Search results for the GEO ID: GSE31727  |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM787650 | GPL1261 |
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Mice fed with a n-3 PUFA-depleted diet and supplemented with FOS during the last 10 days of experiment
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liver tissue
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treatment: deficient diet + FOS supplementation during the last 10 days of treatment
tissue: liver
strain: C57Bl/6J
gender: male
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gene expression data from mice fed with n-3 PUFA depleted diet and supplemented with FOS during the last 10 days of experiment
|
| Sample_geo_accession | GSM787650
| | Sample_status | Public on Dec 12 2012
| | Sample_submission_date | Aug 29 2011
| | Sample_last_update_date | Dec 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | At the end of the study period, mice fed the CT (n=4), DEF (n=7), DEF/CT (n=8) or DEF/FOS diet (n=8) were anesthetized (ketamine/xylazine i.p., 100 and 10 mg/kg of body weight, respectively). The liver tissue was immediately clamped in liquid N2 and kept at -80°C until analysis.
| | Sample_growth_protocol_ch1 | Male C57Bl/6J mice (9 weeks old; Charles River, Brussels, Belgium) were housed in groups of 4 mice per cage at 22°C in a 12 h light/dark cycle and given free access to diet and water. After an acclimatisation period of 1 week, mice were fed a control (CT) (D08041805, Research Diets, New Brunswick, USA) or an n-3 PUFA-depleted diet (DEF) (D08041806, Research Diets, New Brunswick, USA) for 112 days ad libitum. The CT diet contained the following (percent w/w): casein 20, total carbohydrate 72.4 (including corn starch 44.2, sucrose 10, maltodextrin 13.2, cellulose 5), soybean oil 5, mineral mix 3.5 and vitamin mix 1. The depletion was induced by replacing the soybean oil with sunflower oil, which exhibited a higher n-6/n-3 PUFA ratio. The n-6/n-3 PUFA ratio was 6.9 and 127.2 for the CT diet and the DEF diet, respectively. Ten days before the end of the experiment, DEF mice were divided into three groups: DEF, DEF/FOS and DEF/CT mice. The DEF mice were still fed with the n-3 PUFA depleted diet (DEF). The DEF/FOS mice were still fed the DEF diet and were supplemented for 10 days with fructooligosaccharides (DEF/FOS). FOS (Beneo P95 gift from Orafti; Tienen, Belgium) was added to tap water in a concentration adequate to reach an intake of 0.25g of FOS per day. For DEF/CT mice, the DEF diet was replaced by the CT diet during the last 10 days of treatment. At the end of the study period, mice fed the CT (n=4), DEF (n=7), DEF/CT (n=8) or DEF/FOS diet (n=8) were anesthetized (ketamine/xylazine i.p., 100 and 10 mg/kg of body weight, respectively).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from liver tissue using the TriPure reagent (Roche, Basel, Switzerland). RNA quality was checked using Bioanalyzer (Agilent). Equal amounts RNA from each mice (n | 4 to 8 mice per group) were pooled within each group.Double-stranded cDNA was synthesized from total RNA using the One-cycle cDNA synthesis kit (Affymetrix, Santa Clara, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was synthesized using GeneChip IVT labelling kit (Affymetrix, Santa Clara, USA)
| | Sample_hyb_protocol | cRNA was hybridized to mouse genome 430 2.0 array (Affymetrix, Santa Clara, USA)
| | Sample_scan_protocol | Affymetrix standard protocol
| | Sample_data_processing | The MAS5 algorithm was run using GCOS® Affymetrix software as follows: the scaling factor using all probe sets was set to 100, the normalize factor was set to 1 and the baseline comparison was done on the CT diet hybridization samples
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Jean-Baptiste,,Demoulin
| | Sample_contact_email | Jean-Baptiste.Demoulin@uclouvain.be
| | Sample_contact_laboratory | MEXP unit
| | Sample_contact_department | de Duve Institute
| | Sample_contact_institute | Université catholique de Louvain
| | Sample_contact_address | av Hippocrate 75, UCL74.30
| | Sample_contact_city | Brussels
| | Sample_contact_zip/postal_code | B-1200
| | Sample_contact_country | Belgium
| | Sample_contact_web_link | www.icp.ucl.ac.be/mexp
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM787nnn/GSM787650/suppl/GSM787650_BP_16072009_FOS.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM787nnn/GSM787650/suppl/GSM787650_BP_16072009_FOS.CHP.gz
| | Sample_series_id | GSE31727
| | Sample_data_row_count | 45101
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GSM787651 | GPL1261 |
|
Mice fed with a n-3 PUFA-depleted diet and returned on a control diet during the last 10 days of experiment
|
liver tissue
|
treatment: deficient diet + control diet during the last 10 days of treatment
tissue: liver
strain: C57Bl/6J
gender: male
|
gene expression data from mice fed with n-3 PUFA depleted diet and returned on a control diet during the last 10 days of experiment
|
| Sample_geo_accession | GSM787651
| | Sample_status | Public on Dec 12 2012
| | Sample_submission_date | Aug 29 2011
| | Sample_last_update_date | Dec 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | At the end of the study period, mice fed the CT (n=4), DEF (n=7), DEF/CT (n=8) or DEF/FOS diet (n=8) were anesthetized (ketamine/xylazine i.p., 100 and 10 mg/kg of body weight, respectively). The liver tissue was immediately clamped in liquid N2 and kept at -80°C until analysis.
| | Sample_growth_protocol_ch1 | Male C57Bl/6J mice (9 weeks old; Charles River, Brussels, Belgium) were housed in groups of 4 mice per cage at 22°C in a 12 h light/dark cycle and given free access to diet and water. After an acclimatisation period of 1 week, mice were fed a control (CT) (D08041805, Research Diets, New Brunswick, USA) or an n-3 PUFA-depleted diet (DEF) (D08041806, Research Diets, New Brunswick, USA) for 112 days ad libitum. The CT diet contained the following (percent w/w): casein 20, total carbohydrate 72.4 (including corn starch 44.2, sucrose 10, maltodextrin 13.2, cellulose 5), soybean oil 5, mineral mix 3.5 and vitamin mix 1. The depletion was induced by replacing the soybean oil with sunflower oil, which exhibited a higher n-6/n-3 PUFA ratio. The n-6/n-3 PUFA ratio was 6.9 and 127.2 for the CT diet and the DEF diet, respectively. Ten days before the end of the experiment, DEF mice were divided into three groups: DEF, DEF/FOS and DEF/CT mice. The DEF mice were still fed with the n-3 PUFA depleted diet (DEF). The DEF/FOS mice were still fed the DEF diet and were supplemented for 10 days with fructooligosaccharides (DEF/FOS). FOS (Beneo P95 gift from Orafti; Tienen, Belgium) was added to tap water in a concentration adequate to reach an intake of 0.25g of FOS per day. For DEF/CT mice, the DEF diet was replaced by the CT diet during the last 10 days of treatment. At the end of the study period, mice fed the CT (n=4), DEF (n=7), DEF/CT (n=8) or DEF/FOS diet (n=8) were anesthetized (ketamine/xylazine i.p., 100 and 10 mg/kg of body weight, respectively).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 = Total RNA was isolated from liver tissue using the TriPure reagent (Roche, Basel, Switzerland). RNA quality was checked using Bioanalyzer (Agilent). Equal amounts RNA from each mice (n | 4 to 8 mice per group) were pooled within each group.Double-stranded cDNA was synthesized from total RNA using the One-cycle cDNA synthesis kit (Affymetrix, Santa Clara, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was synthesized using GeneChip IVT labelling kit (Affymetrix, Santa Clara, USA)
| | Sample_hyb_protocol | cRNA was hybridized to mouse genome 430 2.0 array (Affymetrix, Santa Clara, USA)
| | Sample_scan_protocol | Affymetrix standard protocol
| | Sample_data_processing | The MAS5 algorithm was run using GCOS® Affymetrix software as follows: the scaling factor using all probe sets was set to 100, the normalize factor was set to 1 and the baseline comparison was done on the CT diet hybridization samples
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Jean-Baptiste,,Demoulin
| | Sample_contact_email | Jean-Baptiste.Demoulin@uclouvain.be
| | Sample_contact_laboratory | MEXP unit
| | Sample_contact_department | de Duve Institute
| | Sample_contact_institute | Université catholique de Louvain
| | Sample_contact_address | av Hippocrate 75, UCL74.30
| | Sample_contact_city | Brussels
| | Sample_contact_zip/postal_code | B-1200
| | Sample_contact_country | Belgium
| | Sample_contact_web_link | www.icp.ucl.ac.be/mexp
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM787nnn/GSM787651/suppl/GSM787651_BP_16072009_CT.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM787nnn/GSM787651/suppl/GSM787651_BP_16072009_CT.CHP.gz
| | Sample_series_id | GSE31727
| | Sample_data_row_count | 45101
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