Search results for the GEO ID: GSE17119  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM428146 | GPL570 |
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Control cells, 1 h post-supplementation.
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Human microvascular endothelial cells (HMVEC), 1 h post-supplementation with 0.6% dimethyl sulfoxide (DMSO) vehicle control.
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cell line: HMVEC
|
HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 0.6% dimethyl sulfoxide (DMSO) vehicle control was added to the sample. Total RNA from the cultures was isolated 1 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
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| Sample_geo_accession | GSM428146
| | Sample_status | Public on Jul 17 2009
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from the cultures was isolated 1 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA samples were prepared for hybridization using the GeneChip One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA, USA). Total RNA integrity was assessed by analysis with an Agilent Bioanalyzer using RNA 6000 Nano chips (Agilent Technologies, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was generated from the total RNA samples and fragmented in preparation for array hybridization, according to standard Affymetrix GeneChip protocols. Fragmented cRNA (10 µg) was hybridized to Affymetrix Human Genome U133 Plus 2.0 probe arrays for 16 h.
| | Sample_scan_protocol | The arrays were washed and stained in an Affymetrix Automated Fluidics Station 400 and scanned with the Affymetrix GeneArray Scanner. Scanned images were examined for visible defects and checked for proper grid alignment, and acceptable image files were analyzed to generate raw data in the form of ‘CEL’ files. Quality control, including replicate analysis, measurement of noise and background levels, and assessment of the 3'/5' ratio of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and beta-actin (β-actin) was performed with Microarray Analysis Suite 5.0 (MAS 5.0, Affymetrix).
| | Sample_data_processing | Using MAS 5.0, each gene transcript was detected as ‘present’, ‘absent’ or ‘marginal’, and the change between the experimental (PNF1-stimulated) and baseline (control) conditions at each timepoint was assigned to one of several standard categories, i.e., increase, marginal increase, no change, marginal decrease and decrease, depending on the P-value (calculated using the Wilcoxon signed rank test). The ranges for each call were 0.0000–0.0025, 0.0025–0.0030, 0.0030–0.9970, 0.9970–0.9975 and 0.9975 to 1.0000, respectively. These data were then inputted into dChip version 1.3 (Li and Wong, 2001), where they were normalized using the invariant set approach.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Erwin,P,Gianchandani
| | Sample_contact_email | erwin@virginia.edu
| | Sample_contact_department | Office of the Vice President for Research
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | Box 400301
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22904
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428146/suppl/GSM428146_ctrl_1hr.CEL.gz
| | Sample_series_id | GSE17119
| | Sample_data_row_count | 54675
| | |
|
GSM428147 | GPL570 |
|
Control cells, 2 h post-supplementation.
|
Human microvascular endothelial cells (HMVEC), 2 h post-supplementation with 0.6% dimethyl sulfoxide (DMSO) vehicle control.
|
cell line: HMVEC
|
HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 0.6% dimethyl sulfoxide (DMSO) vehicle control was added to the sample. Total RNA from the cultures was isolated 2 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
|
| Sample_geo_accession | GSM428147
| | Sample_status | Public on Jul 17 2009
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from the cultures was isolated 2 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA samples were prepared for hybridization using the GeneChip One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA, USA). Total RNA integrity was assessed by analysis with an Agilent Bioanalyzer using RNA 6000 Nano chips (Agilent Technologies, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was generated from the total RNA samples and fragmented in preparation for array hybridization, according to standard Affymetrix GeneChip protocols. Fragmented cRNA (10 µg) was hybridized to Affymetrix Human Genome U133 Plus 2.0 probe arrays for 16 h.
| | Sample_scan_protocol | The arrays were washed and stained in an Affymetrix Automated Fluidics Station 400 and scanned with the Affymetrix GeneArray Scanner. Scanned images were examined for visible defects and checked for proper grid alignment, and acceptable image files were analyzed to generate raw data in the form of ‘CEL’ files. Quality control, including replicate analysis, measurement of noise and background levels, and assessment of the 3'/5' ratio of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and beta-actin (β-actin) was performed with Microarray Analysis Suite 5.0 (MAS 5.0, Affymetrix).
| | Sample_data_processing | Using MAS 5.0, each gene transcript was detected as ‘present’, ‘absent’ or ‘marginal’, and the change between the experimental (PNF1-stimulated) and baseline (control) conditions at each timepoint was assigned to one of several standard categories, i.e., increase, marginal increase, no change, marginal decrease and decrease, depending on the P-value (calculated using the Wilcoxon signed rank test). The ranges for each call were 0.0000–0.0025, 0.0025–0.0030, 0.0030–0.9970, 0.9970–0.9975 and 0.9975 to 1.0000, respectively. These data were then inputted into dChip version 1.3 (Li and Wong, 2001), where they were normalized using the invariant set approach.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Erwin,P,Gianchandani
| | Sample_contact_email | erwin@virginia.edu
| | Sample_contact_department | Office of the Vice President for Research
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | Box 400301
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22904
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428147/suppl/GSM428147_ctrl_2hr.CEL.gz
| | Sample_series_id | GSE17119
| | Sample_data_row_count | 54675
| | |
|
GSM428148 | GPL570 |
|
Control cells, 4 h post-supplementation.
|
Human microvascular endothelial cells (HMVEC), 4 h post-supplementation with 0.6% dimethyl sulfoxide (DMSO) vehicle control.
|
cell line: HMVEC
|
HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 0.6% dimethyl sulfoxide (DMSO) vehicle control was added to the sample. Total RNA from the cultures was isolated 4 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
|
| Sample_geo_accession | GSM428148
| | Sample_status | Public on Jul 17 2009
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from the cultures was isolated 4 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA samples were prepared for hybridization using the GeneChip One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA, USA). Total RNA integrity was assessed by analysis with an Agilent Bioanalyzer using RNA 6000 Nano chips (Agilent Technologies, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was generated from the total RNA samples and fragmented in preparation for array hybridization, according to standard Affymetrix GeneChip protocols. Fragmented cRNA (10 µg) was hybridized to Affymetrix Human Genome U133 Plus 2.0 probe arrays for 16 h.
| | Sample_scan_protocol | The arrays were washed and stained in an Affymetrix Automated Fluidics Station 400 and scanned with the Affymetrix GeneArray Scanner. Scanned images were examined for visible defects and checked for proper grid alignment, and acceptable image files were analyzed to generate raw data in the form of ‘CEL’ files. Quality control, including replicate analysis, measurement of noise and background levels, and assessment of the 3'/5' ratio of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and beta-actin (β-actin) was performed with Microarray Analysis Suite 5.0 (MAS 5.0, Affymetrix).
| | Sample_data_processing | Using MAS 5.0, each gene transcript was detected as ‘present’, ‘absent’ or ‘marginal’, and the change between the experimental (PNF1-stimulated) and baseline (control) conditions at each timepoint was assigned to one of several standard categories, i.e., increase, marginal increase, no change, marginal decrease and decrease, depending on the P-value (calculated using the Wilcoxon signed rank test). The ranges for each call were 0.0000–0.0025, 0.0025–0.0030, 0.0030–0.9970, 0.9970–0.9975 and 0.9975 to 1.0000, respectively. These data were then inputted into dChip version 1.3 (Li and Wong, 2001), where they were normalized using the invariant set approach.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Erwin,P,Gianchandani
| | Sample_contact_email | erwin@virginia.edu
| | Sample_contact_department | Office of the Vice President for Research
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | Box 400301
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22904
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428148/suppl/GSM428148_ctrl_4hr.CEL.gz
| | Sample_series_id | GSE17119
| | Sample_data_row_count | 54675
| | |
|
GSM428149 | GPL570 |
|
Control cells, 8 h post-supplementation.
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Human microvascular endothelial cells (HMVEC), 8 h post-supplementation with 0.6% dimethyl sulfoxide (DMSO) vehicle control.
|
cell line: HMVEC
|
HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 0.6% dimethyl sulfoxide (DMSO) vehicle control was added to the sample. Total RNA from the cultures was isolated 8 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
|
| Sample_geo_accession | GSM428149
| | Sample_status | Public on Jul 17 2009
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from the cultures was isolated 8 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA samples were prepared for hybridization using the GeneChip One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA, USA). Total RNA integrity was assessed by analysis with an Agilent Bioanalyzer using RNA 6000 Nano chips (Agilent Technologies, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was generated from the total RNA samples and fragmented in preparation for array hybridization, according to standard Affymetrix GeneChip protocols. Fragmented cRNA (10 µg) was hybridized to Affymetrix Human Genome U133 Plus 2.0 probe arrays for 16 h.
| | Sample_scan_protocol | The arrays were washed and stained in an Affymetrix Automated Fluidics Station 400 and scanned with the Affymetrix GeneArray Scanner. Scanned images were examined for visible defects and checked for proper grid alignment, and acceptable image files were analyzed to generate raw data in the form of ‘CEL’ files. Quality control, including replicate analysis, measurement of noise and background levels, and assessment of the 3'/5' ratio of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and beta-actin (β-actin) was performed with Microarray Analysis Suite 5.0 (MAS 5.0, Affymetrix).
| | Sample_data_processing | Using MAS 5.0, each gene transcript was detected as ‘present’, ‘absent’ or ‘marginal’, and the change between the experimental (PNF1-stimulated) and baseline (control) conditions at each timepoint was assigned to one of several standard categories, i.e., increase, marginal increase, no change, marginal decrease and decrease, depending on the P-value (calculated using the Wilcoxon signed rank test). The ranges for each call were 0.0000–0.0025, 0.0025–0.0030, 0.0030–0.9970, 0.9970–0.9975 and 0.9975 to 1.0000, respectively. These data were then inputted into dChip version 1.3 (Li and Wong, 2001), where they were normalized using the invariant set approach.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Erwin,P,Gianchandani
| | Sample_contact_email | erwin@virginia.edu
| | Sample_contact_department | Office of the Vice President for Research
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | Box 400301
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22904
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428149/suppl/GSM428149_ctrl_8hr.CEL.gz
| | Sample_series_id | GSE17119
| | Sample_data_row_count | 54675
| | |
|
GSM428150 | GPL570 |
|
Control cells, 16 h post-supplementation.
|
Human microvascular endothelial cells (HMVEC), 16 h post-supplementation with 0.6% dimethyl sulfoxide (DMSO) vehicle control.
|
cell line: HMVEC
|
HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 0.6% dimethyl sulfoxide (DMSO) vehicle control was added to the sample. Total RNA from the cultures was isolated 16 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
|
| Sample_geo_accession | GSM428150
| | Sample_status | Public on Jul 17 2009
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from the cultures was isolated 16 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA samples were prepared for hybridization using the GeneChip One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA, USA). Total RNA integrity was assessed by analysis with an Agilent Bioanalyzer using RNA 6000 Nano chips (Agilent Technologies, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was generated from the total RNA samples and fragmented in preparation for array hybridization, according to standard Affymetrix GeneChip protocols. Fragmented cRNA (10 µg) was hybridized to Affymetrix Human Genome U133 Plus 2.0 probe arrays for 16 h.
| | Sample_scan_protocol | The arrays were washed and stained in an Affymetrix Automated Fluidics Station 400 and scanned with the Affymetrix GeneArray Scanner. Scanned images were examined for visible defects and checked for proper grid alignment, and acceptable image files were analyzed to generate raw data in the form of ‘CEL’ files. Quality control, including replicate analysis, measurement of noise and background levels, and assessment of the 3'/5' ratio of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and beta-actin (β-actin) was performed with Microarray Analysis Suite 5.0 (MAS 5.0, Affymetrix).
| | Sample_data_processing | Using MAS 5.0, each gene transcript was detected as ‘present’, ‘absent’ or ‘marginal’, and the change between the experimental (PNF1-stimulated) and baseline (control) conditions at each timepoint was assigned to one of several standard categories, i.e., increase, marginal increase, no change, marginal decrease and decrease, depending on the P-value (calculated using the Wilcoxon signed rank test). The ranges for each call were 0.0000–0.0025, 0.0025–0.0030, 0.0030–0.9970, 0.9970–0.9975 and 0.9975 to 1.0000, respectively. These data were then inputted into dChip version 1.3 (Li and Wong, 2001), where they were normalized using the invariant set approach.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Erwin,P,Gianchandani
| | Sample_contact_email | erwin@virginia.edu
| | Sample_contact_department | Office of the Vice President for Research
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | Box 400301
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22904
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428150/suppl/GSM428150_ctrl_16hr.CEL.gz
| | Sample_series_id | GSE17119
| | Sample_data_row_count | 54675
| | |
|
GSM428151 | GPL570 |
|
Control cells, 24 h post-supplementation.
|
Human microvascular endothelial cells (HMVEC), 24 h post-supplementation with 0.6% dimethyl sulfoxide (DMSO) vehicle control.
|
cell line: HMVEC
|
HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 0.6% dimethyl sulfoxide (DMSO) vehicle control was added to the sample. Total RNA from the cultures was isolated 24 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
|
| Sample_geo_accession | GSM428151
| | Sample_status | Public on Jul 17 2009
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from the cultures was isolated 24 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA samples were prepared for hybridization using the GeneChip One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA, USA). Total RNA integrity was assessed by analysis with an Agilent Bioanalyzer using RNA 6000 Nano chips (Agilent Technologies, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was generated from the total RNA samples and fragmented in preparation for array hybridization, according to standard Affymetrix GeneChip protocols. Fragmented cRNA (10 µg) was hybridized to Affymetrix Human Genome U133 Plus 2.0 probe arrays for 16 h.
| | Sample_scan_protocol | The arrays were washed and stained in an Affymetrix Automated Fluidics Station 400 and scanned with the Affymetrix GeneArray Scanner. Scanned images were examined for visible defects and checked for proper grid alignment, and acceptable image files were analyzed to generate raw data in the form of ‘CEL’ files. Quality control, including replicate analysis, measurement of noise and background levels, and assessment of the 3'/5' ratio of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and beta-actin (β-actin) was performed with Microarray Analysis Suite 5.0 (MAS 5.0, Affymetrix).
| | Sample_data_processing | Using MAS 5.0, each gene transcript was detected as ‘present’, ‘absent’ or ‘marginal’, and the change between the experimental (PNF1-stimulated) and baseline (control) conditions at each timepoint was assigned to one of several standard categories, i.e., increase, marginal increase, no change, marginal decrease and decrease, depending on the P-value (calculated using the Wilcoxon signed rank test). The ranges for each call were 0.0000–0.0025, 0.0025–0.0030, 0.0030–0.9970, 0.9970–0.9975 and 0.9975 to 1.0000, respectively. These data were then inputted into dChip version 1.3 (Li and Wong, 2001), where they were normalized using the invariant set approach.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Erwin,P,Gianchandani
| | Sample_contact_email | erwin@virginia.edu
| | Sample_contact_department | Office of the Vice President for Research
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | Box 400301
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22904
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428151/suppl/GSM428151_ctrl_24hr.CEL.gz
| | Sample_series_id | GSE17119
| | Sample_data_row_count | 54675
| | |
|
GSM428152 | GPL570 |
|
Control cells, 48 h post-supplementation.
|
Human microvascular endothelial cells (HMVEC), 48 h post-supplementation with 0.6% dimethyl sulfoxide (DMSO) vehicle control.
|
cell line: HMVEC
|
HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 0.6% dimethyl sulfoxide (DMSO) vehicle control was added to the sample. Total RNA from the cultures was isolated 48 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
|
| Sample_geo_accession | GSM428152
| | Sample_status | Public on Jul 17 2009
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from the cultures was isolated 48 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA samples were prepared for hybridization using the GeneChip One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA, USA). Total RNA integrity was assessed by analysis with an Agilent Bioanalyzer using RNA 6000 Nano chips (Agilent Technologies, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was generated from the total RNA samples and fragmented in preparation for array hybridization, according to standard Affymetrix GeneChip protocols. Fragmented cRNA (10 µg) was hybridized to Affymetrix Human Genome U133 Plus 2.0 probe arrays for 16 h.
| | Sample_scan_protocol | The arrays were washed and stained in an Affymetrix Automated Fluidics Station 400 and scanned with the Affymetrix GeneArray Scanner. Scanned images were examined for visible defects and checked for proper grid alignment, and acceptable image files were analyzed to generate raw data in the form of ‘CEL’ files. Quality control, including replicate analysis, measurement of noise and background levels, and assessment of the 3'/5' ratio of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and beta-actin (β-actin) was performed with Microarray Analysis Suite 5.0 (MAS 5.0, Affymetrix).
| | Sample_data_processing | Using MAS 5.0, each gene transcript was detected as ‘present’, ‘absent’ or ‘marginal’, and the change between the experimental (PNF1-stimulated) and baseline (control) conditions at each timepoint was assigned to one of several standard categories, i.e., increase, marginal increase, no change, marginal decrease and decrease, depending on the P-value (calculated using the Wilcoxon signed rank test). The ranges for each call were 0.0000–0.0025, 0.0025–0.0030, 0.0030–0.9970, 0.9970–0.9975 and 0.9975 to 1.0000, respectively. These data were then inputted into dChip version 1.3 (Li and Wong, 2001), where they were normalized using the invariant set approach.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Erwin,P,Gianchandani
| | Sample_contact_email | erwin@virginia.edu
| | Sample_contact_department | Office of the Vice President for Research
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | Box 400301
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22904
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428152/suppl/GSM428152_ctrl_48hr.CEL.gz
| | Sample_series_id | GSE17119
| | Sample_data_row_count | 54675
| | |
|
GSM428153 | GPL570 |
|
PNF1-treated cells, 1 h post-supplementation.
|
Human microvascular endothelial cells (HMVEC), 1 h post-supplementation with 30 µM phthalimide neovascular factor 1 (PNF1).
|
cell line: HMVEC
|
HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 30 µM PNF1 was added to the sample. Total RNA from the cultures was isolated 1 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
|
| Sample_geo_accession | GSM428153
| | Sample_status | Public on Jul 17 2009
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from the cultures was isolated 1 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA samples were prepared for hybridization using the GeneChip One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA, USA). Total RNA integrity was assessed by analysis with an Agilent Bioanalyzer using RNA 6000 Nano chips (Agilent Technologies, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was generated from the total RNA samples and fragmented in preparation for array hybridization, according to standard Affymetrix GeneChip protocols. Fragmented cRNA (10 µg) was hybridized to Affymetrix Human Genome U133 Plus 2.0 probe arrays for 16 h.
| | Sample_scan_protocol | The arrays were washed and stained in an Affymetrix Automated Fluidics Station 400 and scanned with the Affymetrix GeneArray Scanner. Scanned images were examined for visible defects and checked for proper grid alignment, and acceptable image files were analyzed to generate raw data in the form of ‘CEL’ files. Quality control, including replicate analysis, measurement of noise and background levels, and assessment of the 3'/5' ratio of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and beta-actin (β-actin) was performed with Microarray Analysis Suite 5.0 (MAS 5.0, Affymetrix).
| | Sample_data_processing | Using MAS 5.0, each gene transcript was detected as ‘present’, ‘absent’ or ‘marginal’, and the change between the experimental (PNF1-stimulated) and baseline (control) conditions at each timepoint was assigned to one of several standard categories, i.e., increase, marginal increase, no change, marginal decrease and decrease, depending on the P-value (calculated using the Wilcoxon signed rank test). The ranges for each call were 0.0000–0.0025, 0.0025–0.0030, 0.0030–0.9970, 0.9970–0.9975 and 0.9975 to 1.0000, respectively. These data were then inputted into dChip version 1.3 (Li and Wong, 2001), where they were normalized using the invariant set approach.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Erwin,P,Gianchandani
| | Sample_contact_email | erwin@virginia.edu
| | Sample_contact_department | Office of the Vice President for Research
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | Box 400301
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22904
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428153/suppl/GSM428153_pnf1_1hr.CEL.gz
| | Sample_series_id | GSE17119
| | Sample_data_row_count | 54675
| | |
|
GSM428154 | GPL570 |
|
PNF1-treated cells, 2 h post-supplementation.
|
Human microvascular endothelial cells (HMVEC), 2 h post-supplementation with 30 µM phthalimide neovascular factor 1 (PNF1).
|
cell line: HMVEC
|
HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 30 µM PNF1 was added to the sample. Total RNA from the cultures was isolated 2 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
|
| Sample_geo_accession | GSM428154
| | Sample_status | Public on Jul 17 2009
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from the cultures was isolated 2 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA samples were prepared for hybridization using the GeneChip One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA, USA). Total RNA integrity was assessed by analysis with an Agilent Bioanalyzer using RNA 6000 Nano chips (Agilent Technologies, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was generated from the total RNA samples and fragmented in preparation for array hybridization, according to standard Affymetrix GeneChip protocols. Fragmented cRNA (10 µg) was hybridized to Affymetrix Human Genome U133 Plus 2.0 probe arrays for 16 h.
| | Sample_scan_protocol | The arrays were washed and stained in an Affymetrix Automated Fluidics Station 400 and scanned with the Affymetrix GeneArray Scanner. Scanned images were examined for visible defects and checked for proper grid alignment, and acceptable image files were analyzed to generate raw data in the form of ‘CEL’ files. Quality control, including replicate analysis, measurement of noise and background levels, and assessment of the 3'/5' ratio of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and beta-actin (β-actin) was performed with Microarray Analysis Suite 5.0 (MAS 5.0, Affymetrix).
| | Sample_data_processing | Using MAS 5.0, each gene transcript was detected as ‘present’, ‘absent’ or ‘marginal’, and the change between the experimental (PNF1-stimulated) and baseline (control) conditions at each timepoint was assigned to one of several standard categories, i.e., increase, marginal increase, no change, marginal decrease and decrease, depending on the P-value (calculated using the Wilcoxon signed rank test). The ranges for each call were 0.0000–0.0025, 0.0025–0.0030, 0.0030–0.9970, 0.9970–0.9975 and 0.9975 to 1.0000, respectively. These data were then inputted into dChip version 1.3 (Li and Wong, 2001), where they were normalized using the invariant set approach.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Erwin,P,Gianchandani
| | Sample_contact_email | erwin@virginia.edu
| | Sample_contact_department | Office of the Vice President for Research
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | Box 400301
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22904
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428154/suppl/GSM428154_pnf1_2hr.CEL.gz
| | Sample_series_id | GSE17119
| | Sample_data_row_count | 54675
| | |
|
GSM428155 | GPL570 |
|
PNF1-treated cells, 4 h post-supplementation.
|
Human microvascular endothelial cells (HMVEC), 4 h post-supplementation with 30 µM phthalimide neovascular factor 1 (PNF1).
|
cell line: HMVEC
|
HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 30 µM PNF1 was added to the sample. Total RNA from the cultures was isolated 4 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
|
| Sample_geo_accession | GSM428155
| | Sample_status | Public on Jul 17 2009
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from the cultures was isolated 4 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA samples were prepared for hybridization using the GeneChip One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA, USA). Total RNA integrity was assessed by analysis with an Agilent Bioanalyzer using RNA 6000 Nano chips (Agilent Technologies, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was generated from the total RNA samples and fragmented in preparation for array hybridization, according to standard Affymetrix GeneChip protocols. Fragmented cRNA (10 µg) was hybridized to Affymetrix Human Genome U133 Plus 2.0 probe arrays for 16 h.
| | Sample_scan_protocol | The arrays were washed and stained in an Affymetrix Automated Fluidics Station 400 and scanned with the Affymetrix GeneArray Scanner. Scanned images were examined for visible defects and checked for proper grid alignment, and acceptable image files were analyzed to generate raw data in the form of ‘CEL’ files. Quality control, including replicate analysis, measurement of noise and background levels, and assessment of the 3'/5' ratio of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and beta-actin (β-actin) was performed with Microarray Analysis Suite 5.0 (MAS 5.0, Affymetrix).
| | Sample_data_processing | Using MAS 5.0, each gene transcript was detected as ‘present’, ‘absent’ or ‘marginal’, and the change between the experimental (PNF1-stimulated) and baseline (control) conditions at each timepoint was assigned to one of several standard categories, i.e., increase, marginal increase, no change, marginal decrease and decrease, depending on the P-value (calculated using the Wilcoxon signed rank test). The ranges for each call were 0.0000–0.0025, 0.0025–0.0030, 0.0030–0.9970, 0.9970–0.9975 and 0.9975 to 1.0000, respectively. These data were then inputted into dChip version 1.3 (Li and Wong, 2001), where they were normalized using the invariant set approach.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Erwin,P,Gianchandani
| | Sample_contact_email | erwin@virginia.edu
| | Sample_contact_department | Office of the Vice President for Research
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | Box 400301
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22904
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428155/suppl/GSM428155_pnf1_4hr.CEL.gz
| | Sample_series_id | GSE17119
| | Sample_data_row_count | 54675
| | |
|
GSM428156 | GPL570 |
|
PNF1-treated cells, 8 h post-supplementation.
|
Human microvascular endothelial cells (HMVEC), 8 h post-supplementation with 30 µM phthalimide neovascular factor 1 (PNF1).
|
cell line: HMVEC
|
HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 30 µM PNF1 was added to the sample. Total RNA from the cultures was isolated 8 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
|
| Sample_geo_accession | GSM428156
| | Sample_status | Public on Jul 17 2009
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from the cultures was isolated 8 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA samples were prepared for hybridization using the GeneChip One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA, USA). Total RNA integrity was assessed by analysis with an Agilent Bioanalyzer using RNA 6000 Nano chips (Agilent Technologies, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was generated from the total RNA samples and fragmented in preparation for array hybridization, according to standard Affymetrix GeneChip protocols. Fragmented cRNA (10 µg) was hybridized to Affymetrix Human Genome U133 Plus 2.0 probe arrays for 16 h.
| | Sample_scan_protocol | The arrays were washed and stained in an Affymetrix Automated Fluidics Station 400 and scanned with the Affymetrix GeneArray Scanner. Scanned images were examined for visible defects and checked for proper grid alignment, and acceptable image files were analyzed to generate raw data in the form of ‘CEL’ files. Quality control, including replicate analysis, measurement of noise and background levels, and assessment of the 3'/5' ratio of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and beta-actin (β-actin) was performed with Microarray Analysis Suite 5.0 (MAS 5.0, Affymetrix).
| | Sample_data_processing | Using MAS 5.0, each gene transcript was detected as ‘present’, ‘absent’ or ‘marginal’, and the change between the experimental (PNF1-stimulated) and baseline (control) conditions at each timepoint was assigned to one of several standard categories, i.e., increase, marginal increase, no change, marginal decrease and decrease, depending on the P-value (calculated using the Wilcoxon signed rank test). The ranges for each call were 0.0000–0.0025, 0.0025–0.0030, 0.0030–0.9970, 0.9970–0.9975 and 0.9975 to 1.0000, respectively. These data were then inputted into dChip version 1.3 (Li and Wong, 2001), where they were normalized using the invariant set approach.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Erwin,P,Gianchandani
| | Sample_contact_email | erwin@virginia.edu
| | Sample_contact_department | Office of the Vice President for Research
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | Box 400301
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22904
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428156/suppl/GSM428156_pnf1_8hr.CEL.gz
| | Sample_series_id | GSE17119
| | Sample_data_row_count | 54675
| | |
|
GSM428157 | GPL570 |
|
PNF1-treated cells, 16 h post-supplementation.
|
Human microvascular endothelial cells (HMVEC), 16 h post-supplementation with 30 µM phthalimide neovascular factor 1 (PNF1).
|
cell line: HMVEC
|
HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 30 µM PNF1 was added to the sample. Total RNA from the cultures was isolated 16 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
|
| Sample_geo_accession | GSM428157
| | Sample_status | Public on Jul 17 2009
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from the cultures was isolated 16 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA samples were prepared for hybridization using the GeneChip One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA, USA). Total RNA integrity was assessed by analysis with an Agilent Bioanalyzer using RNA 6000 Nano chips (Agilent Technologies, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was generated from the total RNA samples and fragmented in preparation for array hybridization, according to standard Affymetrix GeneChip protocols. Fragmented cRNA (10 µg) was hybridized to Affymetrix Human Genome U133 Plus 2.0 probe arrays for 16 h.
| | Sample_scan_protocol | The arrays were washed and stained in an Affymetrix Automated Fluidics Station 400 and scanned with the Affymetrix GeneArray Scanner. Scanned images were examined for visible defects and checked for proper grid alignment, and acceptable image files were analyzed to generate raw data in the form of ‘CEL’ files. Quality control, including replicate analysis, measurement of noise and background levels, and assessment of the 3'/5' ratio of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and beta-actin (β-actin) was performed with Microarray Analysis Suite 5.0 (MAS 5.0, Affymetrix).
| | Sample_data_processing | Using MAS 5.0, each gene transcript was detected as ‘present’, ‘absent’ or ‘marginal’, and the change between the experimental (PNF1-stimulated) and baseline (control) conditions at each timepoint was assigned to one of several standard categories, i.e., increase, marginal increase, no change, marginal decrease and decrease, depending on the P-value (calculated using the Wilcoxon signed rank test). The ranges for each call were 0.0000–0.0025, 0.0025–0.0030, 0.0030–0.9970, 0.9970–0.9975 and 0.9975 to 1.0000, respectively. These data were then inputted into dChip version 1.3 (Li and Wong, 2001), where they were normalized using the invariant set approach.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Erwin,P,Gianchandani
| | Sample_contact_email | erwin@virginia.edu
| | Sample_contact_department | Office of the Vice President for Research
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | Box 400301
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22904
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428157/suppl/GSM428157_pnf1_16hr.CEL.gz
| | Sample_series_id | GSE17119
| | Sample_data_row_count | 54675
| | |
|
GSM428158 | GPL570 |
|
PNF1-treated cells, 24 h post-supplementation.
|
Human microvascular endothelial cells (HMVEC), 24 h post-supplementation with 30 µM phthalimide neovascular factor 1 (PNF1).
|
cell line: HMVEC
|
HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 30 µM PNF1 was added to the sample. Total RNA from the cultures was isolated 24 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
|
| Sample_geo_accession | GSM428158
| | Sample_status | Public on Jul 17 2009
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from the cultures was isolated 24 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA samples were prepared for hybridization using the GeneChip One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA, USA). Total RNA integrity was assessed by analysis with an Agilent Bioanalyzer using RNA 6000 Nano chips (Agilent Technologies, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was generated from the total RNA samples and fragmented in preparation for array hybridization, according to standard Affymetrix GeneChip protocols. Fragmented cRNA (10 µg) was hybridized to Affymetrix Human Genome U133 Plus 2.0 probe arrays for 16 h.
| | Sample_scan_protocol | The arrays were washed and stained in an Affymetrix Automated Fluidics Station 400 and scanned with the Affymetrix GeneArray Scanner. Scanned images were examined for visible defects and checked for proper grid alignment, and acceptable image files were analyzed to generate raw data in the form of ‘CEL’ files. Quality control, including replicate analysis, measurement of noise and background levels, and assessment of the 3'/5' ratio of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and beta-actin (β-actin) was performed with Microarray Analysis Suite 5.0 (MAS 5.0, Affymetrix).
| | Sample_data_processing | Using MAS 5.0, each gene transcript was detected as ‘present’, ‘absent’ or ‘marginal’, and the change between the experimental (PNF1-stimulated) and baseline (control) conditions at each timepoint was assigned to one of several standard categories, i.e., increase, marginal increase, no change, marginal decrease and decrease, depending on the P-value (calculated using the Wilcoxon signed rank test). The ranges for each call were 0.0000–0.0025, 0.0025–0.0030, 0.0030–0.9970, 0.9970–0.9975 and 0.9975 to 1.0000, respectively. These data were then inputted into dChip version 1.3 (Li and Wong, 2001), where they were normalized using the invariant set approach.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Erwin,P,Gianchandani
| | Sample_contact_email | erwin@virginia.edu
| | Sample_contact_department | Office of the Vice President for Research
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | Box 400301
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22904
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428158/suppl/GSM428158_pnf1_24hr.CEL.gz
| | Sample_series_id | GSE17119
| | Sample_data_row_count | 54675
| | |
|
GSM428159 | GPL570 |
|
PNF1-treated cells, 48 h post-supplementation.
|
Human microvascular endothelial cells (HMVEC), 48 h post-supplementation with 30 µM phthalimide neovascular factor 1 (PNF1).
|
cell line: HMVEC
|
HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 30 µM PNF1 was added to the sample. Total RNA from the cultures was isolated 48 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
|
| Sample_geo_accession | GSM428159
| | Sample_status | Public on Jul 17 2009
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from the cultures was isolated 48 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | RNA samples were prepared for hybridization using the GeneChip One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA, USA). Total RNA integrity was assessed by analysis with an Agilent Bioanalyzer using RNA 6000 Nano chips (Agilent Technologies, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Biotin-labeled cRNA was generated from the total RNA samples and fragmented in preparation for array hybridization, according to standard Affymetrix GeneChip protocols. Fragmented cRNA (10 µg) was hybridized to Affymetrix Human Genome U133 Plus 2.0 probe arrays for 16 h.
| | Sample_scan_protocol | The arrays were washed and stained in an Affymetrix Automated Fluidics Station 400 and scanned with the Affymetrix GeneArray Scanner. Scanned images were examined for visible defects and checked for proper grid alignment, and acceptable image files were analyzed to generate raw data in the form of ‘CEL’ files. Quality control, including replicate analysis, measurement of noise and background levels, and assessment of the 3'/5' ratio of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and beta-actin (β-actin) was performed with Microarray Analysis Suite 5.0 (MAS 5.0, Affymetrix).
| | Sample_data_processing | Using MAS 5.0, each gene transcript was detected as ‘present’, ‘absent’ or ‘marginal’, and the change between the experimental (PNF1-stimulated) and baseline (control) conditions at each timepoint was assigned to one of several standard categories, i.e., increase, marginal increase, no change, marginal decrease and decrease, depending on the P-value (calculated using the Wilcoxon signed rank test). The ranges for each call were 0.0000–0.0025, 0.0025–0.0030, 0.0030–0.9970, 0.9970–0.9975 and 0.9975 to 1.0000, respectively. These data were then inputted into dChip version 1.3 (Li and Wong, 2001), where they were normalized using the invariant set approach.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Erwin,P,Gianchandani
| | Sample_contact_email | erwin@virginia.edu
| | Sample_contact_department | Office of the Vice President for Research
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | Box 400301
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22904
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428159/suppl/GSM428159_pnf1_48hr.CEL.gz
| | Sample_series_id | GSE17119
| | Sample_data_row_count | 54675
| | |
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