Search results for the GEO ID: GSE33166  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM821250 | GPL85 |
|
Corn_oil_fed_5perc-pool1
|
rat liver
|
strain: Sprague-Dawley
dietary oil: Corn oil
oil concentration: 5%
gender: male
|
Corn_oil_5p_1
hepatic gene expression
5-CO-P1.CEL
|
| Sample_geo_accession | GSM821250
| | Sample_status | Public on Oct 24 2011
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Oct 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiment protocol: Groups of male 150 g Sprague Dawley rats were intragastrically cannulated and overfed by 17% of total calories using total enteral nutrition for 21 days. Isocaloric diets varied in fat/carbohydrate ratio and dietary fat type: 5% or 70% fat made of olive, corn or echium oil. At sacrifice livers collected and fresh frozen in liquid nitrogen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Collection protocol: Liver tissues collected from rats at sacrifice and flash frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total liver RNA was isolated from the olive and corn oil fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring v 11.0.2 with RMA for background correction, normalization and log transformation of the PM probe level values
| | Sample_platform_id | GPL85
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821250/suppl/GSM821250.CEL.gz
| | Sample_series_id | GSE33166
| | Sample_data_row_count | 8799
| | |
|
GSM821251 | GPL85 |
|
Corn_oil_fed_5perc-pool2
|
rat liver
|
strain: Sprague-Dawley
dietary oil: Corn oil
oil concentration: 5%
gender: male
|
Corn_oil_5p_2
hepatic gene expression
5-CO-P2.CEL
|
| Sample_geo_accession | GSM821251
| | Sample_status | Public on Oct 24 2011
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Oct 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiment protocol: Groups of male 150 g Sprague Dawley rats were intragastrically cannulated and overfed by 17% of total calories using total enteral nutrition for 21 days. Isocaloric diets varied in fat/carbohydrate ratio and dietary fat type: 5% or 70% fat made of olive, corn or echium oil. At sacrifice livers collected and fresh frozen in liquid nitrogen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Collection protocol: Liver tissues collected from rats at sacrifice and flash frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total liver RNA was isolated from the olive and corn oil fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring v 11.0.2 with RMA for background correction, normalization and log transformation of the PM probe level values
| | Sample_platform_id | GPL85
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821251/suppl/GSM821251.CEL.gz
| | Sample_series_id | GSE33166
| | Sample_data_row_count | 8799
| | |
|
GSM821252 | GPL85 |
|
Corn_oil_fed_5perc-pool3
|
rat liver
|
strain: Sprague-Dawley
dietary oil: Corn oil
oil concentration: 5%
gender: male
|
Corn_oil_5p_3
hepatic gene expression
5-CO-P3.CEL
|
| Sample_geo_accession | GSM821252
| | Sample_status | Public on Oct 24 2011
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Oct 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiment protocol: Groups of male 150 g Sprague Dawley rats were intragastrically cannulated and overfed by 17% of total calories using total enteral nutrition for 21 days. Isocaloric diets varied in fat/carbohydrate ratio and dietary fat type: 5% or 70% fat made of olive, corn or echium oil. At sacrifice livers collected and fresh frozen in liquid nitrogen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Collection protocol: Liver tissues collected from rats at sacrifice and flash frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total liver RNA was isolated from the olive and corn oil fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring v 11.0.2 with RMA for background correction, normalization and log transformation of the PM probe level values
| | Sample_platform_id | GPL85
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821252/suppl/GSM821252.CEL.gz
| | Sample_series_id | GSE33166
| | Sample_data_row_count | 8799
| | |
|
GSM821253 | GPL85 |
|
Olive_oil_fed_5perc-pool1
|
rat liver
|
strain: Sprague-Dawley
dietary oil: Olive oil
oil concentration: 5%
gender: male
|
Olive_oil_5p_1
hepatic gene expression
5-OO-P4.CEL
|
| Sample_geo_accession | GSM821253
| | Sample_status | Public on Oct 24 2011
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Oct 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiment protocol: Groups of male 150 g Sprague Dawley rats were intragastrically cannulated and overfed by 17% of total calories using total enteral nutrition for 21 days. Isocaloric diets varied in fat/carbohydrate ratio and dietary fat type: 5% or 70% fat made of olive, corn or echium oil. At sacrifice livers collected and fresh frozen in liquid nitrogen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Collection protocol: Liver tissues collected from rats at sacrifice and flash frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total liver RNA was isolated from the olive and corn oil fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring v 11.0.2 with RMA for background correction, normalization and log transformation of the PM probe level values
| | Sample_platform_id | GPL85
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821253/suppl/GSM821253.CEL.gz
| | Sample_series_id | GSE33166
| | Sample_data_row_count | 8799
| | |
|
GSM821254 | GPL85 |
|
Olive_oil_fed_5perc-pool2
|
rat liver
|
strain: Sprague-Dawley
dietary oil: Olive oil
oil concentration: 5%
gender: male
|
Olive_oil_5p_2
hepatic gene expression
5-OO-P5.CEL
|
| Sample_geo_accession | GSM821254
| | Sample_status | Public on Oct 24 2011
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Oct 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiment protocol: Groups of male 150 g Sprague Dawley rats were intragastrically cannulated and overfed by 17% of total calories using total enteral nutrition for 21 days. Isocaloric diets varied in fat/carbohydrate ratio and dietary fat type: 5% or 70% fat made of olive, corn or echium oil. At sacrifice livers collected and fresh frozen in liquid nitrogen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Collection protocol: Liver tissues collected from rats at sacrifice and flash frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total liver RNA was isolated from the olive and corn oil fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring v 11.0.2 with RMA for background correction, normalization and log transformation of the PM probe level values
| | Sample_platform_id | GPL85
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821254/suppl/GSM821254.CEL.gz
| | Sample_series_id | GSE33166
| | Sample_data_row_count | 8799
| | |
|
GSM821255 | GPL85 |
|
Olive_oil_fed_5perc-pool3
|
rat liver
|
strain: Sprague-Dawley
dietary oil: Olive oil
oil concentration: 5%
gender: male
|
Olive_oil_5p_3
hepatic gene expression
5-OO-P6.CEL
|
| Sample_geo_accession | GSM821255
| | Sample_status | Public on Oct 24 2011
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Oct 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiment protocol: Groups of male 150 g Sprague Dawley rats were intragastrically cannulated and overfed by 17% of total calories using total enteral nutrition for 21 days. Isocaloric diets varied in fat/carbohydrate ratio and dietary fat type: 5% or 70% fat made of olive, corn or echium oil. At sacrifice livers collected and fresh frozen in liquid nitrogen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Collection protocol: Liver tissues collected from rats at sacrifice and flash frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total liver RNA was isolated from the olive and corn oil fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring v 11.0.2 with RMA for background correction, normalization and log transformation of the PM probe level values
| | Sample_platform_id | GPL85
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821255/suppl/GSM821255.CEL.gz
| | Sample_series_id | GSE33166
| | Sample_data_row_count | 8799
| | |
|
GSM821256 | GPL85 |
|
Corn_oil_fed_70perc-pool1
|
rat liver
|
strain: Sprague-Dawley
dietary oil: Corn oil
oil concentration: 70%
gender: male
|
Corn_oil_70p_1
hepatic gene expression
70-CO-P7.CEL
|
| Sample_geo_accession | GSM821256
| | Sample_status | Public on Oct 24 2011
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Oct 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiment protocol: Groups of male 150 g Sprague Dawley rats were intragastrically cannulated and overfed by 17% of total calories using total enteral nutrition for 21 days. Isocaloric diets varied in fat/carbohydrate ratio and dietary fat type: 5% or 70% fat made of olive, corn or echium oil. At sacrifice livers collected and fresh frozen in liquid nitrogen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Collection protocol: Liver tissues collected from rats at sacrifice and flash frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total liver RNA was isolated from the olive and corn oil fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring v 11.0.2 with RMA for background correction, normalization and log transformation of the PM probe level values
| | Sample_platform_id | GPL85
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821256/suppl/GSM821256.CEL.gz
| | Sample_series_id | GSE33166
| | Sample_data_row_count | 8799
| | |
|
GSM821257 | GPL85 |
|
Corn_oil_fed_70perc-pool2
|
rat liver
|
strain: Sprague-Dawley
dietary oil: Corn oil
oil concentration: 70%
gender: male
|
Corn_oil_70p_2
hepatic gene expression
70-CO-P8.CEL
|
| Sample_geo_accession | GSM821257
| | Sample_status | Public on Oct 24 2011
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Oct 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiment protocol: Groups of male 150 g Sprague Dawley rats were intragastrically cannulated and overfed by 17% of total calories using total enteral nutrition for 21 days. Isocaloric diets varied in fat/carbohydrate ratio and dietary fat type: 5% or 70% fat made of olive, corn or echium oil. At sacrifice livers collected and fresh frozen in liquid nitrogen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Collection protocol: Liver tissues collected from rats at sacrifice and flash frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total liver RNA was isolated from the olive and corn oil fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring v 11.0.2 with RMA for background correction, normalization and log transformation of the PM probe level values
| | Sample_platform_id | GPL85
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821257/suppl/GSM821257.CEL.gz
| | Sample_series_id | GSE33166
| | Sample_data_row_count | 8799
| | |
|
GSM821258 | GPL85 |
|
Corn_oil_fed_70perc-pool3
|
rat liver
|
strain: Sprague-Dawley
dietary oil: Corn oil
oil concentration: 70%
gender: male
|
Corn_oil_70p_3
hepatic gene expression
70-CO-P9.CEL
|
| Sample_geo_accession | GSM821258
| | Sample_status | Public on Oct 24 2011
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Oct 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiment protocol: Groups of male 150 g Sprague Dawley rats were intragastrically cannulated and overfed by 17% of total calories using total enteral nutrition for 21 days. Isocaloric diets varied in fat/carbohydrate ratio and dietary fat type: 5% or 70% fat made of olive, corn or echium oil. At sacrifice livers collected and fresh frozen in liquid nitrogen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Collection protocol: Liver tissues collected from rats at sacrifice and flash frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total liver RNA was isolated from the olive and corn oil fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring v 11.0.2 with RMA for background correction, normalization and log transformation of the PM probe level values
| | Sample_platform_id | GPL85
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821258/suppl/GSM821258.CEL.gz
| | Sample_series_id | GSE33166
| | Sample_data_row_count | 8799
| | |
|
GSM821259 | GPL85 |
|
Olive_oil_fed_70perc-pool1
|
rat liver
|
strain: Sprague-Dawley
dietary oil: Olive oil
oil concentration: 70%
gender: male
|
Olive_oil_70p_1
hepatic gene expression
70-OO-P10.CEL
|
| Sample_geo_accession | GSM821259
| | Sample_status | Public on Oct 24 2011
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Oct 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiment protocol: Groups of male 150 g Sprague Dawley rats were intragastrically cannulated and overfed by 17% of total calories using total enteral nutrition for 21 days. Isocaloric diets varied in fat/carbohydrate ratio and dietary fat type: 5% or 70% fat made of olive, corn or echium oil. At sacrifice livers collected and fresh frozen in liquid nitrogen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Collection protocol: Liver tissues collected from rats at sacrifice and flash frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total liver RNA was isolated from the olive and corn oil fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring v 11.0.2 with RMA for background correction, normalization and log transformation of the PM probe level values
| | Sample_platform_id | GPL85
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821259/suppl/GSM821259.CEL.gz
| | Sample_series_id | GSE33166
| | Sample_data_row_count | 8799
| | |
|
GSM821260 | GPL85 |
|
Olive_oil_fed_70perc-pool2
|
rat liver
|
strain: Sprague-Dawley
dietary oil: Olive oil
oil concentration: 70%
gender: male
|
Olive_oil_70p_2
hepatic gene expression
70-OO-P11.CEL
|
| Sample_geo_accession | GSM821260
| | Sample_status | Public on Oct 24 2011
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Oct 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiment protocol: Groups of male 150 g Sprague Dawley rats were intragastrically cannulated and overfed by 17% of total calories using total enteral nutrition for 21 days. Isocaloric diets varied in fat/carbohydrate ratio and dietary fat type: 5% or 70% fat made of olive, corn or echium oil. At sacrifice livers collected and fresh frozen in liquid nitrogen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Collection protocol: Liver tissues collected from rats at sacrifice and flash frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total liver RNA was isolated from the olive and corn oil fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring v 11.0.2 with RMA for background correction, normalization and log transformation of the PM probe level values
| | Sample_platform_id | GPL85
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821260/suppl/GSM821260.CEL.gz
| | Sample_series_id | GSE33166
| | Sample_data_row_count | 8799
| | |
|
GSM821261 | GPL85 |
|
Olive_oil_fed_70perc-pool3
|
rat liver
|
strain: Sprague-Dawley
dietary oil: Olive oil
oil concentration: 70%
gender: male
|
Olive_oil_70p_3
hepatic gene expression
70-OO-P12.CEL
|
| Sample_geo_accession | GSM821261
| | Sample_status | Public on Oct 24 2011
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Oct 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Experiment protocol: Groups of male 150 g Sprague Dawley rats were intragastrically cannulated and overfed by 17% of total calories using total enteral nutrition for 21 days. Isocaloric diets varied in fat/carbohydrate ratio and dietary fat type: 5% or 70% fat made of olive, corn or echium oil. At sacrifice livers collected and fresh frozen in liquid nitrogen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Collection protocol: Liver tissues collected from rats at sacrifice and flash frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total liver RNA was isolated from the olive and corn oil fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring v 11.0.2 with RMA for background correction, normalization and log transformation of the PM probe level values
| | Sample_platform_id | GPL85
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821261/suppl/GSM821261.CEL.gz
| | Sample_series_id | GSE33166
| | Sample_data_row_count | 8799
| | |
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