Search results for the GEO ID: GSE11936 |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM301569 | GPL1261 |
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intestine_C57BL/6J_flaxseed_pool
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small intestine complete, 4 weeks on diet
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C57BL/6J, male, adult
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Male 4-month-old C57BL/6J mice were maintained for 4 weeks on semisynthetic high-fat (20% wt/wt) diets differing in the composition of n-3 PUFA. Two isocaloric diets were used (n=12): control sHFf diet which contained flax-seed oil (rich in ALA) as the only lipid source, or the sHFf-F2 diet, which had the same composition except that 44 % of the lipids were replaced by a n-3 PUFA concentrate (EPA&DHA) containing 6 % EPA and 51 % DHA (EPAX 1050TG; EPAX AS, Lysaker, Norway). Quality control of RNA samples showed that four samples did not pass quality thresholds, and these samples were excluded from array analysis (two control small intestine samples and one EPA&DHA small intestine sample). The remaining RNA samples were pooled per tissue per diet group. Thus; the flax-seed (control) array was hybridized with RNA pooled from of 10 mice, the PUFA array was hybridized with RNA pooled from 11 mice.
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Sample_geo_accession | GSM301569
| Sample_status | Public on Apr 01 2009
| Sample_submission_date | Jun 30 2008
| Sample_last_update_date | Apr 01 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Small intestines were excised, homogenized in TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | Affymetrix One-cycle Target Labeling Assay. Five μg of total RNA was labelled using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the "Genechip Expression Analysis Technical Manual", section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
| Sample_hyb_protocol | Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the "Genechip Expression Analysis Technical Manual", section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
| Sample_scan_protocol | Arrays were scanned on an Affymetrix 3000 7G scanner, as described n the "Genechip Expression Analysis Technical Manual", section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
| Sample_data_processing | MAS5 expression values
| Sample_platform_id | GPL1261
| Sample_contact_name | Guido,,Hooiveld
| Sample_contact_email | guido.hooiveld@wur.nl
| Sample_contact_laboratory | Nutrition, Metabolism & Genomics Group
| Sample_contact_department | Div. Human Nutrition
| Sample_contact_institute | Wageningen University
| Sample_contact_address | Bomenweg 2
| Sample_contact_city | Wageningen
| Sample_contact_zip/postal_code | NL-6703HD
| Sample_contact_country | Netherlands
| Sample_contact_web_link | http://nutrigene.4t.com
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM301nnn/GSM301569/suppl/GSM301569.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM301nnn/GSM301569/suppl/GSM301569.CHP.gz
| Sample_series_id | GSE11936
| Sample_data_row_count | 45101
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GSM301570 | GPL1261 |
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intestine_C57BL/6J_EPA/DHA_pool
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small intestine complete, 4 weeks on diet
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C57BL/6J, male
|
Male 4-month-old C57BL/6J mice were maintained for 4 weeks on semisynthetic high-fat (20% wt/wt) diets differing in the composition of n-3 PUFA. Two isocaloric diets were used (n=12): control sHFf diet which contained flax-seed oil (rich in ALA) as the only lipid source, or the sHFf-F2 diet, which had the same composition except that 44 % of the lipids were replaced by a n-3 PUFA concentrate (EPA&DHA) containing 6 % EPA and 51 % DHA (EPAX 1050TG; EPAX AS, Lysaker, Norway). Quality control of RNA samples showed that four samples did not pass quality thresholds, and these samples were excluded from array analysis (two control small intestine samples and one EPA&DHA small intestine sample). The remaining RNA samples were pooled per tissue per diet group. Thus; the flax-seed (control) array was hybridized with RNA pooled from of 10 mice, the PUFA array was hybridized with RNA pooled from 11 mice.
|
Sample_geo_accession | GSM301570
| Sample_status | Public on Apr 01 2009
| Sample_submission_date | Jun 30 2008
| Sample_last_update_date | Apr 01 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Small intestines were excised, homogenized in TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | Affymetrix One-cycle Target Labeling Assay. Five μg of total RNA was labelled using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the "Genechip Expression Analysis Technical Manual", section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
| Sample_hyb_protocol | Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the "Genechip Expression Analysis Technical Manual", section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
| Sample_scan_protocol | Arrays were scanned on an Affymetrix 3000 7G scanner, as described n the "Genechip Expression Analysis Technical Manual", section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
| Sample_data_processing | MAS5 expression values
| Sample_platform_id | GPL1261
| Sample_contact_name | Guido,,Hooiveld
| Sample_contact_email | guido.hooiveld@wur.nl
| Sample_contact_laboratory | Nutrition, Metabolism & Genomics Group
| Sample_contact_department | Div. Human Nutrition
| Sample_contact_institute | Wageningen University
| Sample_contact_address | Bomenweg 2
| Sample_contact_city | Wageningen
| Sample_contact_zip/postal_code | NL-6703HD
| Sample_contact_country | Netherlands
| Sample_contact_web_link | http://nutrigene.4t.com
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM301nnn/GSM301570/suppl/GSM301570.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM301nnn/GSM301570/suppl/GSM301570.CHP.gz
| Sample_series_id | GSE11936
| Sample_data_row_count | 45101
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