Search results for the GEO ID: GSE20114  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM502612 | GPL570 |
|
blood-vehicle-control-1
|
blood, vehicle, control
|
tissue: blood
disease: hypertriglyceridemia
lps: vehicle
dha: control
|
Unstimulated control.
101-0-V
|
| Sample_geo_accession | GSM502612
| | Sample_status | Public on Jan 30 2010
| | Sample_submission_date | Jan 29 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Forty moderately hyperlipidemic but otherwise healthy men were enrolled into a double-blind, placebo-controlled, parallel study with 2 metabolic periods – baseline (first 8 d) and intervention (last 90 d). Participants were randomized into one of two groups, where one received 7.5 g/day DHA oil capsules containing 3.0 g/day DHA, produced in Crypthecodinium cohinii (Martek Biosciences Corp., Columbia, MD), and no EPA, and the other group received 7.5 g/day extra virgin olive oil capsules. During the baseline period, participants did not receive supplements.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Blood cells from four subjects in the DHA supplementation group were collected for either lipopolysaccharide (LPS) treatment or no treatment (vehicle) and subsequent RNA isolation. For each subject, two 10 mL heparinized venous blood were collected on days 0 and 91. Whole blood was then diluted 1:2 with sterile RPMI 1640 culture medium containing 25mM HEPES and L-glutamine (Gibco Invitrogen, Carlsbad, CA), then split into two 30 mL and incubated with either 10 microg/mL ultra pure LPS (E. coli O157:H7; List Biological Laboratories, Inc., Campbell, CA) or sterile endotoxin-free water alone for 4 h at 37°C, 5% CO2. To simplify RNA isolation, erythrocytes were lysed by a two-step process (Buffer EL; Qiagen, Valencia, CA) and the resulting leukocyte pellets were lysed with Buffer RLT (Qiagen), homogenized with QIAshredder spin columns (Qiagen), and stored at -80°C. Total cellular RNA from leukocytes was isolated using RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions. RNA quality and integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA (5 microg) was used for cDNA synthesis (SuperScript III First Strand Synthesis System; Invitrogen, Carlsbad, CA) followed by in vitro transcription to incorporate biotin labels and subsequent hybridization to Human Genome U133 Plus 2.0 (Affymetrix, Santa Clara, CA), which represents 38,500 well-characterized genes, per manufacturer’s protocol.
| | Sample_hyb_protocol | The arrays were washed and stained on a GeneChip Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned on a GeneChip Scanner 3000.
| | Sample_data_processing | Affymetrix .CEL files were imported into the Bioconductor Affy R package and subjected to baseline correction, normalization, and calculation of gene expression values using the Robust Multichip Average (RMA) procedure. Genes were considered for further analyses if they were detected in at least 50% of the microarrays (p<0.05 of the signed rank test). Gene expression values were exported into Cluster for hierarchical clustering (HC) and self organizing map (SOM) procedure and visualized as heat maps in Java TreeView. DHA and LPS-specific changes were determined using paired t test. False discovery rate (FDR) was controlled using Bonferroni. Lists of probe sets that were significantly differentially regulated by DHA or LPS or any combinations thereof were exported into the Database for Annotation, Visualization and Integrated Discovery (DAVID) (http://david.abcc.ncifcrf.gov). Gene Ontology (GO) categories and BioCarta and KEGG pathway maps were evaluated against the lists of probe sets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Dawson
| | Sample_contact_laboratory | MCB
| | Sample_contact_department | CCM
| | Sample_contact_institute | UC Davis
| | Sample_contact_address | 2795 Second Street, Suite 400
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95618
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.mousebiology.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502612/suppl/GSM502612.CEL.gz
| | Sample_series_id | GSE20114
| | Sample_data_row_count | 54675
| | |
|
GSM502613 | GPL570 |
|
blood-vehicle-control-2
|
blood, vehicle, control
|
tissue: blood
disease: hypertriglyceridemia
lps: vehicle
dha: control
|
Unstimulated control.
202-0-V
|
| Sample_geo_accession | GSM502613
| | Sample_status | Public on Jan 30 2010
| | Sample_submission_date | Jan 29 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Forty moderately hyperlipidemic but otherwise healthy men were enrolled into a double-blind, placebo-controlled, parallel study with 2 metabolic periods – baseline (first 8 d) and intervention (last 90 d). Participants were randomized into one of two groups, where one received 7.5 g/day DHA oil capsules containing 3.0 g/day DHA, produced in Crypthecodinium cohinii (Martek Biosciences Corp., Columbia, MD), and no EPA, and the other group received 7.5 g/day extra virgin olive oil capsules. During the baseline period, participants did not receive supplements.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Blood cells from four subjects in the DHA supplementation group were collected for either lipopolysaccharide (LPS) treatment or no treatment (vehicle) and subsequent RNA isolation. For each subject, two 10 mL heparinized venous blood were collected on days 0 and 91. Whole blood was then diluted 1:2 with sterile RPMI 1640 culture medium containing 25mM HEPES and L-glutamine (Gibco Invitrogen, Carlsbad, CA), then split into two 30 mL and incubated with either 10 microg/mL ultra pure LPS (E. coli O157:H7; List Biological Laboratories, Inc., Campbell, CA) or sterile endotoxin-free water alone for 4 h at 37°C, 5% CO2. To simplify RNA isolation, erythrocytes were lysed by a two-step process (Buffer EL; Qiagen, Valencia, CA) and the resulting leukocyte pellets were lysed with Buffer RLT (Qiagen), homogenized with QIAshredder spin columns (Qiagen), and stored at -80°C. Total cellular RNA from leukocytes was isolated using RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions. RNA quality and integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA (5 microg) was used for cDNA synthesis (SuperScript III First Strand Synthesis System; Invitrogen, Carlsbad, CA) followed by in vitro transcription to incorporate biotin labels and subsequent hybridization to Human Genome U133 Plus 2.0 (Affymetrix, Santa Clara, CA), which represents 38,500 well-characterized genes, per manufacturer’s protocol.
| | Sample_hyb_protocol | The arrays were washed and stained on a GeneChip Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned on a GeneChip Scanner 3000.
| | Sample_data_processing | Affymetrix .CEL files were imported into the Bioconductor Affy R package and subjected to baseline correction, normalization, and calculation of gene expression values using the Robust Multichip Average (RMA) procedure. Genes were considered for further analyses if they were detected in at least 50% of the microarrays (p<0.05 of the signed rank test). Gene expression values were exported into Cluster for hierarchical clustering (HC) and self organizing map (SOM) procedure and visualized as heat maps in Java TreeView. DHA and LPS-specific changes were determined using paired t test. False discovery rate (FDR) was controlled using Bonferroni. Lists of probe sets that were significantly differentially regulated by DHA or LPS or any combinations thereof were exported into the Database for Annotation, Visualization and Integrated Discovery (DAVID) (http://david.abcc.ncifcrf.gov). Gene Ontology (GO) categories and BioCarta and KEGG pathway maps were evaluated against the lists of probe sets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Dawson
| | Sample_contact_laboratory | MCB
| | Sample_contact_department | CCM
| | Sample_contact_institute | UC Davis
| | Sample_contact_address | 2795 Second Street, Suite 400
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95618
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.mousebiology.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502613/suppl/GSM502613.CEL.gz
| | Sample_series_id | GSE20114
| | Sample_data_row_count | 54675
| | |
|
GSM502614 | GPL570 |
|
blood-vehicle-control-3
|
blood, vehicle, control
|
tissue: blood
disease: hypertriglyceridemia
lps: vehicle
dha: control
|
Unstimulated control.
203-0-V
|
| Sample_geo_accession | GSM502614
| | Sample_status | Public on Jan 30 2010
| | Sample_submission_date | Jan 29 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Forty moderately hyperlipidemic but otherwise healthy men were enrolled into a double-blind, placebo-controlled, parallel study with 2 metabolic periods – baseline (first 8 d) and intervention (last 90 d). Participants were randomized into one of two groups, where one received 7.5 g/day DHA oil capsules containing 3.0 g/day DHA, produced in Crypthecodinium cohinii (Martek Biosciences Corp., Columbia, MD), and no EPA, and the other group received 7.5 g/day extra virgin olive oil capsules. During the baseline period, participants did not receive supplements.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Blood cells from four subjects in the DHA supplementation group were collected for either lipopolysaccharide (LPS) treatment or no treatment (vehicle) and subsequent RNA isolation. For each subject, two 10 mL heparinized venous blood were collected on days 0 and 91. Whole blood was then diluted 1:2 with sterile RPMI 1640 culture medium containing 25mM HEPES and L-glutamine (Gibco Invitrogen, Carlsbad, CA), then split into two 30 mL and incubated with either 10 microg/mL ultra pure LPS (E. coli O157:H7; List Biological Laboratories, Inc., Campbell, CA) or sterile endotoxin-free water alone for 4 h at 37°C, 5% CO2. To simplify RNA isolation, erythrocytes were lysed by a two-step process (Buffer EL; Qiagen, Valencia, CA) and the resulting leukocyte pellets were lysed with Buffer RLT (Qiagen), homogenized with QIAshredder spin columns (Qiagen), and stored at -80°C. Total cellular RNA from leukocytes was isolated using RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions. RNA quality and integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA (5 microg) was used for cDNA synthesis (SuperScript III First Strand Synthesis System; Invitrogen, Carlsbad, CA) followed by in vitro transcription to incorporate biotin labels and subsequent hybridization to Human Genome U133 Plus 2.0 (Affymetrix, Santa Clara, CA), which represents 38,500 well-characterized genes, per manufacturer’s protocol.
| | Sample_hyb_protocol | The arrays were washed and stained on a GeneChip Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned on a GeneChip Scanner 3000.
| | Sample_data_processing | Affymetrix .CEL files were imported into the Bioconductor Affy R package and subjected to baseline correction, normalization, and calculation of gene expression values using the Robust Multichip Average (RMA) procedure. Genes were considered for further analyses if they were detected in at least 50% of the microarrays (p<0.05 of the signed rank test). Gene expression values were exported into Cluster for hierarchical clustering (HC) and self organizing map (SOM) procedure and visualized as heat maps in Java TreeView. DHA and LPS-specific changes were determined using paired t test. False discovery rate (FDR) was controlled using Bonferroni. Lists of probe sets that were significantly differentially regulated by DHA or LPS or any combinations thereof were exported into the Database for Annotation, Visualization and Integrated Discovery (DAVID) (http://david.abcc.ncifcrf.gov). Gene Ontology (GO) categories and BioCarta and KEGG pathway maps were evaluated against the lists of probe sets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Dawson
| | Sample_contact_laboratory | MCB
| | Sample_contact_department | CCM
| | Sample_contact_institute | UC Davis
| | Sample_contact_address | 2795 Second Street, Suite 400
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95618
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.mousebiology.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502614/suppl/GSM502614.CEL.gz
| | Sample_series_id | GSE20114
| | Sample_data_row_count | 54675
| | |
|
GSM502615 | GPL570 |
|
blood-vehicle-control-4
|
blood, vehicle, control
|
tissue: blood
disease: hypertriglyceridemia
lps: vehicle
dha: control
|
Unstimulated control.
418-0-V
|
| Sample_geo_accession | GSM502615
| | Sample_status | Public on Jan 30 2010
| | Sample_submission_date | Jan 29 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Forty moderately hyperlipidemic but otherwise healthy men were enrolled into a double-blind, placebo-controlled, parallel study with 2 metabolic periods – baseline (first 8 d) and intervention (last 90 d). Participants were randomized into one of two groups, where one received 7.5 g/day DHA oil capsules containing 3.0 g/day DHA, produced in Crypthecodinium cohinii (Martek Biosciences Corp., Columbia, MD), and no EPA, and the other group received 7.5 g/day extra virgin olive oil capsules. During the baseline period, participants did not receive supplements.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Blood cells from four subjects in the DHA supplementation group were collected for either lipopolysaccharide (LPS) treatment or no treatment (vehicle) and subsequent RNA isolation. For each subject, two 10 mL heparinized venous blood were collected on days 0 and 91. Whole blood was then diluted 1:2 with sterile RPMI 1640 culture medium containing 25mM HEPES and L-glutamine (Gibco Invitrogen, Carlsbad, CA), then split into two 30 mL and incubated with either 10 microg/mL ultra pure LPS (E. coli O157:H7; List Biological Laboratories, Inc., Campbell, CA) or sterile endotoxin-free water alone for 4 h at 37°C, 5% CO2. To simplify RNA isolation, erythrocytes were lysed by a two-step process (Buffer EL; Qiagen, Valencia, CA) and the resulting leukocyte pellets were lysed with Buffer RLT (Qiagen), homogenized with QIAshredder spin columns (Qiagen), and stored at -80°C. Total cellular RNA from leukocytes was isolated using RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions. RNA quality and integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA (5 microg) was used for cDNA synthesis (SuperScript III First Strand Synthesis System; Invitrogen, Carlsbad, CA) followed by in vitro transcription to incorporate biotin labels and subsequent hybridization to Human Genome U133 Plus 2.0 (Affymetrix, Santa Clara, CA), which represents 38,500 well-characterized genes, per manufacturer’s protocol.
| | Sample_hyb_protocol | The arrays were washed and stained on a GeneChip Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned on a GeneChip Scanner 3000.
| | Sample_data_processing | Affymetrix .CEL files were imported into the Bioconductor Affy R package and subjected to baseline correction, normalization, and calculation of gene expression values using the Robust Multichip Average (RMA) procedure. Genes were considered for further analyses if they were detected in at least 50% of the microarrays (p<0.05 of the signed rank test). Gene expression values were exported into Cluster for hierarchical clustering (HC) and self organizing map (SOM) procedure and visualized as heat maps in Java TreeView. DHA and LPS-specific changes were determined using paired t test. False discovery rate (FDR) was controlled using Bonferroni. Lists of probe sets that were significantly differentially regulated by DHA or LPS or any combinations thereof were exported into the Database for Annotation, Visualization and Integrated Discovery (DAVID) (http://david.abcc.ncifcrf.gov). Gene Ontology (GO) categories and BioCarta and KEGG pathway maps were evaluated against the lists of probe sets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Dawson
| | Sample_contact_laboratory | MCB
| | Sample_contact_department | CCM
| | Sample_contact_institute | UC Davis
| | Sample_contact_address | 2795 Second Street, Suite 400
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95618
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.mousebiology.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502615/suppl/GSM502615.CEL.gz
| | Sample_series_id | GSE20114
| | Sample_data_row_count | 54675
| | |
|
GSM502616 | GPL570 |
|
blood-vehicle-DHA-1
|
blood, vehicle, DHA
|
tissue: blood
disease: hypertriglyceridemia
lps: vehicle
dha: DHA
|
Unstimulated cells, DHA supplementation.
101-91-V
|
| Sample_geo_accession | GSM502616
| | Sample_status | Public on Jan 30 2010
| | Sample_submission_date | Jan 29 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Forty moderately hyperlipidemic but otherwise healthy men were enrolled into a double-blind, placebo-controlled, parallel study with 2 metabolic periods – baseline (first 8 d) and intervention (last 90 d). Participants were randomized into one of two groups, where one received 7.5 g/day DHA oil capsules containing 3.0 g/day DHA, produced in Crypthecodinium cohinii (Martek Biosciences Corp., Columbia, MD), and no EPA, and the other group received 7.5 g/day extra virgin olive oil capsules. During the baseline period, participants did not receive supplements.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Blood cells from four subjects in the DHA supplementation group were collected for either lipopolysaccharide (LPS) treatment or no treatment (vehicle) and subsequent RNA isolation. For each subject, two 10 mL heparinized venous blood were collected on days 0 and 91. Whole blood was then diluted 1:2 with sterile RPMI 1640 culture medium containing 25mM HEPES and L-glutamine (Gibco Invitrogen, Carlsbad, CA), then split into two 30 mL and incubated with either 10 microg/mL ultra pure LPS (E. coli O157:H7; List Biological Laboratories, Inc., Campbell, CA) or sterile endotoxin-free water alone for 4 h at 37°C, 5% CO2. To simplify RNA isolation, erythrocytes were lysed by a two-step process (Buffer EL; Qiagen, Valencia, CA) and the resulting leukocyte pellets were lysed with Buffer RLT (Qiagen), homogenized with QIAshredder spin columns (Qiagen), and stored at -80°C. Total cellular RNA from leukocytes was isolated using RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions. RNA quality and integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA (5 microg) was used for cDNA synthesis (SuperScript III First Strand Synthesis System; Invitrogen, Carlsbad, CA) followed by in vitro transcription to incorporate biotin labels and subsequent hybridization to Human Genome U133 Plus 2.0 (Affymetrix, Santa Clara, CA), which represents 38,500 well-characterized genes, per manufacturer’s protocol.
| | Sample_hyb_protocol | The arrays were washed and stained on a GeneChip Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned on a GeneChip Scanner 3000.
| | Sample_data_processing | Affymetrix .CEL files were imported into the Bioconductor Affy R package and subjected to baseline correction, normalization, and calculation of gene expression values using the Robust Multichip Average (RMA) procedure. Genes were considered for further analyses if they were detected in at least 50% of the microarrays (p<0.05 of the signed rank test). Gene expression values were exported into Cluster for hierarchical clustering (HC) and self organizing map (SOM) procedure and visualized as heat maps in Java TreeView. DHA and LPS-specific changes were determined using paired t test. False discovery rate (FDR) was controlled using Bonferroni. Lists of probe sets that were significantly differentially regulated by DHA or LPS or any combinations thereof were exported into the Database for Annotation, Visualization and Integrated Discovery (DAVID) (http://david.abcc.ncifcrf.gov). Gene Ontology (GO) categories and BioCarta and KEGG pathway maps were evaluated against the lists of probe sets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Dawson
| | Sample_contact_laboratory | MCB
| | Sample_contact_department | CCM
| | Sample_contact_institute | UC Davis
| | Sample_contact_address | 2795 Second Street, Suite 400
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95618
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.mousebiology.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502616/suppl/GSM502616.CEL.gz
| | Sample_series_id | GSE20114
| | Sample_data_row_count | 54675
| | |
|
GSM502617 | GPL570 |
|
blood-vehicle-DHA-2
|
blood, vehicle, DHA
|
tissue: blood
disease: hypertriglyceridemia
lps: vehicle
dha: DHA
|
Unstimulated cells, DHA supplementation.
202-91-V
|
| Sample_geo_accession | GSM502617
| | Sample_status | Public on Jan 30 2010
| | Sample_submission_date | Jan 29 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Forty moderately hyperlipidemic but otherwise healthy men were enrolled into a double-blind, placebo-controlled, parallel study with 2 metabolic periods – baseline (first 8 d) and intervention (last 90 d). Participants were randomized into one of two groups, where one received 7.5 g/day DHA oil capsules containing 3.0 g/day DHA, produced in Crypthecodinium cohinii (Martek Biosciences Corp., Columbia, MD), and no EPA, and the other group received 7.5 g/day extra virgin olive oil capsules. During the baseline period, participants did not receive supplements.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Blood cells from four subjects in the DHA supplementation group were collected for either lipopolysaccharide (LPS) treatment or no treatment (vehicle) and subsequent RNA isolation. For each subject, two 10 mL heparinized venous blood were collected on days 0 and 91. Whole blood was then diluted 1:2 with sterile RPMI 1640 culture medium containing 25mM HEPES and L-glutamine (Gibco Invitrogen, Carlsbad, CA), then split into two 30 mL and incubated with either 10 microg/mL ultra pure LPS (E. coli O157:H7; List Biological Laboratories, Inc., Campbell, CA) or sterile endotoxin-free water alone for 4 h at 37°C, 5% CO2. To simplify RNA isolation, erythrocytes were lysed by a two-step process (Buffer EL; Qiagen, Valencia, CA) and the resulting leukocyte pellets were lysed with Buffer RLT (Qiagen), homogenized with QIAshredder spin columns (Qiagen), and stored at -80°C. Total cellular RNA from leukocytes was isolated using RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions. RNA quality and integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA (5 microg) was used for cDNA synthesis (SuperScript III First Strand Synthesis System; Invitrogen, Carlsbad, CA) followed by in vitro transcription to incorporate biotin labels and subsequent hybridization to Human Genome U133 Plus 2.0 (Affymetrix, Santa Clara, CA), which represents 38,500 well-characterized genes, per manufacturer’s protocol.
| | Sample_hyb_protocol | The arrays were washed and stained on a GeneChip Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned on a GeneChip Scanner 3000.
| | Sample_data_processing | Affymetrix .CEL files were imported into the Bioconductor Affy R package and subjected to baseline correction, normalization, and calculation of gene expression values using the Robust Multichip Average (RMA) procedure. Genes were considered for further analyses if they were detected in at least 50% of the microarrays (p<0.05 of the signed rank test). Gene expression values were exported into Cluster for hierarchical clustering (HC) and self organizing map (SOM) procedure and visualized as heat maps in Java TreeView. DHA and LPS-specific changes were determined using paired t test. False discovery rate (FDR) was controlled using Bonferroni. Lists of probe sets that were significantly differentially regulated by DHA or LPS or any combinations thereof were exported into the Database for Annotation, Visualization and Integrated Discovery (DAVID) (http://david.abcc.ncifcrf.gov). Gene Ontology (GO) categories and BioCarta and KEGG pathway maps were evaluated against the lists of probe sets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Dawson
| | Sample_contact_laboratory | MCB
| | Sample_contact_department | CCM
| | Sample_contact_institute | UC Davis
| | Sample_contact_address | 2795 Second Street, Suite 400
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95618
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.mousebiology.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502617/suppl/GSM502617.CEL.gz
| | Sample_series_id | GSE20114
| | Sample_data_row_count | 54675
| | |
|
GSM502618 | GPL570 |
|
blood-vehicle-DHA-3
|
blood, vehicle, DHA
|
tissue: blood
disease: hypertriglyceridemia
lps: vehicle
dha: DHA
|
Unstimulated cells, DHA supplementation.
203-91-V
|
| Sample_geo_accession | GSM502618
| | Sample_status | Public on Jan 30 2010
| | Sample_submission_date | Jan 29 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Forty moderately hyperlipidemic but otherwise healthy men were enrolled into a double-blind, placebo-controlled, parallel study with 2 metabolic periods – baseline (first 8 d) and intervention (last 90 d). Participants were randomized into one of two groups, where one received 7.5 g/day DHA oil capsules containing 3.0 g/day DHA, produced in Crypthecodinium cohinii (Martek Biosciences Corp., Columbia, MD), and no EPA, and the other group received 7.5 g/day extra virgin olive oil capsules. During the baseline period, participants did not receive supplements.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Blood cells from four subjects in the DHA supplementation group were collected for either lipopolysaccharide (LPS) treatment or no treatment (vehicle) and subsequent RNA isolation. For each subject, two 10 mL heparinized venous blood were collected on days 0 and 91. Whole blood was then diluted 1:2 with sterile RPMI 1640 culture medium containing 25mM HEPES and L-glutamine (Gibco Invitrogen, Carlsbad, CA), then split into two 30 mL and incubated with either 10 microg/mL ultra pure LPS (E. coli O157:H7; List Biological Laboratories, Inc., Campbell, CA) or sterile endotoxin-free water alone for 4 h at 37°C, 5% CO2. To simplify RNA isolation, erythrocytes were lysed by a two-step process (Buffer EL; Qiagen, Valencia, CA) and the resulting leukocyte pellets were lysed with Buffer RLT (Qiagen), homogenized with QIAshredder spin columns (Qiagen), and stored at -80°C. Total cellular RNA from leukocytes was isolated using RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions. RNA quality and integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA (5 microg) was used for cDNA synthesis (SuperScript III First Strand Synthesis System; Invitrogen, Carlsbad, CA) followed by in vitro transcription to incorporate biotin labels and subsequent hybridization to Human Genome U133 Plus 2.0 (Affymetrix, Santa Clara, CA), which represents 38,500 well-characterized genes, per manufacturer’s protocol.
| | Sample_hyb_protocol | The arrays were washed and stained on a GeneChip Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned on a GeneChip Scanner 3000.
| | Sample_data_processing | Affymetrix .CEL files were imported into the Bioconductor Affy R package and subjected to baseline correction, normalization, and calculation of gene expression values using the Robust Multichip Average (RMA) procedure. Genes were considered for further analyses if they were detected in at least 50% of the microarrays (p<0.05 of the signed rank test). Gene expression values were exported into Cluster for hierarchical clustering (HC) and self organizing map (SOM) procedure and visualized as heat maps in Java TreeView. DHA and LPS-specific changes were determined using paired t test. False discovery rate (FDR) was controlled using Bonferroni. Lists of probe sets that were significantly differentially regulated by DHA or LPS or any combinations thereof were exported into the Database for Annotation, Visualization and Integrated Discovery (DAVID) (http://david.abcc.ncifcrf.gov). Gene Ontology (GO) categories and BioCarta and KEGG pathway maps were evaluated against the lists of probe sets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Dawson
| | Sample_contact_laboratory | MCB
| | Sample_contact_department | CCM
| | Sample_contact_institute | UC Davis
| | Sample_contact_address | 2795 Second Street, Suite 400
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95618
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.mousebiology.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502618/suppl/GSM502618.CEL.gz
| | Sample_series_id | GSE20114
| | Sample_data_row_count | 54675
| | |
|
GSM502619 | GPL570 |
|
blood-vehicle-DHA-4
|
blood, vehicle, DHA
|
tissue: blood
disease: hypertriglyceridemia
lps: vehicle
dha: DHA
|
Unstimulated cells, DHA supplementation.
418-91-V
|
| Sample_geo_accession | GSM502619
| | Sample_status | Public on Jan 30 2010
| | Sample_submission_date | Jan 29 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Forty moderately hyperlipidemic but otherwise healthy men were enrolled into a double-blind, placebo-controlled, parallel study with 2 metabolic periods – baseline (first 8 d) and intervention (last 90 d). Participants were randomized into one of two groups, where one received 7.5 g/day DHA oil capsules containing 3.0 g/day DHA, produced in Crypthecodinium cohinii (Martek Biosciences Corp., Columbia, MD), and no EPA, and the other group received 7.5 g/day extra virgin olive oil capsules. During the baseline period, participants did not receive supplements.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Blood cells from four subjects in the DHA supplementation group were collected for either lipopolysaccharide (LPS) treatment or no treatment (vehicle) and subsequent RNA isolation. For each subject, two 10 mL heparinized venous blood were collected on days 0 and 91. Whole blood was then diluted 1:2 with sterile RPMI 1640 culture medium containing 25mM HEPES and L-glutamine (Gibco Invitrogen, Carlsbad, CA), then split into two 30 mL and incubated with either 10 microg/mL ultra pure LPS (E. coli O157:H7; List Biological Laboratories, Inc., Campbell, CA) or sterile endotoxin-free water alone for 4 h at 37°C, 5% CO2. To simplify RNA isolation, erythrocytes were lysed by a two-step process (Buffer EL; Qiagen, Valencia, CA) and the resulting leukocyte pellets were lysed with Buffer RLT (Qiagen), homogenized with QIAshredder spin columns (Qiagen), and stored at -80°C. Total cellular RNA from leukocytes was isolated using RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions. RNA quality and integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA (5 microg) was used for cDNA synthesis (SuperScript III First Strand Synthesis System; Invitrogen, Carlsbad, CA) followed by in vitro transcription to incorporate biotin labels and subsequent hybridization to Human Genome U133 Plus 2.0 (Affymetrix, Santa Clara, CA), which represents 38,500 well-characterized genes, per manufacturer’s protocol.
| | Sample_hyb_protocol | The arrays were washed and stained on a GeneChip Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned on a GeneChip Scanner 3000.
| | Sample_data_processing | Affymetrix .CEL files were imported into the Bioconductor Affy R package and subjected to baseline correction, normalization, and calculation of gene expression values using the Robust Multichip Average (RMA) procedure. Genes were considered for further analyses if they were detected in at least 50% of the microarrays (p<0.05 of the signed rank test). Gene expression values were exported into Cluster for hierarchical clustering (HC) and self organizing map (SOM) procedure and visualized as heat maps in Java TreeView. DHA and LPS-specific changes were determined using paired t test. False discovery rate (FDR) was controlled using Bonferroni. Lists of probe sets that were significantly differentially regulated by DHA or LPS or any combinations thereof were exported into the Database for Annotation, Visualization and Integrated Discovery (DAVID) (http://david.abcc.ncifcrf.gov). Gene Ontology (GO) categories and BioCarta and KEGG pathway maps were evaluated against the lists of probe sets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Dawson
| | Sample_contact_laboratory | MCB
| | Sample_contact_department | CCM
| | Sample_contact_institute | UC Davis
| | Sample_contact_address | 2795 Second Street, Suite 400
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95618
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.mousebiology.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502619/suppl/GSM502619.CEL.gz
| | Sample_series_id | GSE20114
| | Sample_data_row_count | 54675
| | |
|
GSM502620 | GPL570 |
|
blood-LPS-control-1
|
blood, LPS, control
|
tissue: blood
disease: hypertriglyceridemia
lps: LPS
dha: control
|
LPS-stimulated control.
101-0-L
|
| Sample_geo_accession | GSM502620
| | Sample_status | Public on Jan 30 2010
| | Sample_submission_date | Jan 29 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Forty moderately hyperlipidemic but otherwise healthy men were enrolled into a double-blind, placebo-controlled, parallel study with 2 metabolic periods – baseline (first 8 d) and intervention (last 90 d). Participants were randomized into one of two groups, where one received 7.5 g/day DHA oil capsules containing 3.0 g/day DHA, produced in Crypthecodinium cohinii (Martek Biosciences Corp., Columbia, MD), and no EPA, and the other group received 7.5 g/day extra virgin olive oil capsules. During the baseline period, participants did not receive supplements.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Blood cells from four subjects in the DHA supplementation group were collected for either lipopolysaccharide (LPS) treatment or no treatment (vehicle) and subsequent RNA isolation. For each subject, two 10 mL heparinized venous blood were collected on days 0 and 91. Whole blood was then diluted 1:2 with sterile RPMI 1640 culture medium containing 25mM HEPES and L-glutamine (Gibco Invitrogen, Carlsbad, CA), then split into two 30 mL and incubated with either 10 microg/mL ultra pure LPS (E. coli O157:H7; List Biological Laboratories, Inc., Campbell, CA) or sterile endotoxin-free water alone for 4 h at 37°C, 5% CO2. To simplify RNA isolation, erythrocytes were lysed by a two-step process (Buffer EL; Qiagen, Valencia, CA) and the resulting leukocyte pellets were lysed with Buffer RLT (Qiagen), homogenized with QIAshredder spin columns (Qiagen), and stored at -80°C. Total cellular RNA from leukocytes was isolated using RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions. RNA quality and integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA (5 microg) was used for cDNA synthesis (SuperScript III First Strand Synthesis System; Invitrogen, Carlsbad, CA) followed by in vitro transcription to incorporate biotin labels and subsequent hybridization to Human Genome U133 Plus 2.0 (Affymetrix, Santa Clara, CA), which represents 38,500 well-characterized genes, per manufacturer’s protocol.
| | Sample_hyb_protocol | The arrays were washed and stained on a GeneChip Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned on a GeneChip Scanner 3000.
| | Sample_data_processing | Affymetrix .CEL files were imported into the Bioconductor Affy R package and subjected to baseline correction, normalization, and calculation of gene expression values using the Robust Multichip Average (RMA) procedure. Genes were considered for further analyses if they were detected in at least 50% of the microarrays (p<0.05 of the signed rank test). Gene expression values were exported into Cluster for hierarchical clustering (HC) and self organizing map (SOM) procedure and visualized as heat maps in Java TreeView. DHA and LPS-specific changes were determined using paired t test. False discovery rate (FDR) was controlled using Bonferroni. Lists of probe sets that were significantly differentially regulated by DHA or LPS or any combinations thereof were exported into the Database for Annotation, Visualization and Integrated Discovery (DAVID) (http://david.abcc.ncifcrf.gov). Gene Ontology (GO) categories and BioCarta and KEGG pathway maps were evaluated against the lists of probe sets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Dawson
| | Sample_contact_laboratory | MCB
| | Sample_contact_department | CCM
| | Sample_contact_institute | UC Davis
| | Sample_contact_address | 2795 Second Street, Suite 400
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95618
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.mousebiology.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502620/suppl/GSM502620.CEL.gz
| | Sample_series_id | GSE20114
| | Sample_data_row_count | 54675
| | |
|
GSM502621 | GPL570 |
|
blood-LPS-control-2
|
blood, LPS, control
|
tissue: blood
disease: hypertriglyceridemia
lps: LPS
dha: control
|
LPS-stimulated control.
202-0-L
|
| Sample_geo_accession | GSM502621
| | Sample_status | Public on Jan 30 2010
| | Sample_submission_date | Jan 29 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Forty moderately hyperlipidemic but otherwise healthy men were enrolled into a double-blind, placebo-controlled, parallel study with 2 metabolic periods – baseline (first 8 d) and intervention (last 90 d). Participants were randomized into one of two groups, where one received 7.5 g/day DHA oil capsules containing 3.0 g/day DHA, produced in Crypthecodinium cohinii (Martek Biosciences Corp., Columbia, MD), and no EPA, and the other group received 7.5 g/day extra virgin olive oil capsules. During the baseline period, participants did not receive supplements.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Blood cells from four subjects in the DHA supplementation group were collected for either lipopolysaccharide (LPS) treatment or no treatment (vehicle) and subsequent RNA isolation. For each subject, two 10 mL heparinized venous blood were collected on days 0 and 91. Whole blood was then diluted 1:2 with sterile RPMI 1640 culture medium containing 25mM HEPES and L-glutamine (Gibco Invitrogen, Carlsbad, CA), then split into two 30 mL and incubated with either 10 microg/mL ultra pure LPS (E. coli O157:H7; List Biological Laboratories, Inc., Campbell, CA) or sterile endotoxin-free water alone for 4 h at 37°C, 5% CO2. To simplify RNA isolation, erythrocytes were lysed by a two-step process (Buffer EL; Qiagen, Valencia, CA) and the resulting leukocyte pellets were lysed with Buffer RLT (Qiagen), homogenized with QIAshredder spin columns (Qiagen), and stored at -80°C. Total cellular RNA from leukocytes was isolated using RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions. RNA quality and integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA (5 microg) was used for cDNA synthesis (SuperScript III First Strand Synthesis System; Invitrogen, Carlsbad, CA) followed by in vitro transcription to incorporate biotin labels and subsequent hybridization to Human Genome U133 Plus 2.0 (Affymetrix, Santa Clara, CA), which represents 38,500 well-characterized genes, per manufacturer’s protocol.
| | Sample_hyb_protocol | The arrays were washed and stained on a GeneChip Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned on a GeneChip Scanner 3000.
| | Sample_data_processing | Affymetrix .CEL files were imported into the Bioconductor Affy R package and subjected to baseline correction, normalization, and calculation of gene expression values using the Robust Multichip Average (RMA) procedure. Genes were considered for further analyses if they were detected in at least 50% of the microarrays (p<0.05 of the signed rank test). Gene expression values were exported into Cluster for hierarchical clustering (HC) and self organizing map (SOM) procedure and visualized as heat maps in Java TreeView. DHA and LPS-specific changes were determined using paired t test. False discovery rate (FDR) was controlled using Bonferroni. Lists of probe sets that were significantly differentially regulated by DHA or LPS or any combinations thereof were exported into the Database for Annotation, Visualization and Integrated Discovery (DAVID) (http://david.abcc.ncifcrf.gov). Gene Ontology (GO) categories and BioCarta and KEGG pathway maps were evaluated against the lists of probe sets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Dawson
| | Sample_contact_laboratory | MCB
| | Sample_contact_department | CCM
| | Sample_contact_institute | UC Davis
| | Sample_contact_address | 2795 Second Street, Suite 400
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95618
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.mousebiology.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502621/suppl/GSM502621.CEL.gz
| | Sample_series_id | GSE20114
| | Sample_data_row_count | 54675
| | |
|
GSM502622 | GPL570 |
|
blood-LPS-control-3
|
blood, LPS, control
|
tissue: blood
disease: hypertriglyceridemia
lps: LPS
dha: control
|
LPS-stimulated control.
203-0-L
|
| Sample_geo_accession | GSM502622
| | Sample_status | Public on Jan 30 2010
| | Sample_submission_date | Jan 29 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Forty moderately hyperlipidemic but otherwise healthy men were enrolled into a double-blind, placebo-controlled, parallel study with 2 metabolic periods – baseline (first 8 d) and intervention (last 90 d). Participants were randomized into one of two groups, where one received 7.5 g/day DHA oil capsules containing 3.0 g/day DHA, produced in Crypthecodinium cohinii (Martek Biosciences Corp., Columbia, MD), and no EPA, and the other group received 7.5 g/day extra virgin olive oil capsules. During the baseline period, participants did not receive supplements.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Blood cells from four subjects in the DHA supplementation group were collected for either lipopolysaccharide (LPS) treatment or no treatment (vehicle) and subsequent RNA isolation. For each subject, two 10 mL heparinized venous blood were collected on days 0 and 91. Whole blood was then diluted 1:2 with sterile RPMI 1640 culture medium containing 25mM HEPES and L-glutamine (Gibco Invitrogen, Carlsbad, CA), then split into two 30 mL and incubated with either 10 microg/mL ultra pure LPS (E. coli O157:H7; List Biological Laboratories, Inc., Campbell, CA) or sterile endotoxin-free water alone for 4 h at 37°C, 5% CO2. To simplify RNA isolation, erythrocytes were lysed by a two-step process (Buffer EL; Qiagen, Valencia, CA) and the resulting leukocyte pellets were lysed with Buffer RLT (Qiagen), homogenized with QIAshredder spin columns (Qiagen), and stored at -80°C. Total cellular RNA from leukocytes was isolated using RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions. RNA quality and integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA (5 microg) was used for cDNA synthesis (SuperScript III First Strand Synthesis System; Invitrogen, Carlsbad, CA) followed by in vitro transcription to incorporate biotin labels and subsequent hybridization to Human Genome U133 Plus 2.0 (Affymetrix, Santa Clara, CA), which represents 38,500 well-characterized genes, per manufacturer’s protocol.
| | Sample_hyb_protocol | The arrays were washed and stained on a GeneChip Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned on a GeneChip Scanner 3000.
| | Sample_data_processing | Affymetrix .CEL files were imported into the Bioconductor Affy R package and subjected to baseline correction, normalization, and calculation of gene expression values using the Robust Multichip Average (RMA) procedure. Genes were considered for further analyses if they were detected in at least 50% of the microarrays (p<0.05 of the signed rank test). Gene expression values were exported into Cluster for hierarchical clustering (HC) and self organizing map (SOM) procedure and visualized as heat maps in Java TreeView. DHA and LPS-specific changes were determined using paired t test. False discovery rate (FDR) was controlled using Bonferroni. Lists of probe sets that were significantly differentially regulated by DHA or LPS or any combinations thereof were exported into the Database for Annotation, Visualization and Integrated Discovery (DAVID) (http://david.abcc.ncifcrf.gov). Gene Ontology (GO) categories and BioCarta and KEGG pathway maps were evaluated against the lists of probe sets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Dawson
| | Sample_contact_laboratory | MCB
| | Sample_contact_department | CCM
| | Sample_contact_institute | UC Davis
| | Sample_contact_address | 2795 Second Street, Suite 400
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95618
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.mousebiology.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502622/suppl/GSM502622.CEL.gz
| | Sample_series_id | GSE20114
| | Sample_data_row_count | 54675
| | |
|
GSM502623 | GPL570 |
|
blood-LPS-control-4
|
blood, LPS, control
|
tissue: blood
disease: hypertriglyceridemia
lps: LPS
dha: control
|
LPS-stimulated control.
418-0-L
|
| Sample_geo_accession | GSM502623
| | Sample_status | Public on Jan 30 2010
| | Sample_submission_date | Jan 29 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Forty moderately hyperlipidemic but otherwise healthy men were enrolled into a double-blind, placebo-controlled, parallel study with 2 metabolic periods – baseline (first 8 d) and intervention (last 90 d). Participants were randomized into one of two groups, where one received 7.5 g/day DHA oil capsules containing 3.0 g/day DHA, produced in Crypthecodinium cohinii (Martek Biosciences Corp., Columbia, MD), and no EPA, and the other group received 7.5 g/day extra virgin olive oil capsules. During the baseline period, participants did not receive supplements.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Blood cells from four subjects in the DHA supplementation group were collected for either lipopolysaccharide (LPS) treatment or no treatment (vehicle) and subsequent RNA isolation. For each subject, two 10 mL heparinized venous blood were collected on days 0 and 91. Whole blood was then diluted 1:2 with sterile RPMI 1640 culture medium containing 25mM HEPES and L-glutamine (Gibco Invitrogen, Carlsbad, CA), then split into two 30 mL and incubated with either 10 microg/mL ultra pure LPS (E. coli O157:H7; List Biological Laboratories, Inc., Campbell, CA) or sterile endotoxin-free water alone for 4 h at 37°C, 5% CO2. To simplify RNA isolation, erythrocytes were lysed by a two-step process (Buffer EL; Qiagen, Valencia, CA) and the resulting leukocyte pellets were lysed with Buffer RLT (Qiagen), homogenized with QIAshredder spin columns (Qiagen), and stored at -80°C. Total cellular RNA from leukocytes was isolated using RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions. RNA quality and integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA (5 microg) was used for cDNA synthesis (SuperScript III First Strand Synthesis System; Invitrogen, Carlsbad, CA) followed by in vitro transcription to incorporate biotin labels and subsequent hybridization to Human Genome U133 Plus 2.0 (Affymetrix, Santa Clara, CA), which represents 38,500 well-characterized genes, per manufacturer’s protocol.
| | Sample_hyb_protocol | The arrays were washed and stained on a GeneChip Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned on a GeneChip Scanner 3000.
| | Sample_data_processing | Affymetrix .CEL files were imported into the Bioconductor Affy R package and subjected to baseline correction, normalization, and calculation of gene expression values using the Robust Multichip Average (RMA) procedure. Genes were considered for further analyses if they were detected in at least 50% of the microarrays (p<0.05 of the signed rank test). Gene expression values were exported into Cluster for hierarchical clustering (HC) and self organizing map (SOM) procedure and visualized as heat maps in Java TreeView. DHA and LPS-specific changes were determined using paired t test. False discovery rate (FDR) was controlled using Bonferroni. Lists of probe sets that were significantly differentially regulated by DHA or LPS or any combinations thereof were exported into the Database for Annotation, Visualization and Integrated Discovery (DAVID) (http://david.abcc.ncifcrf.gov). Gene Ontology (GO) categories and BioCarta and KEGG pathway maps were evaluated against the lists of probe sets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Dawson
| | Sample_contact_laboratory | MCB
| | Sample_contact_department | CCM
| | Sample_contact_institute | UC Davis
| | Sample_contact_address | 2795 Second Street, Suite 400
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95618
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.mousebiology.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502623/suppl/GSM502623.CEL.gz
| | Sample_series_id | GSE20114
| | Sample_data_row_count | 54675
| | |
|
GSM502624 | GPL570 |
|
blood-LPS-DHA-1
|
blood, LPS, DHA
|
tissue: blood
disease: hypertriglyceridemia
lps: LPS
dha: DHA
|
LPS-stimulated cells, DHA supplementation.
101-91-L
|
| Sample_geo_accession | GSM502624
| | Sample_status | Public on Jan 30 2010
| | Sample_submission_date | Jan 29 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Forty moderately hyperlipidemic but otherwise healthy men were enrolled into a double-blind, placebo-controlled, parallel study with 2 metabolic periods – baseline (first 8 d) and intervention (last 90 d). Participants were randomized into one of two groups, where one received 7.5 g/day DHA oil capsules containing 3.0 g/day DHA, produced in Crypthecodinium cohinii (Martek Biosciences Corp., Columbia, MD), and no EPA, and the other group received 7.5 g/day extra virgin olive oil capsules. During the baseline period, participants did not receive supplements.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Blood cells from four subjects in the DHA supplementation group were collected for either lipopolysaccharide (LPS) treatment or no treatment (vehicle) and subsequent RNA isolation. For each subject, two 10 mL heparinized venous blood were collected on days 0 and 91. Whole blood was then diluted 1:2 with sterile RPMI 1640 culture medium containing 25mM HEPES and L-glutamine (Gibco Invitrogen, Carlsbad, CA), then split into two 30 mL and incubated with either 10 microg/mL ultra pure LPS (E. coli O157:H7; List Biological Laboratories, Inc., Campbell, CA) or sterile endotoxin-free water alone for 4 h at 37°C, 5% CO2. To simplify RNA isolation, erythrocytes were lysed by a two-step process (Buffer EL; Qiagen, Valencia, CA) and the resulting leukocyte pellets were lysed with Buffer RLT (Qiagen), homogenized with QIAshredder spin columns (Qiagen), and stored at -80°C. Total cellular RNA from leukocytes was isolated using RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions. RNA quality and integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA (5 microg) was used for cDNA synthesis (SuperScript III First Strand Synthesis System; Invitrogen, Carlsbad, CA) followed by in vitro transcription to incorporate biotin labels and subsequent hybridization to Human Genome U133 Plus 2.0 (Affymetrix, Santa Clara, CA), which represents 38,500 well-characterized genes, per manufacturer’s protocol.
| | Sample_hyb_protocol | The arrays were washed and stained on a GeneChip Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned on a GeneChip Scanner 3000.
| | Sample_data_processing | Affymetrix .CEL files were imported into the Bioconductor Affy R package and subjected to baseline correction, normalization, and calculation of gene expression values using the Robust Multichip Average (RMA) procedure. Genes were considered for further analyses if they were detected in at least 50% of the microarrays (p<0.05 of the signed rank test). Gene expression values were exported into Cluster for hierarchical clustering (HC) and self organizing map (SOM) procedure and visualized as heat maps in Java TreeView. DHA and LPS-specific changes were determined using paired t test. False discovery rate (FDR) was controlled using Bonferroni. Lists of probe sets that were significantly differentially regulated by DHA or LPS or any combinations thereof were exported into the Database for Annotation, Visualization and Integrated Discovery (DAVID) (http://david.abcc.ncifcrf.gov). Gene Ontology (GO) categories and BioCarta and KEGG pathway maps were evaluated against the lists of probe sets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Dawson
| | Sample_contact_laboratory | MCB
| | Sample_contact_department | CCM
| | Sample_contact_institute | UC Davis
| | Sample_contact_address | 2795 Second Street, Suite 400
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95618
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.mousebiology.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502624/suppl/GSM502624.CEL.gz
| | Sample_series_id | GSE20114
| | Sample_data_row_count | 54675
| | |
|
GSM502625 | GPL570 |
|
blood-LPS-DHA-2
|
blood, LPS, DHA
|
tissue: blood
disease: hypertriglyceridemia
lps: LPS
dha: DHA
|
LPS-stimulated cells, DHA supplementation.
202-91-L
|
| Sample_geo_accession | GSM502625
| | Sample_status | Public on Jan 30 2010
| | Sample_submission_date | Jan 29 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Forty moderately hyperlipidemic but otherwise healthy men were enrolled into a double-blind, placebo-controlled, parallel study with 2 metabolic periods – baseline (first 8 d) and intervention (last 90 d). Participants were randomized into one of two groups, where one received 7.5 g/day DHA oil capsules containing 3.0 g/day DHA, produced in Crypthecodinium cohinii (Martek Biosciences Corp., Columbia, MD), and no EPA, and the other group received 7.5 g/day extra virgin olive oil capsules. During the baseline period, participants did not receive supplements.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Blood cells from four subjects in the DHA supplementation group were collected for either lipopolysaccharide (LPS) treatment or no treatment (vehicle) and subsequent RNA isolation. For each subject, two 10 mL heparinized venous blood were collected on days 0 and 91. Whole blood was then diluted 1:2 with sterile RPMI 1640 culture medium containing 25mM HEPES and L-glutamine (Gibco Invitrogen, Carlsbad, CA), then split into two 30 mL and incubated with either 10 microg/mL ultra pure LPS (E. coli O157:H7; List Biological Laboratories, Inc., Campbell, CA) or sterile endotoxin-free water alone for 4 h at 37°C, 5% CO2. To simplify RNA isolation, erythrocytes were lysed by a two-step process (Buffer EL; Qiagen, Valencia, CA) and the resulting leukocyte pellets were lysed with Buffer RLT (Qiagen), homogenized with QIAshredder spin columns (Qiagen), and stored at -80°C. Total cellular RNA from leukocytes was isolated using RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions. RNA quality and integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA (5 microg) was used for cDNA synthesis (SuperScript III First Strand Synthesis System; Invitrogen, Carlsbad, CA) followed by in vitro transcription to incorporate biotin labels and subsequent hybridization to Human Genome U133 Plus 2.0 (Affymetrix, Santa Clara, CA), which represents 38,500 well-characterized genes, per manufacturer’s protocol.
| | Sample_hyb_protocol | The arrays were washed and stained on a GeneChip Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned on a GeneChip Scanner 3000.
| | Sample_data_processing | Affymetrix .CEL files were imported into the Bioconductor Affy R package and subjected to baseline correction, normalization, and calculation of gene expression values using the Robust Multichip Average (RMA) procedure. Genes were considered for further analyses if they were detected in at least 50% of the microarrays (p<0.05 of the signed rank test). Gene expression values were exported into Cluster for hierarchical clustering (HC) and self organizing map (SOM) procedure and visualized as heat maps in Java TreeView. DHA and LPS-specific changes were determined using paired t test. False discovery rate (FDR) was controlled using Bonferroni. Lists of probe sets that were significantly differentially regulated by DHA or LPS or any combinations thereof were exported into the Database for Annotation, Visualization and Integrated Discovery (DAVID) (http://david.abcc.ncifcrf.gov). Gene Ontology (GO) categories and BioCarta and KEGG pathway maps were evaluated against the lists of probe sets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Dawson
| | Sample_contact_laboratory | MCB
| | Sample_contact_department | CCM
| | Sample_contact_institute | UC Davis
| | Sample_contact_address | 2795 Second Street, Suite 400
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95618
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.mousebiology.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502625/suppl/GSM502625.CEL.gz
| | Sample_series_id | GSE20114
| | Sample_data_row_count | 54675
| | |
|
GSM502626 | GPL570 |
|
blood-LPS-DHA-3
|
blood, LPS, DHA
|
tissue: blood
disease: hypertriglyceridemia
lps: LPS
dha: DHA
|
LPS-stimulated cells, DHA supplementation.
203-91-L
|
| Sample_geo_accession | GSM502626
| | Sample_status | Public on Jan 30 2010
| | Sample_submission_date | Jan 29 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Forty moderately hyperlipidemic but otherwise healthy men were enrolled into a double-blind, placebo-controlled, parallel study with 2 metabolic periods – baseline (first 8 d) and intervention (last 90 d). Participants were randomized into one of two groups, where one received 7.5 g/day DHA oil capsules containing 3.0 g/day DHA, produced in Crypthecodinium cohinii (Martek Biosciences Corp., Columbia, MD), and no EPA, and the other group received 7.5 g/day extra virgin olive oil capsules. During the baseline period, participants did not receive supplements.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Blood cells from four subjects in the DHA supplementation group were collected for either lipopolysaccharide (LPS) treatment or no treatment (vehicle) and subsequent RNA isolation. For each subject, two 10 mL heparinized venous blood were collected on days 0 and 91. Whole blood was then diluted 1:2 with sterile RPMI 1640 culture medium containing 25mM HEPES and L-glutamine (Gibco Invitrogen, Carlsbad, CA), then split into two 30 mL and incubated with either 10 microg/mL ultra pure LPS (E. coli O157:H7; List Biological Laboratories, Inc., Campbell, CA) or sterile endotoxin-free water alone for 4 h at 37°C, 5% CO2. To simplify RNA isolation, erythrocytes were lysed by a two-step process (Buffer EL; Qiagen, Valencia, CA) and the resulting leukocyte pellets were lysed with Buffer RLT (Qiagen), homogenized with QIAshredder spin columns (Qiagen), and stored at -80°C. Total cellular RNA from leukocytes was isolated using RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions. RNA quality and integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified total RNA (5 microg) was used for cDNA synthesis (SuperScript III First Strand Synthesis System; Invitrogen, Carlsbad, CA) followed by in vitro transcription to incorporate biotin labels and subsequent hybridization to Human Genome U133 Plus 2.0 (Affymetrix, Santa Clara, CA), which represents 38,500 well-characterized genes, per manufacturer’s protocol.
| | Sample_hyb_protocol | The arrays were washed and stained on a GeneChip Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned on a GeneChip Scanner 3000.
| | Sample_data_processing | Affymetrix .CEL files were imported into the Bioconductor Affy R package and subjected to baseline correction, normalization, and calculation of gene expression values using the Robust Multichip Average (RMA) procedure. Genes were considered for further analyses if they were detected in at least 50% of the microarrays (p<0.05 of the signed rank test). Gene expression values were exported into Cluster for hierarchical clustering (HC) and self organizing map (SOM) procedure and visualized as heat maps in Java TreeView. DHA and LPS-specific changes were determined using paired t test. False discovery rate (FDR) was controlled using Bonferroni. Lists of probe sets that were significantly differentially regulated by DHA or LPS or any combinations thereof were exported into the Database for Annotation, Visualization and Integrated Discovery (DAVID) (http://david.abcc.ncifcrf.gov). Gene Ontology (GO) categories and BioCarta and KEGG pathway maps were evaluated against the lists of probe sets.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kevin,,Dawson
| | Sample_contact_laboratory | MCB
| | Sample_contact_department | CCM
| | Sample_contact_institute | UC Davis
| | Sample_contact_address | 2795 Second Street, Suite 400
| | Sample_contact_city | Davis
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 95618
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.mousebiology.org
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502626/suppl/GSM502626.CEL.gz
| | Sample_series_id | GSE20114
| | Sample_data_row_count | 54675
| | |
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