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Search results for the GEO ID: GSE16899

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Description

Characteristics

GSM423650

GPL1355

Iron-deficient diet, biological rep 1

Liver of rat fed iron-deficient diet

strain: Strain: Sprague-Dawley gender: male age: 7 weeks tissue: liver

No additional information

Sample_geo_accession	GSM423650
Sample_status	Public on Apr 22 2010
Sample_submission_date	Jun 30 2009
Sample_last_update_date	Apr 21 2010
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 = Male 3-week-old Sprague Dawley rats were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room conditioned at 24 ± 1°C and 40 ± 5% humidity with a 12-h light-dark cycle (lights on at 08:00). The rats were given a control diet and water for 24 h ad libitum. Diets for rats were obtained from Research Diets, Inc. (New Brunswick, NJ, USA). The composition of the control diet was based on the AIN93G diet , except that cellulose was replaced by Avicel, since cellulose is an ingredient of variable iron content. The iron-deficient diet was prepared by removal of iron (ferric citrate) from the control diet. At day 8, rats were divided into two groups comprising animals of similar body weights. One group (n = 6) was fed the control diet and the other group (n	7) was fed the iron-deficient diet (iron-deficient diet group). After iron-deficient diet feeding was started, blood hemoglobin levels were measured every two days. Blood samples for hemoglobin measurements were collected from the tail vein, and hemoglobin levels were measured by using the Wako Hemoglobin B test (Wako Pure Chemical Industries, Osaka, Japan). On day 12 of the iron-deficient diet treatment, diets were removed at 17:00, and feeding was conducted between 09:00 and 17:00 for another 4 days. This protocol was intended to synchronize the rats’ feeding behavior. On day 17 of the iron-deficient diet treatment, rats were fed for 1.5 h prior to sacrifice under anesthesia.
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, 2001, 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 the distribution free weighted method (DFW) using 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/GSM423nnn/GSM423650/suppl/GSM423650.CEL.gz
Sample_series_id	GSE16899
Sample_data_row_count	31099

GSM423651

GPL1355

Iron-deficient diet, biological rep 2

Liver of rat fed iron-deficient diet

strain: Strain: Sprague-Dawley gender: male age: 7 weeks tissue: liver

No additional information

Sample_geo_accession	GSM423651
Sample_status	Public on Apr 22 2010
Sample_submission_date	Jun 30 2009
Sample_last_update_date	Apr 21 2010
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 = Male 3-week-old Sprague Dawley rats were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room conditioned at 24 ± 1°C and 40 ± 5% humidity with a 12-h light-dark cycle (lights on at 08:00). The rats were given a control diet and water for 24 h ad libitum. Diets for rats were obtained from Research Diets, Inc. (New Brunswick, NJ, USA). The composition of the control diet was based on the AIN93G diet , except that cellulose was replaced by Avicel, since cellulose is an ingredient of variable iron content. The iron-deficient diet was prepared by removal of iron (ferric citrate) from the control diet. At day 8, rats were divided into two groups comprising animals of similar body weights. One group (n = 6) was fed the control diet and the other group (n	7) was fed the iron-deficient diet (iron-deficient diet group). After iron-deficient diet feeding was started, blood hemoglobin levels were measured every two days. Blood samples for hemoglobin measurements were collected from the tail vein, and hemoglobin levels were measured by using the Wako Hemoglobin B test (Wako Pure Chemical Industries, Osaka, Japan). On day 12 of the iron-deficient diet treatment, diets were removed at 17:00, and feeding was conducted between 09:00 and 17:00 for another 4 days. This protocol was intended to synchronize the rats’ feeding behavior. On day 17 of the iron-deficient diet treatment, rats were fed for 1.5 h prior to sacrifice under anesthesia.
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, 2001, 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 the distribution free weighted method (DFW) using 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/GSM423nnn/GSM423651/suppl/GSM423651.CEL.gz
Sample_series_id	GSE16899
Sample_data_row_count	31099

GSM423652

GPL1355

Iron-deficient diet, biological rep 3

Liver of rat fed iron-deficient diet

strain: Strain: Sprague-Dawley gender: male age: 7 weeks tissue: liver

No additional information

Sample_geo_accession	GSM423652
Sample_status	Public on Apr 22 2010
Sample_submission_date	Jun 30 2009
Sample_last_update_date	Apr 21 2010
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 = Male 3-week-old Sprague Dawley rats were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room conditioned at 24 ± 1°C and 40 ± 5% humidity with a 12-h light-dark cycle (lights on at 08:00). The rats were given a control diet and water for 24 h ad libitum. Diets for rats were obtained from Research Diets, Inc. (New Brunswick, NJ, USA). The composition of the control diet was based on the AIN93G diet , except that cellulose was replaced by Avicel, since cellulose is an ingredient of variable iron content. The iron-deficient diet was prepared by removal of iron (ferric citrate) from the control diet. At day 8, rats were divided into two groups comprising animals of similar body weights. One group (n = 6) was fed the control diet and the other group (n	7) was fed the iron-deficient diet (iron-deficient diet group). After iron-deficient diet feeding was started, blood hemoglobin levels were measured every two days. Blood samples for hemoglobin measurements were collected from the tail vein, and hemoglobin levels were measured by using the Wako Hemoglobin B test (Wako Pure Chemical Industries, Osaka, Japan). On day 12 of the iron-deficient diet treatment, diets were removed at 17:00, and feeding was conducted between 09:00 and 17:00 for another 4 days. This protocol was intended to synchronize the rats’ feeding behavior. On day 17 of the iron-deficient diet treatment, rats were fed for 1.5 h prior to sacrifice under anesthesia.
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, 2001, 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 the distribution free weighted method (DFW) using 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/GSM423nnn/GSM423652/suppl/GSM423652.CEL.gz
Sample_series_id	GSE16899
Sample_data_row_count	31099

GSM423653

GPL1355

Iron-deficient diet, biological rep 4

Liver of rat fed iron-deficient diet

strain: Strain: Sprague-Dawley gender: male age: 7 weeks tissue: liver

No additional information

Sample_geo_accession	GSM423653
Sample_status	Public on Apr 22 2010
Sample_submission_date	Jun 30 2009
Sample_last_update_date	Apr 21 2010
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 = Male 3-week-old Sprague Dawley rats were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room conditioned at 24 ± 1°C and 40 ± 5% humidity with a 12-h light-dark cycle (lights on at 08:00). The rats were given a control diet and water for 24 h ad libitum. Diets for rats were obtained from Research Diets, Inc. (New Brunswick, NJ, USA). The composition of the control diet was based on the AIN93G diet , except that cellulose was replaced by Avicel, since cellulose is an ingredient of variable iron content. The iron-deficient diet was prepared by removal of iron (ferric citrate) from the control diet. At day 8, rats were divided into two groups comprising animals of similar body weights. One group (n = 6) was fed the control diet and the other group (n	7) was fed the iron-deficient diet (iron-deficient diet group). After iron-deficient diet feeding was started, blood hemoglobin levels were measured every two days. Blood samples for hemoglobin measurements were collected from the tail vein, and hemoglobin levels were measured by using the Wako Hemoglobin B test (Wako Pure Chemical Industries, Osaka, Japan). On day 12 of the iron-deficient diet treatment, diets were removed at 17:00, and feeding was conducted between 09:00 and 17:00 for another 4 days. This protocol was intended to synchronize the rats’ feeding behavior. On day 17 of the iron-deficient diet treatment, rats were fed for 1.5 h prior to sacrifice under anesthesia.
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, 2001, 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 the distribution free weighted method (DFW) using 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/GSM423nnn/GSM423653/suppl/GSM423653.CEL.gz
Sample_series_id	GSE16899
Sample_data_row_count	31099

GSM423654

GPL1355

Control diet, biological rep 1

Liver of rat fed control diet

strain: Strain: Sprague-Dawley gender: male age: 7 weeks tissue: liver

No additional information

Sample_geo_accession	GSM423654
Sample_status	Public on Apr 22 2010
Sample_submission_date	Jun 30 2009
Sample_last_update_date	Apr 21 2010
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 = Male 3-week-old Sprague Dawley rats were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room conditioned at 24 ± 1°C and 40 ± 5% humidity with a 12-h light-dark cycle (lights on at 08:00). The rats were given a control diet and water for 24 h ad libitum. Diets for rats were obtained from Research Diets, Inc. (New Brunswick, NJ, USA). The composition of the control diet was based on the AIN93G diet , except that cellulose was replaced by Avicel, since cellulose is an ingredient of variable iron content. The iron-deficient diet was prepared by removal of iron (ferric citrate) from the control diet. At day 8, rats were divided into two groups comprising animals of similar body weights. One group (n = 6) was fed the control diet and the other group (n	7) was fed the iron-deficient diet (iron-deficient diet group). After iron-deficient diet feeding was started, blood hemoglobin levels were measured every two days. Blood samples for hemoglobin measurements were collected from the tail vein, and hemoglobin levels were measured by using the Wako Hemoglobin B test (Wako Pure Chemical Industries, Osaka, Japan). On day 12 of the iron-deficient diet treatment, diets were removed at 17:00, and feeding was conducted between 09:00 and 17:00 for another 4 days. This protocol was intended to synchronize the rats’ feeding behavior. On day 17 of the iron-deficient diet treatment, rats were fed for 1.5 h prior to sacrifice under anesthesia.
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, 2001, 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 the distribution free weighted method (DFW) using 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/GSM423nnn/GSM423654/suppl/GSM423654.CEL.gz
Sample_series_id	GSE16899
Sample_data_row_count	31099

GSM423655

GPL1355

Control diet, biological rep 2

Liver of rat fed control diet

strain: Strain: Sprague-Dawley gender: male age: 7 weeks tissue: liver

No additional information

Sample_geo_accession	GSM423655
Sample_status	Public on Apr 22 2010
Sample_submission_date	Jun 30 2009
Sample_last_update_date	Apr 21 2010
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 = Male 3-week-old Sprague Dawley rats were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room conditioned at 24 ± 1°C and 40 ± 5% humidity with a 12-h light-dark cycle (lights on at 08:00). The rats were given a control diet and water for 24 h ad libitum. Diets for rats were obtained from Research Diets, Inc. (New Brunswick, NJ, USA). The composition of the control diet was based on the AIN93G diet , except that cellulose was replaced by Avicel, since cellulose is an ingredient of variable iron content. The iron-deficient diet was prepared by removal of iron (ferric citrate) from the control diet. At day 8, rats were divided into two groups comprising animals of similar body weights. One group (n = 6) was fed the control diet and the other group (n	7) was fed the iron-deficient diet (iron-deficient diet group). After iron-deficient diet feeding was started, blood hemoglobin levels were measured every two days. Blood samples for hemoglobin measurements were collected from the tail vein, and hemoglobin levels were measured by using the Wako Hemoglobin B test (Wako Pure Chemical Industries, Osaka, Japan). On day 12 of the iron-deficient diet treatment, diets were removed at 17:00, and feeding was conducted between 09:00 and 17:00 for another 4 days. This protocol was intended to synchronize the rats’ feeding behavior. On day 17 of the iron-deficient diet treatment, rats were fed for 1.5 h prior to sacrifice under anesthesia.
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, 2001, 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 the distribution free weighted method (DFW) using 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/GSM423nnn/GSM423655/suppl/GSM423655.CEL.gz
Sample_series_id	GSE16899
Sample_data_row_count	31099

GSM423656

GPL1355

Control diet, biological rep 3

Liver of rat fed control diet

strain: Strain: Sprague-Dawley gender: male age: 7 weeks tissue: liver

No additional information

Sample_geo_accession	GSM423656
Sample_status	Public on Apr 22 2010
Sample_submission_date	Jun 30 2009
Sample_last_update_date	Apr 21 2010
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 = Male 3-week-old Sprague Dawley rats were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room conditioned at 24 ± 1°C and 40 ± 5% humidity with a 12-h light-dark cycle (lights on at 08:00). The rats were given a control diet and water for 24 h ad libitum. Diets for rats were obtained from Research Diets, Inc. (New Brunswick, NJ, USA). The composition of the control diet was based on the AIN93G diet , except that cellulose was replaced by Avicel, since cellulose is an ingredient of variable iron content. The iron-deficient diet was prepared by removal of iron (ferric citrate) from the control diet. At day 8, rats were divided into two groups comprising animals of similar body weights. One group (n = 6) was fed the control diet and the other group (n	7) was fed the iron-deficient diet (iron-deficient diet group). After iron-deficient diet feeding was started, blood hemoglobin levels were measured every two days. Blood samples for hemoglobin measurements were collected from the tail vein, and hemoglobin levels were measured by using the Wako Hemoglobin B test (Wako Pure Chemical Industries, Osaka, Japan). On day 12 of the iron-deficient diet treatment, diets were removed at 17:00, and feeding was conducted between 09:00 and 17:00 for another 4 days. This protocol was intended to synchronize the rats’ feeding behavior. On day 17 of the iron-deficient diet treatment, rats were fed for 1.5 h prior to sacrifice under anesthesia.
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, 2001, 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 the distribution free weighted method (DFW) using 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/GSM423nnn/GSM423656/suppl/GSM423656.CEL.gz
Sample_series_id	GSE16899
Sample_data_row_count	31099

GSM423657

GPL1355

Control diet, biological rep 4

Liver of rat fed control diet

strain: Strain: Sprague-Dawley gender: male age: 7 weeks tissue: liver

No additional information

Sample_geo_accession	GSM423657
Sample_status	Public on Apr 22 2010
Sample_submission_date	Jun 30 2009
Sample_last_update_date	Apr 21 2010
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 = Male 3-week-old Sprague Dawley rats were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room conditioned at 24 ± 1°C and 40 ± 5% humidity with a 12-h light-dark cycle (lights on at 08:00). The rats were given a control diet and water for 24 h ad libitum. Diets for rats were obtained from Research Diets, Inc. (New Brunswick, NJ, USA). The composition of the control diet was based on the AIN93G diet , except that cellulose was replaced by Avicel, since cellulose is an ingredient of variable iron content. The iron-deficient diet was prepared by removal of iron (ferric citrate) from the control diet. At day 8, rats were divided into two groups comprising animals of similar body weights. One group (n = 6) was fed the control diet and the other group (n	7) was fed the iron-deficient diet (iron-deficient diet group). After iron-deficient diet feeding was started, blood hemoglobin levels were measured every two days. Blood samples for hemoglobin measurements were collected from the tail vein, and hemoglobin levels were measured by using the Wako Hemoglobin B test (Wako Pure Chemical Industries, Osaka, Japan). On day 12 of the iron-deficient diet treatment, diets were removed at 17:00, and feeding was conducted between 09:00 and 17:00 for another 4 days. This protocol was intended to synchronize the rats’ feeding behavior. On day 17 of the iron-deficient diet treatment, rats were fed for 1.5 h prior to sacrifice under anesthesia.
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, 2001, 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 the distribution free weighted method (DFW) using 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/GSM423nnn/GSM423657/suppl/GSM423657.CEL.gz
Sample_series_id	GSE16899
Sample_data_row_count	31099

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