Search results for the GEO ID: GSE30533  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM757155 | GPL1355 |
|
iron-deficient diet, biological rep 1
|
Liver of rat fed iron-deficient diet
|
strain: Strain: Sprague-Dawley
gender: male
age: 5 weeks
tissue: liver
treatment: iron-deficient diet
|
|
| Sample_geo_accession | GSM757155
| | Sample_status | Public on Mar 21 2013
| | Sample_submission_date | Jul 08 2011
| | Sample_last_update_date | Mar 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Livers were excised and subsequently immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan).
| | Sample_growth_protocol_ch1 = Three-week-old male rats (Sprague Dawley) were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room maintained at 24 ± 1°C and 40 ± 5% humidity with a 12-h light/dark cycle (light 08:00–20:00; dark 20:00–08:00). Rats were given a normal diet (Research Diets, Inc., New Brunswick, NJ, USA) as control and water for 24 h ad libitum. The composition of the control diet, 48 ppm iron, was based on the AIN-93G diet; Avicel was used in place of cellulose which may contain a trace amount of iron. On day 3, diet was removed at 18:00 and the feeding was conducted between 09:00 and 17:00 for another 4 days to synchronize the feeding behaviors. On day 8, rats were divided into two groups with similar average body weights. Rats in the one group (n = 5) were given ad libitum an iron-deficient diet, ca. 3 ppm iron, that was prepared by removal of iron (ferric citrate) from the control diet, and those in the other group (n | 5) were fed the control diet by pair feeding. On day 1 and day 3 of feeding with the experiment diet, the hemoglobin level of each rat was measured for the blood samples collected from the tail vein. On day 3, each rat was sacrificed under anesthesia after 1.5 h feeding, prior to excising the liver which was soon immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol (Invitrogen Life Technologies, Carlsbad, CA, USA), then purified with an RNeasy mini kit (Qiagen, Valencia, CA, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 2 µg total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | The Affymetrix AGCC system was used to reduce the array images to the intensity values for each probe. These values were then stored in Affymatrix CEL format files and quantified with using a robust multiarray average (RMA) the statistical language R (http://www.r-project.org/), version 2.7.1.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Asuka,,Kamei
| | Sample_contact_email | fp-kamei@newkast.or.jp
| | Sample_contact_phone | +81-44-280-2187
| | Sample_contact_department | Project on Health and Anti-aging
| | Sample_contact_institute | Kanagawa Academy of Science and technology
| | Sample_contact_address | LiSE 4F C-4, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi
| | Sample_contact_city | Kanagawa
| | Sample_contact_zip/postal_code | 210-0821
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM757nnn/GSM757155/suppl/GSM757155_-Fe_short_27.CEL.gz
| | Sample_series_id | GSE30533
| | Sample_data_row_count | 31099
| | |
|
GSM757156 | GPL1355 |
|
iron-deficient diet, biological rep 2
|
Liver of rat fed iron-deficient diet
|
strain: Strain: Sprague-Dawley
gender: male
age: 5 weeks
tissue: liver
treatment: iron-deficient diet
|
|
| Sample_geo_accession | GSM757156
| | Sample_status | Public on Mar 21 2013
| | Sample_submission_date | Jul 08 2011
| | Sample_last_update_date | Mar 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Livers were excised and subsequently immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan).
| | Sample_growth_protocol_ch1 = Three-week-old male rats (Sprague Dawley) were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room maintained at 24 ± 1°C and 40 ± 5% humidity with a 12-h light/dark cycle (light 08:00–20:00; dark 20:00–08:00). Rats were given a normal diet (Research Diets, Inc., New Brunswick, NJ, USA) as control and water for 24 h ad libitum. The composition of the control diet, 48 ppm iron, was based on the AIN-93G diet; Avicel was used in place of cellulose which may contain a trace amount of iron. On day 3, diet was removed at 18:00 and the feeding was conducted between 09:00 and 17:00 for another 4 days to synchronize the feeding behaviors. On day 8, rats were divided into two groups with similar average body weights. Rats in the one group (n = 5) were given ad libitum an iron-deficient diet, ca. 3 ppm iron, that was prepared by removal of iron (ferric citrate) from the control diet, and those in the other group (n | 5) were fed the control diet by pair feeding. On day 1 and day 3 of feeding with the experiment diet, the hemoglobin level of each rat was measured for the blood samples collected from the tail vein. On day 3, each rat was sacrificed under anesthesia after 1.5 h feeding, prior to excising the liver which was soon immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol (Invitrogen Life Technologies, Carlsbad, CA, USA), then purified with an RNeasy mini kit (Qiagen, Valencia, CA, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 2 µg total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | The Affymetrix AGCC system was used to reduce the array images to the intensity values for each probe. These values were then stored in Affymatrix CEL format files and quantified with using a robust multiarray average (RMA) the statistical language R (http://www.r-project.org/), version 2.7.1.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Asuka,,Kamei
| | Sample_contact_email | fp-kamei@newkast.or.jp
| | Sample_contact_phone | +81-44-280-2187
| | Sample_contact_department | Project on Health and Anti-aging
| | Sample_contact_institute | Kanagawa Academy of Science and technology
| | Sample_contact_address | LiSE 4F C-4, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi
| | Sample_contact_city | Kanagawa
| | Sample_contact_zip/postal_code | 210-0821
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM757nnn/GSM757156/suppl/GSM757156_-Fe_short_31.CEL.gz
| | Sample_series_id | GSE30533
| | Sample_data_row_count | 31099
| | |
|
GSM757157 | GPL1355 |
|
iron-deficient diet, biological rep 3
|
Liver of rat fed iron-deficient diet
|
strain: Strain: Sprague-Dawley
gender: male
age: 5 weeks
tissue: liver
treatment: iron-deficient diet
|
|
| Sample_geo_accession | GSM757157
| | Sample_status | Public on Mar 21 2013
| | Sample_submission_date | Jul 08 2011
| | Sample_last_update_date | Mar 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Livers were excised and subsequently immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan).
| | Sample_growth_protocol_ch1 = Three-week-old male rats (Sprague Dawley) were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room maintained at 24 ± 1°C and 40 ± 5% humidity with a 12-h light/dark cycle (light 08:00–20:00; dark 20:00–08:00). Rats were given a normal diet (Research Diets, Inc., New Brunswick, NJ, USA) as control and water for 24 h ad libitum. The composition of the control diet, 48 ppm iron, was based on the AIN-93G diet; Avicel was used in place of cellulose which may contain a trace amount of iron. On day 3, diet was removed at 18:00 and the feeding was conducted between 09:00 and 17:00 for another 4 days to synchronize the feeding behaviors. On day 8, rats were divided into two groups with similar average body weights. Rats in the one group (n = 5) were given ad libitum an iron-deficient diet, ca. 3 ppm iron, that was prepared by removal of iron (ferric citrate) from the control diet, and those in the other group (n | 5) were fed the control diet by pair feeding. On day 1 and day 3 of feeding with the experiment diet, the hemoglobin level of each rat was measured for the blood samples collected from the tail vein. On day 3, each rat was sacrificed under anesthesia after 1.5 h feeding, prior to excising the liver which was soon immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol (Invitrogen Life Technologies, Carlsbad, CA, USA), then purified with an RNeasy mini kit (Qiagen, Valencia, CA, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 2 µg total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | The Affymetrix AGCC system was used to reduce the array images to the intensity values for each probe. These values were then stored in Affymatrix CEL format files and quantified with using a robust multiarray average (RMA) the statistical language R (http://www.r-project.org/), version 2.7.1.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Asuka,,Kamei
| | Sample_contact_email | fp-kamei@newkast.or.jp
| | Sample_contact_phone | +81-44-280-2187
| | Sample_contact_department | Project on Health and Anti-aging
| | Sample_contact_institute | Kanagawa Academy of Science and technology
| | Sample_contact_address | LiSE 4F C-4, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi
| | Sample_contact_city | Kanagawa
| | Sample_contact_zip/postal_code | 210-0821
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM757nnn/GSM757157/suppl/GSM757157_-Fe_short_33.CEL.gz
| | Sample_series_id | GSE30533
| | Sample_data_row_count | 31099
| | |
|
GSM757158 | GPL1355 |
|
iron-deficient diet, biological rep 4
|
Liver of rat fed iron-deficient diet
|
strain: Strain: Sprague-Dawley
gender: male
age: 5 weeks
tissue: liver
treatment: iron-deficient diet
|
|
| Sample_geo_accession | GSM757158
| | Sample_status | Public on Mar 21 2013
| | Sample_submission_date | Jul 08 2011
| | Sample_last_update_date | Mar 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Livers were excised and subsequently immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan).
| | Sample_growth_protocol_ch1 = Three-week-old male rats (Sprague Dawley) were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room maintained at 24 ± 1°C and 40 ± 5% humidity with a 12-h light/dark cycle (light 08:00–20:00; dark 20:00–08:00). Rats were given a normal diet (Research Diets, Inc., New Brunswick, NJ, USA) as control and water for 24 h ad libitum. The composition of the control diet, 48 ppm iron, was based on the AIN-93G diet; Avicel was used in place of cellulose which may contain a trace amount of iron. On day 3, diet was removed at 18:00 and the feeding was conducted between 09:00 and 17:00 for another 4 days to synchronize the feeding behaviors. On day 8, rats were divided into two groups with similar average body weights. Rats in the one group (n = 5) were given ad libitum an iron-deficient diet, ca. 3 ppm iron, that was prepared by removal of iron (ferric citrate) from the control diet, and those in the other group (n | 5) were fed the control diet by pair feeding. On day 1 and day 3 of feeding with the experiment diet, the hemoglobin level of each rat was measured for the blood samples collected from the tail vein. On day 3, each rat was sacrificed under anesthesia after 1.5 h feeding, prior to excising the liver which was soon immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol (Invitrogen Life Technologies, Carlsbad, CA, USA), then purified with an RNeasy mini kit (Qiagen, Valencia, CA, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 2 µg total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | The Affymetrix AGCC system was used to reduce the array images to the intensity values for each probe. These values were then stored in Affymatrix CEL format files and quantified with using a robust multiarray average (RMA) the statistical language R (http://www.r-project.org/), version 2.7.1.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Asuka,,Kamei
| | Sample_contact_email | fp-kamei@newkast.or.jp
| | Sample_contact_phone | +81-44-280-2187
| | Sample_contact_department | Project on Health and Anti-aging
| | Sample_contact_institute | Kanagawa Academy of Science and technology
| | Sample_contact_address | LiSE 4F C-4, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi
| | Sample_contact_city | Kanagawa
| | Sample_contact_zip/postal_code | 210-0821
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM757nnn/GSM757158/suppl/GSM757158_-Fe_short_35.CEL.gz
| | Sample_series_id | GSE30533
| | Sample_data_row_count | 31099
| | |
|
GSM757159 | GPL1355 |
|
iron-deficient diet, biological rep 5
|
Liver of rat fed iron-deficient diet
|
strain: Strain: Sprague-Dawley
gender: male
age: 5 weeks
tissue: liver
treatment: iron-deficient diet
|
|
| Sample_geo_accession | GSM757159
| | Sample_status | Public on Mar 21 2013
| | Sample_submission_date | Jul 08 2011
| | Sample_last_update_date | Mar 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Livers were excised and subsequently immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan).
| | Sample_growth_protocol_ch1 = Three-week-old male rats (Sprague Dawley) were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room maintained at 24 ± 1°C and 40 ± 5% humidity with a 12-h light/dark cycle (light 08:00–20:00; dark 20:00–08:00). Rats were given a normal diet (Research Diets, Inc., New Brunswick, NJ, USA) as control and water for 24 h ad libitum. The composition of the control diet, 48 ppm iron, was based on the AIN-93G diet; Avicel was used in place of cellulose which may contain a trace amount of iron. On day 3, diet was removed at 18:00 and the feeding was conducted between 09:00 and 17:00 for another 4 days to synchronize the feeding behaviors. On day 8, rats were divided into two groups with similar average body weights. Rats in the one group (n = 5) were given ad libitum an iron-deficient diet, ca. 3 ppm iron, that was prepared by removal of iron (ferric citrate) from the control diet, and those in the other group (n | 5) were fed the control diet by pair feeding. On day 1 and day 3 of feeding with the experiment diet, the hemoglobin level of each rat was measured for the blood samples collected from the tail vein. On day 3, each rat was sacrificed under anesthesia after 1.5 h feeding, prior to excising the liver which was soon immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol (Invitrogen Life Technologies, Carlsbad, CA, USA), then purified with an RNeasy mini kit (Qiagen, Valencia, CA, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 2 µg total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | The Affymetrix AGCC system was used to reduce the array images to the intensity values for each probe. These values were then stored in Affymatrix CEL format files and quantified with using a robust multiarray average (RMA) the statistical language R (http://www.r-project.org/), version 2.7.1.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Asuka,,Kamei
| | Sample_contact_email | fp-kamei@newkast.or.jp
| | Sample_contact_phone | +81-44-280-2187
| | Sample_contact_department | Project on Health and Anti-aging
| | Sample_contact_institute | Kanagawa Academy of Science and technology
| | Sample_contact_address | LiSE 4F C-4, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi
| | Sample_contact_city | Kanagawa
| | Sample_contact_zip/postal_code | 210-0821
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM757nnn/GSM757159/suppl/GSM757159_-Fe_short_37.CEL.gz
| | Sample_series_id | GSE30533
| | Sample_data_row_count | 31099
| | |
|
GSM757160 | GPL1355 |
|
control diet, biological rep 1
|
Liver of rat fed iron-deficient diet
|
strain: Strain: Sprague-Dawley
gender: male
age: 5 weeks
tissue: liver
treatment: control diet
|
|
| Sample_geo_accession | GSM757160
| | Sample_status | Public on Mar 21 2013
| | Sample_submission_date | Jul 08 2011
| | Sample_last_update_date | Mar 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Livers were excised and subsequently immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan).
| | Sample_growth_protocol_ch1 = Three-week-old male rats (Sprague Dawley) were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room maintained at 24 ± 1°C and 40 ± 5% humidity with a 12-h light/dark cycle (light 08:00–20:00; dark 20:00–08:00). Rats were given a normal diet (Research Diets, Inc., New Brunswick, NJ, USA) as control and water for 24 h ad libitum. The composition of the control diet, 48 ppm iron, was based on the AIN-93G diet; Avicel was used in place of cellulose which may contain a trace amount of iron. On day 3, diet was removed at 18:00 and the feeding was conducted between 09:00 and 17:00 for another 4 days to synchronize the feeding behaviors. On day 8, rats were divided into two groups with similar average body weights. Rats in the one group (n = 5) were given ad libitum an iron-deficient diet, ca. 3 ppm iron, that was prepared by removal of iron (ferric citrate) from the control diet, and those in the other group (n | 5) were fed the control diet by pair feeding. On day 1 and day 3 of feeding with the experiment diet, the hemoglobin level of each rat was measured for the blood samples collected from the tail vein. On day 3, each rat was sacrificed under anesthesia after 1.5 h feeding, prior to excising the liver which was soon immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol (Invitrogen Life Technologies, Carlsbad, CA, USA), then purified with an RNeasy mini kit (Qiagen, Valencia, CA, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 2 µg total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | The Affymetrix AGCC system was used to reduce the array images to the intensity values for each probe. These values were then stored in Affymatrix CEL format files and quantified with using a robust multiarray average (RMA) the statistical language R (http://www.r-project.org/), version 2.7.1.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Asuka,,Kamei
| | Sample_contact_email | fp-kamei@newkast.or.jp
| | Sample_contact_phone | +81-44-280-2187
| | Sample_contact_department | Project on Health and Anti-aging
| | Sample_contact_institute | Kanagawa Academy of Science and technology
| | Sample_contact_address | LiSE 4F C-4, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi
| | Sample_contact_city | Kanagawa
| | Sample_contact_zip/postal_code | 210-0821
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM757nnn/GSM757160/suppl/GSM757160_control_28.CEL.gz
| | Sample_series_id | GSE30533
| | Sample_data_row_count | 31099
| | |
|
GSM757161 | GPL1355 |
|
control diet, biological rep 2
|
Liver of rat fed iron-deficient diet
|
strain: Strain: Sprague-Dawley
gender: male
age: 5 weeks
tissue: liver
treatment: control diet
|
|
| Sample_geo_accession | GSM757161
| | Sample_status | Public on Mar 21 2013
| | Sample_submission_date | Jul 08 2011
| | Sample_last_update_date | Mar 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Livers were excised and subsequently immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan).
| | Sample_growth_protocol_ch1 = Three-week-old male rats (Sprague Dawley) were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room maintained at 24 ± 1°C and 40 ± 5% humidity with a 12-h light/dark cycle (light 08:00–20:00; dark 20:00–08:00). Rats were given a normal diet (Research Diets, Inc., New Brunswick, NJ, USA) as control and water for 24 h ad libitum. The composition of the control diet, 48 ppm iron, was based on the AIN-93G diet; Avicel was used in place of cellulose which may contain a trace amount of iron. On day 3, diet was removed at 18:00 and the feeding was conducted between 09:00 and 17:00 for another 4 days to synchronize the feeding behaviors. On day 8, rats were divided into two groups with similar average body weights. Rats in the one group (n = 5) were given ad libitum an iron-deficient diet, ca. 3 ppm iron, that was prepared by removal of iron (ferric citrate) from the control diet, and those in the other group (n | 5) were fed the control diet by pair feeding. On day 1 and day 3 of feeding with the experiment diet, the hemoglobin level of each rat was measured for the blood samples collected from the tail vein. On day 3, each rat was sacrificed under anesthesia after 1.5 h feeding, prior to excising the liver which was soon immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol (Invitrogen Life Technologies, Carlsbad, CA, USA), then purified with an RNeasy mini kit (Qiagen, Valencia, CA, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 2 µg total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | The Affymetrix AGCC system was used to reduce the array images to the intensity values for each probe. These values were then stored in Affymatrix CEL format files and quantified with using a robust multiarray average (RMA) the statistical language R (http://www.r-project.org/), version 2.7.1.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Asuka,,Kamei
| | Sample_contact_email | fp-kamei@newkast.or.jp
| | Sample_contact_phone | +81-44-280-2187
| | Sample_contact_department | Project on Health and Anti-aging
| | Sample_contact_institute | Kanagawa Academy of Science and technology
| | Sample_contact_address | LiSE 4F C-4, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi
| | Sample_contact_city | Kanagawa
| | Sample_contact_zip/postal_code | 210-0821
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM757nnn/GSM757161/suppl/GSM757161_control_30.CEL.gz
| | Sample_series_id | GSE30533
| | Sample_data_row_count | 31099
| | |
|
GSM757162 | GPL1355 |
|
control diet, biological rep 3
|
Liver of rat fed iron-deficient diet
|
strain: Strain: Sprague-Dawley
gender: male
age: 5 weeks
tissue: liver
treatment: control diet
|
|
| Sample_geo_accession | GSM757162
| | Sample_status | Public on Mar 21 2013
| | Sample_submission_date | Jul 08 2011
| | Sample_last_update_date | Mar 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Livers were excised and subsequently immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan).
| | Sample_growth_protocol_ch1 = Three-week-old male rats (Sprague Dawley) were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room maintained at 24 ± 1°C and 40 ± 5% humidity with a 12-h light/dark cycle (light 08:00–20:00; dark 20:00–08:00). Rats were given a normal diet (Research Diets, Inc., New Brunswick, NJ, USA) as control and water for 24 h ad libitum. The composition of the control diet, 48 ppm iron, was based on the AIN-93G diet; Avicel was used in place of cellulose which may contain a trace amount of iron. On day 3, diet was removed at 18:00 and the feeding was conducted between 09:00 and 17:00 for another 4 days to synchronize the feeding behaviors. On day 8, rats were divided into two groups with similar average body weights. Rats in the one group (n = 5) were given ad libitum an iron-deficient diet, ca. 3 ppm iron, that was prepared by removal of iron (ferric citrate) from the control diet, and those in the other group (n | 5) were fed the control diet by pair feeding. On day 1 and day 3 of feeding with the experiment diet, the hemoglobin level of each rat was measured for the blood samples collected from the tail vein. On day 3, each rat was sacrificed under anesthesia after 1.5 h feeding, prior to excising the liver which was soon immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol (Invitrogen Life Technologies, Carlsbad, CA, USA), then purified with an RNeasy mini kit (Qiagen, Valencia, CA, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 2 µg total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | The Affymetrix AGCC system was used to reduce the array images to the intensity values for each probe. These values were then stored in Affymatrix CEL format files and quantified with using a robust multiarray average (RMA) the statistical language R (http://www.r-project.org/), version 2.7.1.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Asuka,,Kamei
| | Sample_contact_email | fp-kamei@newkast.or.jp
| | Sample_contact_phone | +81-44-280-2187
| | Sample_contact_department | Project on Health and Anti-aging
| | Sample_contact_institute | Kanagawa Academy of Science and technology
| | Sample_contact_address | LiSE 4F C-4, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi
| | Sample_contact_city | Kanagawa
| | Sample_contact_zip/postal_code | 210-0821
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM757nnn/GSM757162/suppl/GSM757162_control_32.CEL.gz
| | Sample_series_id | GSE30533
| | Sample_data_row_count | 31099
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GSM757163 | GPL1355 |
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control diet, biological rep 4
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Liver of rat fed iron-deficient diet
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strain: Strain: Sprague-Dawley
gender: male
age: 5 weeks
tissue: liver
treatment: control diet
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|
| Sample_geo_accession | GSM757163
| | Sample_status | Public on Mar 21 2013
| | Sample_submission_date | Jul 08 2011
| | Sample_last_update_date | Mar 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Livers were excised and subsequently immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan).
| | Sample_growth_protocol_ch1 = Three-week-old male rats (Sprague Dawley) were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room maintained at 24 ± 1°C and 40 ± 5% humidity with a 12-h light/dark cycle (light 08:00–20:00; dark 20:00–08:00). Rats were given a normal diet (Research Diets, Inc., New Brunswick, NJ, USA) as control and water for 24 h ad libitum. The composition of the control diet, 48 ppm iron, was based on the AIN-93G diet; Avicel was used in place of cellulose which may contain a trace amount of iron. On day 3, diet was removed at 18:00 and the feeding was conducted between 09:00 and 17:00 for another 4 days to synchronize the feeding behaviors. On day 8, rats were divided into two groups with similar average body weights. Rats in the one group (n = 5) were given ad libitum an iron-deficient diet, ca. 3 ppm iron, that was prepared by removal of iron (ferric citrate) from the control diet, and those in the other group (n | 5) were fed the control diet by pair feeding. On day 1 and day 3 of feeding with the experiment diet, the hemoglobin level of each rat was measured for the blood samples collected from the tail vein. On day 3, each rat was sacrificed under anesthesia after 1.5 h feeding, prior to excising the liver which was soon immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol (Invitrogen Life Technologies, Carlsbad, CA, USA), then purified with an RNeasy mini kit (Qiagen, Valencia, CA, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 2 µg total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | The Affymetrix AGCC system was used to reduce the array images to the intensity values for each probe. These values were then stored in Affymatrix CEL format files and quantified with using a robust multiarray average (RMA) the statistical language R (http://www.r-project.org/), version 2.7.1.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Asuka,,Kamei
| | Sample_contact_email | fp-kamei@newkast.or.jp
| | Sample_contact_phone | +81-44-280-2187
| | Sample_contact_department | Project on Health and Anti-aging
| | Sample_contact_institute | Kanagawa Academy of Science and technology
| | Sample_contact_address | LiSE 4F C-4, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi
| | Sample_contact_city | Kanagawa
| | Sample_contact_zip/postal_code | 210-0821
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM757nnn/GSM757163/suppl/GSM757163_control_34.CEL.gz
| | Sample_series_id | GSE30533
| | Sample_data_row_count | 31099
| | |
|
GSM757164 | GPL1355 |
|
control diet, biological rep 5
|
Liver of rat fed iron-deficient diet
|
strain: Strain: Sprague-Dawley
gender: male
age: 5 weeks
tissue: liver
treatment: control diet
|
|
| Sample_geo_accession | GSM757164
| | Sample_status | Public on Mar 21 2013
| | Sample_submission_date | Jul 08 2011
| | Sample_last_update_date | Mar 21 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Livers were excised and subsequently immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan).
| | Sample_growth_protocol_ch1 = Three-week-old male rats (Sprague Dawley) were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room maintained at 24 ± 1°C and 40 ± 5% humidity with a 12-h light/dark cycle (light 08:00–20:00; dark 20:00–08:00). Rats were given a normal diet (Research Diets, Inc., New Brunswick, NJ, USA) as control and water for 24 h ad libitum. The composition of the control diet, 48 ppm iron, was based on the AIN-93G diet; Avicel was used in place of cellulose which may contain a trace amount of iron. On day 3, diet was removed at 18:00 and the feeding was conducted between 09:00 and 17:00 for another 4 days to synchronize the feeding behaviors. On day 8, rats were divided into two groups with similar average body weights. Rats in the one group (n = 5) were given ad libitum an iron-deficient diet, ca. 3 ppm iron, that was prepared by removal of iron (ferric citrate) from the control diet, and those in the other group (n | 5) were fed the control diet by pair feeding. On day 1 and day 3 of feeding with the experiment diet, the hemoglobin level of each rat was measured for the blood samples collected from the tail vein. On day 3, each rat was sacrificed under anesthesia after 1.5 h feeding, prior to excising the liver which was soon immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol (Invitrogen Life Technologies, Carlsbad, CA, USA), then purified with an RNeasy mini kit (Qiagen, Valencia, CA, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 2 µg total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | The Affymetrix AGCC system was used to reduce the array images to the intensity values for each probe. These values were then stored in Affymatrix CEL format files and quantified with using a robust multiarray average (RMA) the statistical language R (http://www.r-project.org/), version 2.7.1.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Asuka,,Kamei
| | Sample_contact_email | fp-kamei@newkast.or.jp
| | Sample_contact_phone | +81-44-280-2187
| | Sample_contact_department | Project on Health and Anti-aging
| | Sample_contact_institute | Kanagawa Academy of Science and technology
| | Sample_contact_address | LiSE 4F C-4, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi
| | Sample_contact_city | Kanagawa
| | Sample_contact_zip/postal_code | 210-0821
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM757nnn/GSM757164/suppl/GSM757164_control_36.CEL.gz
| | Sample_series_id | GSE30533
| | Sample_data_row_count | 31099
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