | Sample_contact_department | Medicine/Cardiology
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 675 Charles E Young Dr South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM959nnn/GSM959068/suppl/GSM959068_BL6_wt_4_wk-12.cel.gz
| | Sample_series_id | GSE39264
| | Sample_data_row_count | 22626
| | |
|
GSM959069 | GPL8759 |
|
BL6_wt_4 wk-13
|
MAECs isolated from 4 week wild-type mice
|
strain: C57BL/6
genotype: wild-type
cell type: aortic endothelial cells
treatment: no treatment
disease state: control normal-lipidemic
|
Gene expression data from amplified RNA isolated directly from the intima of mouse aortas.
|
| Sample_geo_accession | GSM959069
| | Sample_status | Public on Jul 11 2012
| | Sample_submission_date | Jul 11 2012
| | Sample_last_update_date | Jul 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | DMEM with 1% FBS was used as the cell culture medium; vessels were incubated for 4 hours in a cell culture incubator at 37 C, 5% CO2. 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) and oxLDL were prepared as previously described 28, 29 Lipopolysaccharide (LPS) was purchased from List Biological Laboratories. OxPAPC and oxLDL were added to DMEM for a final concentration of 50 ug/mL, LPS was formulated for a final concentration of 4 ng/mL. After aortas were opened en face, each was placed in one well of a 12-well cell culture plate along with 1 mL of the appropriate DMEM formulation pre-warmed to 37C. After the 4 hour treatment, aortas were removed from media and placed lumen side up on a glass slide; isolation continued as described above, beginning with hematoxylin treatment.
| | Sample_growth_protocol_ch1 | Mice were maintained in the UCLA barrier facility on chow diet prior to euthanization
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNAqueous®-Micro Kit by Ambion. The buffer and collagenase solution containing scraped endothelial cells was pipetted directly into 100 uL of Lysis buffer in a 200 uL PCR tube, vortexed, then incubated at 42 C for 30 minutes on a PCR thermalcycler. RNA isolation continued following the manufacturer’s protocol, including suggestions to pre-wet the filter assembly with 30 uL Lysis buffer prior to isolation and to preheat elution solution to 95 C. RNA was stored at -80 C after isolation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The products of RNA amplification were treated with the NuGEN Encore Biotin Module prior to hybridization according to manufacturer’s protocol
| | Sample_hyb_protocol | Entire sample was hybridized for 40 hr on a 96 well HTA plate according to manufacturer protocol.
| | Sample_scan_protocol | GeneChips were processed using GCOS.
| | Sample_data_processing | Microarray results were normalized using RMA in the “affy” package
| | Sample_platform_id | GPL8759
| | Sample_contact_name | Ayca,,Erbilgin
| | Sample_contact_email | ayca.erbilgin@gmail.com
| | Sample_contact_phone | 310 825 1595
| | Sample_contact_laboratory | Lusis
| | Sample_contact_department | Medicine/Cardiology
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 675 Charles E Young Dr South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM959nnn/GSM959069/suppl/GSM959069_BL6_wt_4_wk-13.cel.gz
| | Sample_series_id | GSE39264
| | Sample_data_row_count | 22626
| | |
|
GSM959070 | GPL8759 |
|
BL6_wt_4 wk-14
|
MAECs isolated from 4 week wild-type mice
|
strain: C57BL/6
genotype: wild-type
cell type: aortic endothelial cells
treatment: no treatment
disease state: control normal-lipidemic
|
Gene expression data from amplified RNA isolated directly from the intima of mouse aortas.
|
| Sample_geo_accession | GSM959070
| | Sample_status | Public on Jul 11 2012
| | Sample_submission_date | Jul 11 2012
| | Sample_last_update_date | Jul 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | DMEM with 1% FBS was used as the cell culture medium; vessels were incubated for 4 hours in a cell culture incubator at 37 C, 5% CO2. 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) and oxLDL were prepared as previously described 28, 29 Lipopolysaccharide (LPS) was purchased from List Biological Laboratories. OxPAPC and oxLDL were added to DMEM for a final concentration of 50 ug/mL, LPS was formulated for a final concentration of 4 ng/mL. After aortas were opened en face, each was placed in one well of a 12-well cell culture plate along with 1 mL of the appropriate DMEM formulation pre-warmed to 37C. After the 4 hour treatment, aortas were removed from media and placed lumen side up on a glass slide; isolation continued as described above, beginning with hematoxylin treatment.
| | Sample_growth_protocol_ch1 | Mice were maintained in the UCLA barrier facility on chow diet prior to euthanization
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNAqueous®-Micro Kit by Ambion. The buffer and collagenase solution containing scraped endothelial cells was pipetted directly into 100 uL of Lysis buffer in a 200 uL PCR tube, vortexed, then incubated at 42 C for 30 minutes on a PCR thermalcycler. RNA isolation continued following the manufacturer’s protocol, including suggestions to pre-wet the filter assembly with 30 uL Lysis buffer prior to isolation and to preheat elution solution to 95 C. RNA was stored at -80 C after isolation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The products of RNA amplification were treated with the NuGEN Encore Biotin Module prior to hybridization according to manufacturer’s protocol
| | Sample_hyb_protocol | Entire sample was hybridized for 40 hr on a 96 well HTA plate according to manufacturer protocol.
| | Sample_scan_protocol | GeneChips were processed using GCOS.
| | Sample_data_processing | Microarray results were normalized using RMA in the “affy” package
| | Sample_platform_id | GPL8759
| | Sample_contact_name | Ayca,,Erbilgin
| | Sample_contact_email | ayca.erbilgin@gmail.com
| | Sample_contact_phone | 310 825 1595
| | Sample_contact_laboratory | Lusis
| | Sample_contact_department | Medicine/Cardiology
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 675 Charles E Young Dr South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM959nnn/GSM959070/suppl/GSM959070_BL6_wt_4_wk-14.cel.gz
| | Sample_series_id | GSE39264
| | Sample_data_row_count | 22626
| | |
|
GSM959071 | GPL8759 |
|
BL6_wt_4 wk-15
|
MAECs isolated from 4 week wild-type mice
|
strain: C57BL/6
genotype: wild-type
cell type: aortic endothelial cells
treatment: no treatment
disease state: control normal-lipidemic
|
Gene expression data from amplified RNA isolated directly from the intima of mouse aortas.
|
| Sample_geo_accession | GSM959071
| | Sample_status | Public on Jul 11 2012
| | Sample_submission_date | Jul 11 2012
| | Sample_last_update_date | Jul 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | DMEM with 1% FBS was used as the cell culture medium; vessels were incubated for 4 hours in a cell culture incubator at 37 C, 5% CO2. 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) and oxLDL were prepared as previously described 28, 29 Lipopolysaccharide (LPS) was purchased from List Biological Laboratories. OxPAPC and oxLDL were added to DMEM for a final concentration of 50 ug/mL, LPS was formulated for a final concentration of 4 ng/mL. After aortas were opened en face, each was placed in one well of a 12-well cell culture plate along with 1 mL of the appropriate DMEM formulation pre-warmed to 37C. After the 4 hour treatment, aortas were removed from media and placed lumen side up on a glass slide; isolation continued as described above, beginning with hematoxylin treatment.
| | Sample_growth_protocol_ch1 | Mice were maintained in the UCLA barrier facility on chow diet prior to euthanization
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNAqueous®-Micro Kit by Ambion. The buffer and collagenase solution containing scraped endothelial cells was pipetted directly into 100 uL of Lysis buffer in a 200 uL PCR tube, vortexed, then incubated at 42 C for 30 minutes on a PCR thermalcycler. RNA isolation continued following the manufacturer’s protocol, including suggestions to pre-wet the filter assembly with 30 uL Lysis buffer prior to isolation and to preheat elution solution to 95 C. RNA was stored at -80 C after isolation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The products of RNA amplification were treated with the NuGEN Encore Biotin Module prior to hybridization according to manufacturer’s protocol
| | Sample_hyb_protocol | Entire sample was hybridized for 40 hr on a 96 well HTA plate according to manufacturer protocol.
| | Sample_scan_protocol | GeneChips were processed using GCOS.
| | Sample_data_processing | Microarray results were normalized using RMA in the “affy” package
| | Sample_platform_id | GPL8759
| | Sample_contact_name | Ayca,,Erbilgin
| | Sample_contact_email | ayca.erbilgin@gmail.com
| | Sample_contact_phone | 310 825 1595
| | Sample_contact_laboratory | Lusis
| | Sample_contact_department | Medicine/Cardiology
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 675 Charles E Young Dr South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM959nnn/GSM959071/suppl/GSM959071_BL6_wt_4_wk-15.cel.gz
| | Sample_series_id | GSE39264
| | Sample_data_row_count | 22626
| | |
|
GSM959072 | GPL8759 |
|
DMEM-9
|
MAECs isolated from aortas treated with media for 4 hours
|
strain: C57BL/6
genotype: wild-type
cell type: aortic endothelial cells
treatment: DMEM cell media, 4 hrs
disease state: control
|
Gene expression data from amplified RNA isolated directly from the intima of mouse aortas.
|
| Sample_geo_accession | GSM959072
| | Sample_status | Public on Jul 11 2012
| | Sample_submission_date | Jul 11 2012
| | Sample_last_update_date | Jul 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | DMEM with 1% FBS was used as the cell culture medium; vessels were incubated for 4 hours in a cell culture incubator at 37 C, 5% CO2. 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) and oxLDL were prepared as previously described 28, 29 Lipopolysaccharide (LPS) was purchased from List Biological Laboratories. OxPAPC and oxLDL were added to DMEM for a final concentration of 50 ug/mL, LPS was formulated for a final concentration of 4 ng/mL. After aortas were opened en face, each was placed in one well of a 12-well cell culture plate along with 1 mL of the appropriate DMEM formulation pre-warmed to 37C. After the 4 hour treatment, aortas were removed from media and placed lumen side up on a glass slide; isolation continued as described above, beginning with hematoxylin treatment.
| | Sample_growth_protocol_ch1 | Mice were maintained in the UCLA barrier facility on chow diet prior to euthanization
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNAqueous®-Micro Kit by Ambion. The buffer and collagenase solution containing scraped endothelial cells was pipetted directly into 100 uL of Lysis buffer in a 200 uL PCR tube, vortexed, then incubated at 42 C for 30 minutes on a PCR thermalcycler. RNA isolation continued following the manufacturer’s protocol, including suggestions to pre-wet the filter assembly with 30 uL Lysis buffer prior to isolation and to preheat elution solution to 95 C. RNA was stored at -80 C after isolation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The products of RNA amplification were treated with the NuGEN Encore Biotin Module prior to hybridization according to manufacturer’s protocol
| | Sample_hyb_protocol | Entire sample was hybridized for 40 hr on a 96 well HTA plate according to manufacturer protocol.
| | Sample_scan_protocol | GeneChips were processed using GCOS.
| | Sample_data_processing | Microarray results were normalized using RMA in the “affy” package
| | Sample_platform_id | GPL8759
| | Sample_contact_name | Ayca,,Erbilgin
| | Sample_contact_email | ayca.erbilgin@gmail.com
| | Sample_contact_phone | 310 825 1595
| | Sample_contact_laboratory | Lusis
| | Sample_contact_department | Medicine/Cardiology
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 675 Charles E Young Dr South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM959nnn/GSM959072/suppl/GSM959072_DMEM-9.cel.gz
| | Sample_series_id | GSE39264
| | Sample_data_row_count | 22626
| | |
|
GSM959073 | GPL8759 |
|
DMEM-10
|
MAECs isolated from aortas treated with media for 4 hours
|
strain: C57BL/6
genotype: wild-type
cell type: aortic endothelial cells
treatment: DMEM cell media, 4 hrs
disease state: control
|
Gene expression data from amplified RNA isolated directly from the intima of mouse aortas.
|
| Sample_geo_accession | GSM959073
| | Sample_status | Public on Jul 11 2012
| | Sample_submission_date | Jul 11 2012
| | Sample_last_update_date | Jul 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | DMEM with 1% FBS was used as the cell culture medium; vessels were incubated for 4 hours in a cell culture incubator at 37 C, 5% CO2. 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) and oxLDL were prepared as previously described 28, 29 Lipopolysaccharide (LPS) was purchased from List Biological Laboratories. OxPAPC and oxLDL were added to DMEM for a final concentration of 50 ug/mL, LPS was formulated for a final concentration of 4 ng/mL. After aortas were opened en face, each was placed in one well of a 12-well cell culture plate along with 1 mL of the appropriate DMEM formulation pre-warmed to 37C. After the 4 hour treatment, aortas were removed from media and placed lumen side up on a glass slide; isolation continued as described above, beginning with hematoxylin treatment.
| | Sample_growth_protocol_ch1 | Mice were maintained in the UCLA barrier facility on chow diet prior to euthanization
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNAqueous®-Micro Kit by Ambion. The buffer and collagenase solution containing scraped endothelial cells was pipetted directly into 100 uL of Lysis buffer in a 200 uL PCR tube, vortexed, then incubated at 42 C for 30 minutes on a PCR thermalcycler. RNA isolation continued following the manufacturer’s protocol, including suggestions to pre-wet the filter assembly with 30 uL Lysis buffer prior to isolation and to preheat elution solution to 95 C. RNA was stored at -80 C after isolation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The products of RNA amplification were treated with the NuGEN Encore Biotin Module prior to hybridization according to manufacturer’s protocol
| | Sample_hyb_protocol | Entire sample was hybridized for 40 hr on a 96 well HTA plate according to manufacturer protocol.
| | Sample_scan_protocol | GeneChips were processed using GCOS.
| | Sample_data_processing | Microarray results were normalized using RMA in the “affy” package
| | Sample_platform_id | GPL8759
| | Sample_contact_name | Ayca,,Erbilgin
| | Sample_contact_email | ayca.erbilgin@gmail.com
| | Sample_contact_phone | 310 825 1595
| | Sample_contact_laboratory | Lusis
| | Sample_contact_department | Medicine/Cardiology
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 675 Charles E Young Dr South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM959nnn/GSM959073/suppl/GSM959073_DMEM-10.cel.gz
| | Sample_series_id | GSE39264
| | Sample_data_row_count | 22626
| | |
|
GSM959074 | GPL8759 |
|
DMEM-11
|
MAECs isolated from aortas treated with media for 4 hours
|
strain: C57BL/6
genotype: wild-type
cell type: aortic endothelial cells
treatment: DMEM cell media, 4 hrs
disease state: control
|
Gene expression data from amplified RNA isolated directly from the intima of mouse aortas.
|
| Sample_geo_accession | GSM959074
| | Sample_status | Public on Jul 11 2012
| | Sample_submission_date | Jul 11 2012
| | Sample_last_update_date | Jul 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | DMEM with 1% FBS was used as the cell culture medium; vessels were incubated for 4 hours in a cell culture incubator at 37 C, 5% CO2. 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) and oxLDL were prepared as previously described 28, 29 Lipopolysaccharide (LPS) was purchased from List Biological Laboratories. OxPAPC and oxLDL were added to DMEM for a final concentration of 50 ug/mL, LPS was formulated for a final concentration of 4 ng/mL. After aortas were opened en face, each was placed in one well of a 12-well cell culture plate along with 1 mL of the appropriate DMEM formulation pre-warmed to 37C. After the 4 hour treatment, aortas were removed from media and placed lumen side up on a glass slide; isolation continued as described above, beginning with hematoxylin treatment.
| | Sample_growth_protocol_ch1 | Mice were maintained in the UCLA barrier facility on chow diet prior to euthanization
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNAqueous®-Micro Kit by Ambion. The buffer and collagenase solution containing scraped endothelial cells was pipetted directly into 100 uL of Lysis buffer in a 200 uL PCR tube, vortexed, then incubated at 42 C for 30 minutes on a PCR thermalcycler. RNA isolation continued following the manufacturer’s protocol, including suggestions to pre-wet the filter assembly with 30 uL Lysis buffer prior to isolation and to preheat elution solution to 95 C. RNA was stored at -80 C after isolation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The products of RNA amplification were treated with the NuGEN Encore Biotin Module prior to hybridization according to manufacturer’s protocol
| | Sample_hyb_protocol | Entire sample was hybridized for 40 hr on a 96 well HTA plate according to manufacturer protocol.
| | Sample_scan_protocol | GeneChips were processed using GCOS.
| | Sample_data_processing | Microarray results were normalized using RMA in the “affy” package
| | Sample_platform_id | GPL8759
| | Sample_contact_name | Ayca,,Erbilgin
| | Sample_contact_email | ayca.erbilgin@gmail.com
| | Sample_contact_phone | 310 825 1595
| | Sample_contact_laboratory | Lusis
| | Sample_contact_department | Medicine/Cardiology
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 675 Charles E Young Dr South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM959nnn/GSM959074/suppl/GSM959074_DMEM-11.cel.gz
| | Sample_series_id | GSE39264
| | Sample_data_row_count | 22626
| | |
|
GSM959075 | GPL8759 |
|
LPS-3
|
MAECs isolated from aortas treated with media + LPS for 4 hours
|
strain: C57BL/6
genotype: wild-type
cell type: aortic endothelial cells
treatment: DMEM + LPS, 4 hrs
disease state: atherosclerotic treatment
|
Gene expression data from amplified RNA isolated directly from the intima of mouse aortas.
|
| Sample_geo_accession | GSM959075
| | Sample_status | Public on Jul 11 2012
| | Sample_submission_date | Jul 11 2012
| | Sample_last_update_date | Jul 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | DMEM with 1% FBS was used as the cell culture medium; vessels were incubated for 4 hours in a cell culture incubator at 37 C, 5% CO2. 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) and oxLDL were prepared as previously described 28, 29 Lipopolysaccharide (LPS) was purchased from List Biological Laboratories. OxPAPC and oxLDL were added to DMEM for a final concentration of 50 ug/mL, LPS was formulated for a final concentration of 4 ng/mL. After aortas were opened en face, each was placed in one well of a 12-well cell culture plate along with 1 mL of the appropriate DMEM formulation pre-warmed to 37C. After the 4 hour treatment, aortas were removed from media and placed lumen side up on a glass slide; isolation continued as described above, beginning with hematoxylin treatment.
| | Sample_growth_protocol_ch1 | Mice were maintained in the UCLA barrier facility on chow diet prior to euthanization
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNAqueous®-Micro Kit by Ambion. The buffer and collagenase solution containing scraped endothelial cells was pipetted directly into 100 uL of Lysis buffer in a 200 uL PCR tube, vortexed, then incubated at 42 C for 30 minutes on a PCR thermalcycler. RNA isolation continued following the manufacturer’s protocol, including suggestions to pre-wet the filter assembly with 30 uL Lysis buffer prior to isolation and to preheat elution solution to 95 C. RNA was stored at -80 C after isolation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The products of RNA amplification were treated with the NuGEN Encore Biotin Module prior to hybridization according to manufacturer’s protocol
| | Sample_hyb_protocol | Entire sample was hybridized for 40 hr on a 96 well HTA plate according to manufacturer protocol.
| | Sample_scan_protocol | GeneChips were processed using GCOS.
| | Sample_data_processing | Microarray results were normalized using RMA in the “affy” package
| | Sample_platform_id | GPL8759
| | Sample_contact_name | Ayca,,Erbilgin
| | Sample_contact_email | ayca.erbilgin@gmail.com
| | Sample_contact_phone | 310 825 1595
| | Sample_contact_laboratory | Lusis
| | Sample_contact_department | Medicine/Cardiology
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 675 Charles E Young Dr South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM959nnn/GSM959075/suppl/GSM959075_LPS-3.cel.gz
| | Sample_series_id | GSE39264
| | Sample_data_row_count | 22626
| | |
|
GSM959076 | GPL8759 |
|
LPS-4
|
MAECs isolated from aortas treated with media + LPS for 4 hours
|
strain: C57BL/6
genotype: wild-type
cell type: aortic endothelial cells
treatment: DMEM + LPS, 4 hrs
disease state: atherosclerotic treatment
|
Gene expression data from amplified RNA isolated directly from the intima of mouse aortas.
|
| Sample_geo_accession | GSM959076
| | Sample_status | Public on Jul 11 2012
| | Sample_submission_date | Jul 11 2012
| | Sample_last_update_date | Jul 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | DMEM with 1% FBS was used as the cell culture medium; vessels were incubated for 4 hours in a cell culture incubator at 37 C, 5% CO2. 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) and oxLDL were prepared as previously described 28, 29 Lipopolysaccharide (LPS) was purchased from List Biological Laboratories. OxPAPC and oxLDL were added to DMEM for a final concentration of 50 ug/mL, LPS was formulated for a final concentration of 4 ng/mL. After aortas were opened en face, each was placed in one well of a 12-well cell culture plate along with 1 mL of the appropriate DMEM formulation pre-warmed to 37C. After the 4 hour treatment, aortas were removed from media and placed lumen side up on a glass slide; isolation continued as described above, beginning with hematoxylin treatment.
| | Sample_growth_protocol_ch1 | Mice were maintained in the UCLA barrier facility on chow diet prior to euthanization
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNAqueous®-Micro Kit by Ambion. The buffer and collagenase solution containing scraped endothelial cells was pipetted directly into 100 uL of Lysis buffer in a 200 uL PCR tube, vortexed, then incubated at 42 C for 30 minutes on a PCR thermalcycler. RNA isolation continued following the manufacturer’s protocol, including suggestions to pre-wet the filter assembly with 30 uL Lysis buffer prior to isolation and to preheat elution solution to 95 C. RNA was stored at -80 C after isolation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The products of RNA amplification were treated with the NuGEN Encore Biotin Module prior to hybridization according to manufacturer’s protocol
| | Sample_hyb_protocol | Entire sample was hybridized for 40 hr on a 96 well HTA plate according to manufacturer protocol.
| | Sample_scan_protocol | GeneChips were processed using GCOS.
| | Sample_data_processing | Microarray results were normalized using RMA in the “affy” package
| | Sample_platform_id | GPL8759
| | Sample_contact_name | Ayca,,Erbilgin
| | Sample_contact_email | ayca.erbilgin@gmail.com
| | Sample_contact_phone | 310 825 1595
| | Sample_contact_laboratory | Lusis
| | Sample_contact_department | Medicine/Cardiology
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 675 Charles E Young Dr South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM959nnn/GSM959076/suppl/GSM959076_LPS-4.cel.gz
| | Sample_series_id | GSE39264
| | Sample_data_row_count | 22626
| | |
|
GSM959077 | GPL8759 |
|
LPS-10
|
MAECs isolated from aortas treated with media + LPS for 4 hours
|
strain: C57BL/6
genotype: wild-type
cell type: aortic endothelial cells
treatment: DMEM + LPS, 4 hrs
disease state: atherosclerotic treatment
|
Gene expression data from amplified RNA isolated directly from the intima of mouse aortas.
|
| Sample_geo_accession | GSM959077
| | Sample_status | Public on Jul 11 2012
| | Sample_submission_date | Jul 11 2012
| | Sample_last_update_date | Jul 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | DMEM with 1% FBS was used as the cell culture medium; vessels were incubated for 4 hours in a cell culture incubator at 37 C, 5% CO2. 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) and oxLDL were prepared as previously described 28, 29 Lipopolysaccharide (LPS) was purchased from List Biological Laboratories. OxPAPC and oxLDL were added to DMEM for a final concentration of 50 ug/mL, LPS was formulated for a final concentration of 4 ng/mL. After aortas were opened en face, each was placed in one well of a 12-well cell culture plate along with 1 mL of the appropriate DMEM formulation pre-warmed to 37C. After the 4 hour treatment, aortas were removed from media and placed lumen side up on a glass slide; isolation continued as described above, beginning with hematoxylin treatment.
| | Sample_growth_protocol_ch1 | Mice were maintained in the UCLA barrier facility on chow diet prior to euthanization
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNAqueous®-Micro Kit by Ambion. The buffer and collagenase solution containing scraped endothelial cells was pipetted directly into 100 uL of Lysis buffer in a 200 uL PCR tube, vortexed, then incubated at 42 C for 30 minutes on a PCR thermalcycler. RNA isolation continued following the manufacturer’s protocol, including suggestions to pre-wet the filter assembly with 30 uL Lysis buffer prior to isolation and to preheat elution solution to 95 C. RNA was stored at -80 C after isolation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The products of RNA amplification were treated with the NuGEN Encore Biotin Module prior to hybridization according to manufacturer’s protocol
| | Sample_hyb_protocol | Entire sample was hybridized for 40 hr on a 96 well HTA plate according to manufacturer protocol.
| | Sample_scan_protocol | GeneChips were processed using GCOS.
| | Sample_data_processing | Microarray results were normalized using RMA in the “affy” package
| | Sample_platform_id | GPL8759
| | Sample_contact_name | Ayca,,Erbilgin
| | Sample_contact_email | ayca.erbilgin@gmail.com
| | Sample_contact_phone | 310 825 1595
| | Sample_contact_laboratory | Lusis
| | Sample_contact_department | Medicine/Cardiology
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 675 Charles E Young Dr South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM959nnn/GSM959077/suppl/GSM959077_LPS-10.cel.gz
| | Sample_series_id | GSE39264
| | Sample_data_row_count | 22626
| | |
|
GSM959078 | GPL8759 |
|
oxLDL-14
|
MAECs isolated from aortas treated with media + oxLDL for 4 hours
|
strain: C57BL/6
genotype: wild-type
cell type: aortic endothelial cells
treatment: DMEM + oxLDL, 4 hrs
disease state: atherosclerotic treatment
|
Gene expression data from amplified RNA isolated directly from the intima of mouse aortas.
|
| Sample_geo_accession | GSM959078
| | Sample_status | Public on Jul 11 2012
| | Sample_submission_date | Jul 11 2012
| | Sample_last_update_date | Jul 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | DMEM with 1% FBS was used as the cell culture medium; vessels were incubated for 4 hours in a cell culture incubator at 37 C, 5% CO2. 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) and oxLDL were prepared as previously described 28, 29 Lipopolysaccharide (LPS) was purchased from List Biological Laboratories. OxPAPC and oxLDL were added to DMEM for a final concentration of 50 ug/mL, LPS was formulated for a final concentration of 4 ng/mL. After aortas were opened en face, each was placed in one well of a 12-well cell culture plate along with 1 mL of the appropriate DMEM formulation pre-warmed to 37C. After the 4 hour treatment, aortas were removed from media and placed lumen side up on a glass slide; isolation continued as described above, beginning with hematoxylin treatment.
| | Sample_growth_protocol_ch1 | Mice were maintained in the UCLA barrier facility on chow diet prior to euthanization
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNAqueous®-Micro Kit by Ambion. The buffer and collagenase solution containing scraped endothelial cells was pipetted directly into 100 uL of Lysis buffer in a 200 uL PCR tube, vortexed, then incubated at 42 C for 30 minutes on a PCR thermalcycler. RNA isolation continued following the manufacturer’s protocol, including suggestions to pre-wet the filter assembly with 30 uL Lysis buffer prior to isolation and to preheat elution solution to 95 C. RNA was stored at -80 C after isolation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The products of RNA amplification were treated with the NuGEN Encore Biotin Module prior to hybridization according to manufacturer’s protocol
| | Sample_hyb_protocol | Entire sample was hybridized for 40 hr on a 96 well HTA plate according to manufacturer protocol.
| | Sample_scan_protocol | GeneChips were processed using GCOS.
| | Sample_data_processing | Microarray results were normalized using RMA in the “affy” package
| | Sample_platform_id | GPL8759
| | Sample_contact_name | Ayca,,Erbilgin
| | Sample_contact_email | ayca.erbilgin@gmail.com
| | Sample_contact_phone | 310 825 1595
| | Sample_contact_laboratory | Lusis
| | Sample_contact_department | Medicine/Cardiology
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 675 Charles E Young Dr South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM959nnn/GSM959078/suppl/GSM959078_oxLDL-14.cel.gz
| | Sample_series_id | GSE39264
| | Sample_data_row_count | 22626
| | |
|
GSM959079 | GPL8759 |
|
oxLDL-15
|
MAECs isolated from aortas treated with media + oxLDL for 4 hours
|
strain: C57BL/6
genotype: wild-type
cell type: aortic endothelial cells
treatment: DMEM + oxLDL, 4 hrs
disease state: atherosclerotic treatment
|
Gene expression data from amplified RNA isolated directly from the intima of mouse aortas.
|
| Sample_geo_accession | GSM959079
| | Sample_status | Public on Jul 11 2012
| | Sample_submission_date | Jul 11 2012
| | Sample_last_update_date | Jul 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | DMEM with 1% FBS was used as the cell culture medium; vessels were incubated for 4 hours in a cell culture incubator at 37 C, 5% CO2. 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) and oxLDL were prepared as previously described 28, 29 Lipopolysaccharide (LPS) was purchased from List Biological Laboratories. OxPAPC and oxLDL were added to DMEM for a final concentration of 50 ug/mL, LPS was formulated for a final concentration of 4 ng/mL. After aortas were opened en face, each was placed in one well of a 12-well cell culture plate along with 1 mL of the appropriate DMEM formulation pre-warmed to 37C. After the 4 hour treatment, aortas were removed from media and placed lumen side up on a glass slide; isolation continued as described above, beginning with hematoxylin treatment.
| | Sample_growth_protocol_ch1 | Mice were maintained in the UCLA barrier facility on chow diet prior to euthanization
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNAqueous®-Micro Kit by Ambion. The buffer and collagenase solution containing scraped endothelial cells was pipetted directly into 100 uL of Lysis buffer in a 200 uL PCR tube, vortexed, then incubated at 42 C for 30 minutes on a PCR thermalcycler. RNA isolation continued following the manufacturer’s protocol, including suggestions to pre-wet the filter assembly with 30 uL Lysis buffer prior to isolation and to preheat elution solution to 95 C. RNA was stored at -80 C after isolation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The products of RNA amplification were treated with the NuGEN Encore Biotin Module prior to hybridization according to manufacturer’s protocol
| | Sample_hyb_protocol | Entire sample was hybridized for 40 hr on a 96 well HTA plate according to manufacturer protocol.
| | Sample_scan_protocol | GeneChips were processed using GCOS.
| | Sample_data_processing | Microarray results were normalized using RMA in the “affy” package
| | Sample_platform_id | GPL8759
| | Sample_contact_name | Ayca,,Erbilgin
| | Sample_contact_email | ayca.erbilgin@gmail.com
| | Sample_contact_phone | 310 825 1595
| | Sample_contact_laboratory | Lusis
| | Sample_contact_department | Medicine/Cardiology
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 675 Charles E Young Dr South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM959nnn/GSM959079/suppl/GSM959079_oxLDL-15.cel.gz
| | Sample_series_id | GSE39264
| | Sample_data_row_count | 22626
| | |
|
GSM959080 | GPL8759 |
|
oxLDL-16
|
MAECs isolated from aortas treated with media + oxLDL for 4 hours
|
strain: C57BL/6
genotype: wild-type
cell type: aortic endothelial cells
treatment: DMEM + oxLDL, 4 hrs
disease state: atherosclerotic treatment
|
Gene expression data from amplified RNA isolated directly from the intima of mouse aortas.
|
| Sample_geo_accession | GSM959080
| | Sample_status | Public on Jul 11 2012
| | Sample_submission_date | Jul 11 2012
| | Sample_last_update_date | Jul 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | DMEM with 1% FBS was used as the cell culture medium; vessels were incubated for 4 hours in a cell culture incubator at 37 C, 5% CO2. 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) and oxLDL were prepared as previously described 28, 29 Lipopolysaccharide (LPS) was purchased from List Biological Laboratories. OxPAPC and oxLDL were added to DMEM for a final concentration of 50 ug/mL, LPS was formulated for a final concentration of 4 ng/mL. After aortas were opened en face, each was placed in one well of a 12-well cell culture plate along with 1 mL of the appropriate DMEM formulation pre-warmed to 37C. After the 4 hour treatment, aortas were removed from media and placed lumen side up on a glass slide; isolation continued as described above, beginning with hematoxylin treatment.
| | Sample_growth_protocol_ch1 | Mice were maintained in the UCLA barrier facility on chow diet prior to euthanization
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNAqueous®-Micro Kit by Ambion. The buffer and collagenase solution containing scraped endothelial cells was pipetted directly into 100 uL of Lysis buffer in a 200 uL PCR tube, vortexed, then incubated at 42 C for 30 minutes on a PCR thermalcycler. RNA isolation continued following the manufacturer’s protocol, including suggestions to pre-wet the filter assembly with 30 uL Lysis buffer prior to isolation and to preheat elution solution to 95 C. RNA was stored at -80 C after isolation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The products of RNA amplification were treated with the NuGEN Encore Biotin Module prior to hybridization according to manufacturer’s protocol
| | Sample_hyb_protocol | Entire sample was hybridized for 40 hr on a 96 well HTA plate according to manufacturer protocol.
| | Sample_scan_protocol | GeneChips were processed using GCOS.
| | Sample_data_processing | Microarray results were normalized using RMA in the “affy” package
| | Sample_platform_id | GPL8759
| | Sample_contact_name | Ayca,,Erbilgin
| | Sample_contact_email | ayca.erbilgin@gmail.com
| | Sample_contact_phone | 310 825 1595
| | Sample_contact_laboratory | Lusis
| | Sample_contact_department | Medicine/Cardiology
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 675 Charles E Young Dr South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM959nnn/GSM959080/suppl/GSM959080_oxLDL-16.cel.gz
| | Sample_series_id | GSE39264
| | Sample_data_row_count | 22626
| | |
|
GSM959081 | GPL8759 |
|
oxPAPC-11
|
MAECs isolated from aortas treated with media + oxPAPC for 4 hours
|
strain: C57BL/6
genotype: wild-type
cell type: aortic endothelial cells
treatment: DMEM + oxPAPC, 4 hrs
disease state: atherosclerotic treatment
|
Gene expression data from amplified RNA isolated directly from the intima of mouse aortas.
|
| Sample_geo_accession | GSM959081
| | Sample_status | Public on Jul 11 2012
| | Sample_submission_date | Jul 11 2012
| | Sample_last_update_date | Jul 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | DMEM with 1% FBS was used as the cell culture medium; vessels were incubated for 4 hours in a cell culture incubator at 37 C, 5% CO2. 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) and oxLDL were prepared as previously described 28, 29 Lipopolysaccharide (LPS) was purchased from List Biological Laboratories. OxPAPC and oxLDL were added to DMEM for a final concentration of 50 ug/mL, LPS was formulated for a final concentration of 4 ng/mL. After aortas were opened en face, each was placed in one well of a 12-well cell culture plate along with 1 mL of the appropriate DMEM formulation pre-warmed to 37C. After the 4 hour treatment, aortas were removed from media and placed lumen side up on a glass slide; isolation continued as described above, beginning with hematoxylin treatment.
| | Sample_growth_protocol_ch1 | Mice were maintained in the UCLA barrier facility on chow diet prior to euthanization
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNAqueous®-Micro Kit by Ambion. The buffer and collagenase solution containing scraped endothelial cells was pipetted directly into 100 uL of Lysis buffer in a 200 uL PCR tube, vortexed, then incubated at 42 C for 30 minutes on a PCR thermalcycler. RNA isolation continued following the manufacturer’s protocol, including suggestions to pre-wet the filter assembly with 30 uL Lysis buffer prior to isolation and to preheat elution solution to 95 C. RNA was stored at -80 C after isolation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The products of RNA amplification were treated with the NuGEN Encore Biotin Module prior to hybridization according to manufacturer’s protocol
| | Sample_hyb_protocol | Entire sample was hybridized for 40 hr on a 96 well HTA plate according to manufacturer protocol.
| | Sample_scan_protocol | GeneChips were processed using GCOS.
| | Sample_data_processing | Microarray results were normalized using RMA in the “affy” package
| | Sample_platform_id | GPL8759
| | Sample_contact_name | Ayca,,Erbilgin
| | Sample_contact_email | ayca.erbilgin@gmail.com
| | Sample_contact_phone | 310 825 1595
| | Sample_contact_laboratory | Lusis
| | Sample_contact_department | Medicine/Cardiology
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 675 Charles E Young Dr South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM959nnn/GSM959081/suppl/GSM959081_oxPAPC-11.cel.gz
| | Sample_series_id | GSE39264
| | Sample_data_row_count | 22626
| | |
|
GSM959082 | GPL8759 |
|
oxPAPC-12
|
MAECs isolated from aortas treated with media + oxPAPC for 4 hours
|
strain: C57BL/6
genotype: wild-type
cell type: aortic endothelial cells
treatment: DMEM + oxPAPC, 4 hrs
disease state: atherosclerotic treatment
|
Gene expression data from amplified RNA isolated directly from the intima of mouse aortas.
|
| Sample_geo_accession | GSM959082
| | Sample_status | Public on Jul 11 2012
| | Sample_submission_date | Jul 11 2012
| | Sample_last_update_date | Jul 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | DMEM with 1% FBS was used as the cell culture medium; vessels were incubated for 4 hours in a cell culture incubator at 37 C, 5% CO2. 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) and oxLDL were prepared as previously described 28, 29 Lipopolysaccharide (LPS) was purchased from List Biological Laboratories. OxPAPC and oxLDL were added to DMEM for a final concentration of 50 ug/mL, LPS was formulated for a final concentration of 4 ng/mL. After aortas were opened en face, each was placed in one well of a 12-well cell culture plate along with 1 mL of the appropriate DMEM formulation pre-warmed to 37C. After the 4 hour treatment, aortas were removed from media and placed lumen side up on a glass slide; isolation continued as described above, beginning with hematoxylin treatment.
| | Sample_growth_protocol_ch1 | Mice were maintained in the UCLA barrier facility on chow diet prior to euthanization
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNAqueous®-Micro Kit by Ambion. The buffer and collagenase solution containing scraped endothelial cells was pipetted directly into 100 uL of Lysis buffer in a 200 uL PCR tube, vortexed, then incubated at 42 C for 30 minutes on a PCR thermalcycler. RNA isolation continued following the manufacturer’s protocol, including suggestions to pre-wet the filter assembly with 30 uL Lysis buffer prior to isolation and to preheat elution solution to 95 C. RNA was stored at -80 C after isolation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The products of RNA amplification were treated with the NuGEN Encore Biotin Module prior to hybridization according to manufacturer’s protocol
| | Sample_hyb_protocol | Entire sample was hybridized for 40 hr on a 96 well HTA plate according to manufacturer protocol.
| | Sample_scan_protocol | GeneChips were processed using GCOS.
| | Sample_data_processing | Microarray results were normalized using RMA in the “affy” package
| | Sample_platform_id | GPL8759
| | Sample_contact_name | Ayca,,Erbilgin
| | Sample_contact_email | ayca.erbilgin@gmail.com
| | Sample_contact_phone | 310 825 1595
| | Sample_contact_laboratory | Lusis
| | Sample_contact_department | Medicine/Cardiology
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 675 Charles E Young Dr South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM959nnn/GSM959082/suppl/GSM959082_oxPAPC-12.cel.gz
| | Sample_series_id | GSE39264
| | Sample_data_row_count | 22626
| | |
|
GSM959083 | GPL8759 |
|
oxPAPC-13
|
MAECs isolated from aortas treated with media + oxPAPC for 4 hours
|
strain: C57BL/6
genotype: wild-type
cell type: aortic endothelial cells
treatment: DMEM + oxPAPC, 4 hrs
disease state: atherosclerotic treatment
|
Gene expression data from amplified RNA isolated directly from the intima of mouse aortas.
|
| Sample_geo_accession | GSM959083
| | Sample_status | Public on Jul 11 2012
| | Sample_submission_date | Jul 11 2012
| | Sample_last_update_date | Jul 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | DMEM with 1% FBS was used as the cell culture medium; vessels were incubated for 4 hours in a cell culture incubator at 37 C, 5% CO2. 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) and oxLDL were prepared as previously described 28, 29 Lipopolysaccharide (LPS) was purchased from List Biological Laboratories. OxPAPC and oxLDL were added to DMEM for a final concentration of 50 ug/mL, LPS was formulated for a final concentration of 4 ng/mL. After aortas were opened en face, each was placed in one well of a 12-well cell culture plate along with 1 mL of the appropriate DMEM formulation pre-warmed to 37C. After the 4 hour treatment, aortas were removed from media and placed lumen side up on a glass slide; isolation continued as described above, beginning with hematoxylin treatment.
| | Sample_growth_protocol_ch1 | Mice were maintained in the UCLA barrier facility on chow diet prior to euthanization
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the RNAqueous®-Micro Kit by Ambion. The buffer and collagenase solution containing scraped endothelial cells was pipetted directly into 100 uL of Lysis buffer in a 200 uL PCR tube, vortexed, then incubated at 42 C for 30 minutes on a PCR thermalcycler. RNA isolation continued following the manufacturer’s protocol, including suggestions to pre-wet the filter assembly with 30 uL Lysis buffer prior to isolation and to preheat elution solution to 95 C. RNA was stored at -80 C after isolation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The products of RNA amplification were treated with the NuGEN Encore Biotin Module prior to hybridization according to manufacturer’s protocol
| | Sample_hyb_protocol | Entire sample was hybridized for 40 hr on a 96 well HTA plate according to manufacturer protocol.
| | Sample_scan_protocol | GeneChips were processed using GCOS.
| | Sample_data_processing | Microarray results were normalized using RMA in the “affy” package
| | Sample_platform_id | GPL8759
| | Sample_contact_name | Ayca,,Erbilgin
| | Sample_contact_email | ayca.erbilgin@gmail.com
| | Sample_contact_phone | 310 825 1595
| | Sample_contact_laboratory | Lusis
| | Sample_contact_department | Medicine/Cardiology
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 675 Charles E Young Dr South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM959nnn/GSM959083/suppl/GSM959083_oxPAPC-13.cel.gz
| | Sample_series_id | GSE39264
| | Sample_data_row_count | 22626
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
