Search results for the GEO ID: GSE18581  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM213045 | GPL1261 |
|
SI1_wk2_HF (high fat diet, high calcium)
|
SI1 after 2 wks on a HFD, HCa diet
|
strain: C57Bl/6J
gender: male
tissue: small intestine, SI 1
dietary fat: high
dietary calcium: high
age: 9wks old at start of diet intervention
diet intervention time: 2wks
|
Pooled total RNA sample of 6 mice.
|
|
|
GSM213051 | GPL1261 |
|
SI2_wk2_HF (high fat diet, high calcium)
|
SI2 after 2 wks on a HFD, HCa diet
|
strain: C57Bl/6J
gender: male
tissue: small intestine, SI 2
dietary fat: high
dietary calcium: high
age: 9wks old at start of diet intervention
diet intervention time: 2wks
|
Pooled total RNA sample of 6 mice.
|
|
|
GSM213057 | GPL1261 |
|
SI3_wk2_HF (high fat diet, high calcium)
|
SI3 after 2 wks on a HFD, HCa diet
|
strain: C57Bl/6J
gender: male
tissue: small intestine, SI 3
dietary fat: high
dietary calcium: high
age: 9wks old at start of diet intervention
diet intervention time: 2wks
|
Pooled total RNA sample of 6 mice.
|
|
|
GSM462207 | GPL1261 |
|
SI1_wk2_HF (high fat diet, low calcium)
|
SI1 after 2 wks on a HFD, LCa diet
|
strain: C57Bl/6J
gender: male
tissue: small intestine, SI 1
dietary fat: high
dietary calcium: low
age: 9wks old at start of diet intervention
diet intervention time: 2wks
|
Pooled total RNA sample of 6 mice.
SI1_wk2_LCa
|
| Sample_geo_accession | GSM462207
| | Sample_status | Public on Mar 03 2011
| | Sample_submission_date | Oct 15 2009
| | Sample_last_update_date | Mar 04 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Nine-week-old mice were fed a high-fat purified diet with a low calcium concentration of 50mmol/kg (LCa diet) for 8 weeks.
| | Sample_growth_protocol_ch1 | Male C57BL/6J mice were purchased from Harlan (Horst, The Netherlands) and were housed in the light- and temperature-controlled animal facility of Wageningen University. They had free access to water and prior to the diet intervention they received standard laboratory chow.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol reagent (Invitrogen, Breda, The Netherlands) according to the manufacturer’s instructions. The isolated RNA was further column-purified using the SV total RNA isolation system (Promega, Leiden, The Netherlands). RNA concentration was measured on a NanoDrop ND-1000 UV-Vis spectrophotometer (Isogen, Maarssen, The Netherlands) and analyzed on a bioanalyzer (Agilent Technologies, Amsterdam, the Netherlands) with 6000 Nano Chips according to the manufacturer’s instructions. For each part of small intestine, total RNA was pooled per diet group (n=6).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (described in the eukaryotic section in the GeneChip Expression Analysis Technical Manual Rev. 3 from Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data analysis was performed using Microarray Analysis Suite 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The mean target intensity of each array was set to 500.
| | 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/GSM462nnn/GSM462207/suppl/GSM462207.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM462nnn/GSM462207/suppl/GSM462207.EXP.gz
| | Sample_series_id | GSE18581
| | Sample_data_row_count | 45046
| | |
|
GSM462208 | GPL1261 |
|
SI2_wk2_HF (high fat diet, low calcium)
|
SI2 after 2 wks on a HFD, LCa diet
|
strain: C57Bl/6J
gender: male
tissue: small intestine, SI 2
dietary fat: high
dietary calcium: low
age: 9wks old at start of diet intervention
diet intervention time: 2wks
|
Pooled total RNA sample of 6 mice.
SI2_wk2_LCa
|
| Sample_geo_accession | GSM462208
| | Sample_status | Public on Mar 03 2011
| | Sample_submission_date | Oct 15 2009
| | Sample_last_update_date | Mar 04 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Nine-week-old mice were fed a high-fat purified diet with a low calcium concentration of 50mmol/kg (LCa diet) for 8 weeks.
| | Sample_growth_protocol_ch1 | Male C57BL/6J mice were purchased from Harlan (Horst, The Netherlands) and were housed in the light- and temperature-controlled animal facility of Wageningen University. They had free access to water and prior to the diet intervention they received standard laboratory chow.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol reagent (Invitrogen, Breda, The Netherlands) according to the manufacturer’s instructions. The isolated RNA was further column-purified using the SV total RNA isolation system (Promega, Leiden, The Netherlands). RNA concentration was measured on a NanoDrop ND-1000 UV-Vis spectrophotometer (Isogen, Maarssen, The Netherlands) and analyzed on a bioanalyzer (Agilent Technologies, Amsterdam, the Netherlands) with 6000 Nano Chips according to the manufacturer’s instructions. For each part of small intestine, total RNA was pooled per diet group (n=6).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (described in the eukaryotic section in the GeneChip Expression Analysis Technical Manual Rev. 3 from Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data analysis was performed using Microarray Analysis Suite 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The mean target intensity of each array was set to 500.
| | 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/GSM462nnn/GSM462208/suppl/GSM462208.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM462nnn/GSM462208/suppl/GSM462208.EXP.gz
| | Sample_series_id | GSE18581
| | Sample_data_row_count | 45046
| | |
|
GSM462209 | GPL1261 |
|
SI3_wk2_HF (high fat diet, low calcium)
|
SI3 after 2 wks on a HFD, LCa diet
|
strain: C57Bl/6J
gender: male
tissue: small intestine, SI 3
dietary fat: high
dietary calcium: low
age: 9wks old at start of diet intervention
diet intervention time: 2wks
|
Pooled total RNA sample of 6 mice.
SI3_wk2_LCa
|
| Sample_geo_accession | GSM462209
| | Sample_status | Public on Mar 03 2011
| | Sample_submission_date | Oct 15 2009
| | Sample_last_update_date | Mar 04 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Nine-week-old mice were fed a high-fat purified diet with a low calcium concentration of 50mmol/kg (LCa diet) for 8 weeks.
| | Sample_growth_protocol_ch1 | Male C57BL/6J mice were purchased from Harlan (Horst, The Netherlands) and were housed in the light- and temperature-controlled animal facility of Wageningen University. They had free access to water and prior to the diet intervention they received standard laboratory chow.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol reagent (Invitrogen, Breda, The Netherlands) according to the manufacturer’s instructions. The isolated RNA was further column-purified using the SV total RNA isolation system (Promega, Leiden, The Netherlands). RNA concentration was measured on a NanoDrop ND-1000 UV-Vis spectrophotometer (Isogen, Maarssen, The Netherlands) and analyzed on a bioanalyzer (Agilent Technologies, Amsterdam, the Netherlands) with 6000 Nano Chips according to the manufacturer’s instructions. For each part of small intestine, total RNA was pooled per diet group (n=6).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (described in the eukaryotic section in the GeneChip Expression Analysis Technical Manual Rev. 3 from Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data analysis was performed using Microarray Analysis Suite 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The mean target intensity of each array was set to 500.
| | 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/GSM462nnn/GSM462209/suppl/GSM462209.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM462nnn/GSM462209/suppl/GSM462209.EXP.gz
| | Sample_series_id | GSE18581
| | Sample_data_row_count | 45046
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
