Search results for the GEO ID: GSE29859  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM739648 | GPL1355 |
|
CorticalBone_ExcessVitA_rep1
|
CorticalBone_ExcessVitA
|
breed: Sprague-Dawley
gender: male
age: 8 week
disease status: Hypervitaminosis A
tissue: Humerus, Diaphyseal Cortical Bone
|
a13
|
| Sample_geo_accession | GSM739648
| | Sample_status | Public on Dec 21 2011
| | Sample_submission_date | Jun 09 2011
| | Sample_last_update_date | Dec 21 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The rats were divided into two groups, each with 12 animals. They were fed a standard diet containing 12 IU vitamin A/g pellet (“cont”), or a standard diet supplemented with 1700 IU (“Ex. vitA”) vitamin A/g pellet. The vitamin A was added to the pellets in the form of retinyl palmitate and retinyl acetate. After eight days, the rats were euthanized by exsanguinations from the abdominal aorta under Eqvitesin anesthesia (chloral hydrate 182 mg/kg, pentobarbital 41.7 g/kg).
| | Sample_growth_protocol_ch1 | They were acclimatized for one week and kept in groups of three animals and had free access to water and commercial pellet diet (Lactamin R36, Stockholm, Sweden).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Bones were snap-frozen in liquid nitrogen and quickly crushed into a fine powder using a mortar and pestle followed by total RNA extraction with TRI Reagent® (Sigma-Aldrich). For cortical bone without marrow, diaphyseal bones were cut into pieces, vortexed in ice-cold PBS three times for 10 s to remove marrow cells followed by snap-freezing in liquid nitrogen, crushing into a fine powder and RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Sample preparation and processing were performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_hyb_protocol | Hybridization was performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_scan_protocol | The arrays were washed using Affymetrix fluidics stations, and scanned using the GeneChip® Scanner 3000 7G.
| | Sample_data_processing | Gene expression data were processed in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project. The raw data was normalized using the robust multi-array average (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anders,,Isaksson
| | Sample_contact_email | anders.isaksson@medsci.uu.se
| | Sample_contact_institute | Uppsala Array Platform
| | Sample_contact_address | Akademiska sjukhuset ing61 3tr
| | Sample_contact_city | Uppsala
| | Sample_contact_zip/postal_code | 75185
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM739nnn/GSM739648/suppl/GSM739648.CEL.gz
| | Sample_series_id | GSE29859
| | Sample_data_row_count | 31099
| | |
|
GSM739649 | GPL1355 |
|
CorticalBone_ExcessVitA_rep2
|
CorticalBone_ExcessVitA
|
breed: Sprague-Dawley
gender: male
age: 8 week
disease status: Hypervitaminosis A
tissue: Humerus, Diaphyseal Cortical Bone
|
a17
|
| Sample_geo_accession | GSM739649
| | Sample_status | Public on Dec 21 2011
| | Sample_submission_date | Jun 09 2011
| | Sample_last_update_date | Dec 21 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The rats were divided into two groups, each with 12 animals. They were fed a standard diet containing 12 IU vitamin A/g pellet (“cont”), or a standard diet supplemented with 1700 IU (“Ex. vitA”) vitamin A/g pellet. The vitamin A was added to the pellets in the form of retinyl palmitate and retinyl acetate. After eight days, the rats were euthanized by exsanguinations from the abdominal aorta under Eqvitesin anesthesia (chloral hydrate 182 mg/kg, pentobarbital 41.7 g/kg).
| | Sample_growth_protocol_ch1 | They were acclimatized for one week and kept in groups of three animals and had free access to water and commercial pellet diet (Lactamin R36, Stockholm, Sweden).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Bones were snap-frozen in liquid nitrogen and quickly crushed into a fine powder using a mortar and pestle followed by total RNA extraction with TRI Reagent® (Sigma-Aldrich). For cortical bone without marrow, diaphyseal bones were cut into pieces, vortexed in ice-cold PBS three times for 10 s to remove marrow cells followed by snap-freezing in liquid nitrogen, crushing into a fine powder and RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Sample preparation and processing were performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_hyb_protocol | Hybridization was performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_scan_protocol | The arrays were washed using Affymetrix fluidics stations, and scanned using the GeneChip® Scanner 3000 7G.
| | Sample_data_processing | Gene expression data were processed in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project. The raw data was normalized using the robust multi-array average (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anders,,Isaksson
| | Sample_contact_email | anders.isaksson@medsci.uu.se
| | Sample_contact_institute | Uppsala Array Platform
| | Sample_contact_address | Akademiska sjukhuset ing61 3tr
| | Sample_contact_city | Uppsala
| | Sample_contact_zip/postal_code | 75185
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM739nnn/GSM739649/suppl/GSM739649.CEL.gz
| | Sample_series_id | GSE29859
| | Sample_data_row_count | 31099
| | |
|
GSM739650 | GPL1355 |
|
CorticalBone+Marrow_ExcessVitA_rep1
|
CorticalBone+Marrow_ExcessVitA
|
breed: Sprague-Dawley
gender: male
age: 8 week
disease status: Hypervitaminosis A
tissue: Humerus, Diaphyseal Cortical Bone including Marrow
|
a18
|
| Sample_geo_accession | GSM739650
| | Sample_status | Public on Dec 21 2011
| | Sample_submission_date | Jun 09 2011
| | Sample_last_update_date | Dec 21 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The rats were divided into two groups, each with 12 animals. They were fed a standard diet containing 12 IU vitamin A/g pellet (“cont”), or a standard diet supplemented with 1700 IU (“Ex. vitA”) vitamin A/g pellet. The vitamin A was added to the pellets in the form of retinyl palmitate and retinyl acetate. After eight days, the rats were euthanized by exsanguinations from the abdominal aorta under Eqvitesin anesthesia (chloral hydrate 182 mg/kg, pentobarbital 41.7 g/kg).
| | Sample_growth_protocol_ch1 | They were acclimatized for one week and kept in groups of three animals and had free access to water and commercial pellet diet (Lactamin R36, Stockholm, Sweden).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Bones were snap-frozen in liquid nitrogen and quickly crushed into a fine powder using a mortar and pestle followed by total RNA extraction with TRI Reagent® (Sigma-Aldrich). For cortical bone without marrow, diaphyseal bones were cut into pieces, vortexed in ice-cold PBS three times for 10 s to remove marrow cells followed by snap-freezing in liquid nitrogen, crushing into a fine powder and RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Sample preparation and processing were performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_hyb_protocol | Hybridization was performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_scan_protocol | The arrays were washed using Affymetrix fluidics stations, and scanned using the GeneChip® Scanner 3000 7G.
| | Sample_data_processing | Gene expression data were processed in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project. The raw data was normalized using the robust multi-array average (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anders,,Isaksson
| | Sample_contact_email | anders.isaksson@medsci.uu.se
| | Sample_contact_institute | Uppsala Array Platform
| | Sample_contact_address | Akademiska sjukhuset ing61 3tr
| | Sample_contact_city | Uppsala
| | Sample_contact_zip/postal_code | 75185
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM739nnn/GSM739650/suppl/GSM739650.CEL.gz
| | Sample_series_id | GSE29859
| | Sample_data_row_count | 31099
| | |
|
GSM739651 | GPL1355 |
|
CorticalBone+Marrow_ExcessVitA_rep2
|
CorticalBone+Marrow_ExcessVitA
|
breed: Sprague-Dawley
gender: male
age: 8 week
disease status: Hypervitaminosis A
tissue: Humerus, Diaphyseal Cortical Bone including Marrow
|
a20
|
| Sample_geo_accession | GSM739651
| | Sample_status | Public on Dec 21 2011
| | Sample_submission_date | Jun 09 2011
| | Sample_last_update_date | Dec 21 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The rats were divided into two groups, each with 12 animals. They were fed a standard diet containing 12 IU vitamin A/g pellet (“cont”), or a standard diet supplemented with 1700 IU (“Ex. vitA”) vitamin A/g pellet. The vitamin A was added to the pellets in the form of retinyl palmitate and retinyl acetate. After eight days, the rats were euthanized by exsanguinations from the abdominal aorta under Eqvitesin anesthesia (chloral hydrate 182 mg/kg, pentobarbital 41.7 g/kg).
| | Sample_growth_protocol_ch1 | They were acclimatized for one week and kept in groups of three animals and had free access to water and commercial pellet diet (Lactamin R36, Stockholm, Sweden).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Bones were snap-frozen in liquid nitrogen and quickly crushed into a fine powder using a mortar and pestle followed by total RNA extraction with TRI Reagent® (Sigma-Aldrich). For cortical bone without marrow, diaphyseal bones were cut into pieces, vortexed in ice-cold PBS three times for 10 s to remove marrow cells followed by snap-freezing in liquid nitrogen, crushing into a fine powder and RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Sample preparation and processing were performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_hyb_protocol | Hybridization was performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_scan_protocol | The arrays were washed using Affymetrix fluidics stations, and scanned using the GeneChip® Scanner 3000 7G.
| | Sample_data_processing | Gene expression data were processed in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project. The raw data was normalized using the robust multi-array average (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anders,,Isaksson
| | Sample_contact_email | anders.isaksson@medsci.uu.se
| | Sample_contact_institute | Uppsala Array Platform
| | Sample_contact_address | Akademiska sjukhuset ing61 3tr
| | Sample_contact_city | Uppsala
| | Sample_contact_zip/postal_code | 75185
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM739nnn/GSM739651/suppl/GSM739651.CEL.gz
| | Sample_series_id | GSE29859
| | Sample_data_row_count | 31099
| | |
|
GSM739652 | GPL1355 |
|
CorticalBone_ExcessVitA_rep3
|
CorticalBone_ExcessVitA
|
breed: Sprague-Dawley
gender: male
age: 8 week
disease status: Hypervitaminosis A
tissue: Humerus, Diaphyseal Cortical Bone
|
a21
|
| Sample_geo_accession | GSM739652
| | Sample_status | Public on Dec 21 2011
| | Sample_submission_date | Jun 09 2011
| | Sample_last_update_date | Dec 21 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The rats were divided into two groups, each with 12 animals. They were fed a standard diet containing 12 IU vitamin A/g pellet (“cont”), or a standard diet supplemented with 1700 IU (“Ex. vitA”) vitamin A/g pellet. The vitamin A was added to the pellets in the form of retinyl palmitate and retinyl acetate. After eight days, the rats were euthanized by exsanguinations from the abdominal aorta under Eqvitesin anesthesia (chloral hydrate 182 mg/kg, pentobarbital 41.7 g/kg).
| | Sample_growth_protocol_ch1 | They were acclimatized for one week and kept in groups of three animals and had free access to water and commercial pellet diet (Lactamin R36, Stockholm, Sweden).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Bones were snap-frozen in liquid nitrogen and quickly crushed into a fine powder using a mortar and pestle followed by total RNA extraction with TRI Reagent® (Sigma-Aldrich). For cortical bone without marrow, diaphyseal bones were cut into pieces, vortexed in ice-cold PBS three times for 10 s to remove marrow cells followed by snap-freezing in liquid nitrogen, crushing into a fine powder and RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Sample preparation and processing were performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_hyb_protocol | Hybridization was performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_scan_protocol | The arrays were washed using Affymetrix fluidics stations, and scanned using the GeneChip® Scanner 3000 7G.
| | Sample_data_processing | Gene expression data were processed in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project. The raw data was normalized using the robust multi-array average (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anders,,Isaksson
| | Sample_contact_email | anders.isaksson@medsci.uu.se
| | Sample_contact_institute | Uppsala Array Platform
| | Sample_contact_address | Akademiska sjukhuset ing61 3tr
| | Sample_contact_city | Uppsala
| | Sample_contact_zip/postal_code | 75185
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM739nnn/GSM739652/suppl/GSM739652.CEL.gz
| | Sample_series_id | GSE29859
| | Sample_data_row_count | 31099
| | |
|
GSM739653 | GPL1355 |
|
CorticalBone_ExcessVitA_rep4
|
CorticalBone_ExcessVitA
|
breed: Sprague-Dawley
gender: male
age: 8 week
disease status: Hypervitaminosis A
tissue: Humerus, Diaphyseal Cortical Bone
|
a22
|
| Sample_geo_accession | GSM739653
| | Sample_status | Public on Dec 21 2011
| | Sample_submission_date | Jun 09 2011
| | Sample_last_update_date | Dec 21 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The rats were divided into two groups, each with 12 animals. They were fed a standard diet containing 12 IU vitamin A/g pellet (“cont”), or a standard diet supplemented with 1700 IU (“Ex. vitA”) vitamin A/g pellet. The vitamin A was added to the pellets in the form of retinyl palmitate and retinyl acetate. After eight days, the rats were euthanized by exsanguinations from the abdominal aorta under Eqvitesin anesthesia (chloral hydrate 182 mg/kg, pentobarbital 41.7 g/kg).
| | Sample_growth_protocol_ch1 | They were acclimatized for one week and kept in groups of three animals and had free access to water and commercial pellet diet (Lactamin R36, Stockholm, Sweden).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Bones were snap-frozen in liquid nitrogen and quickly crushed into a fine powder using a mortar and pestle followed by total RNA extraction with TRI Reagent® (Sigma-Aldrich). For cortical bone without marrow, diaphyseal bones were cut into pieces, vortexed in ice-cold PBS three times for 10 s to remove marrow cells followed by snap-freezing in liquid nitrogen, crushing into a fine powder and RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Sample preparation and processing were performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_hyb_protocol | Hybridization was performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_scan_protocol | The arrays were washed using Affymetrix fluidics stations, and scanned using the GeneChip® Scanner 3000 7G.
| | Sample_data_processing | Gene expression data were processed in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project. The raw data was normalized using the robust multi-array average (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anders,,Isaksson
| | Sample_contact_email | anders.isaksson@medsci.uu.se
| | Sample_contact_institute | Uppsala Array Platform
| | Sample_contact_address | Akademiska sjukhuset ing61 3tr
| | Sample_contact_city | Uppsala
| | Sample_contact_zip/postal_code | 75185
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM739nnn/GSM739653/suppl/GSM739653.CEL.gz
| | Sample_series_id | GSE29859
| | Sample_data_row_count | 31099
| | |
|
GSM739654 | GPL1355 |
|
CorticalBone+Marrow_ExcessVitA_rep3
|
CorticalBone+Marrow_ExcessVitA
|
breed: Sprague-Dawley
gender: male
age: 8 week
disease status: Hypervitaminosis A
tissue: Humerus, Diaphyseal Cortical Bone including Marrow
|
a23
|
| Sample_geo_accession | GSM739654
| | Sample_status | Public on Dec 21 2011
| | Sample_submission_date | Jun 09 2011
| | Sample_last_update_date | Dec 21 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The rats were divided into two groups, each with 12 animals. They were fed a standard diet containing 12 IU vitamin A/g pellet (“cont”), or a standard diet supplemented with 1700 IU (“Ex. vitA”) vitamin A/g pellet. The vitamin A was added to the pellets in the form of retinyl palmitate and retinyl acetate. After eight days, the rats were euthanized by exsanguinations from the abdominal aorta under Eqvitesin anesthesia (chloral hydrate 182 mg/kg, pentobarbital 41.7 g/kg).
| | Sample_growth_protocol_ch1 | They were acclimatized for one week and kept in groups of three animals and had free access to water and commercial pellet diet (Lactamin R36, Stockholm, Sweden).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Bones were snap-frozen in liquid nitrogen and quickly crushed into a fine powder using a mortar and pestle followed by total RNA extraction with TRI Reagent® (Sigma-Aldrich). For cortical bone without marrow, diaphyseal bones were cut into pieces, vortexed in ice-cold PBS three times for 10 s to remove marrow cells followed by snap-freezing in liquid nitrogen, crushing into a fine powder and RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Sample preparation and processing were performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_hyb_protocol | Hybridization was performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_scan_protocol | The arrays were washed using Affymetrix fluidics stations, and scanned using the GeneChip® Scanner 3000 7G.
| | Sample_data_processing | Gene expression data were processed in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project. The raw data was normalized using the robust multi-array average (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anders,,Isaksson
| | Sample_contact_email | anders.isaksson@medsci.uu.se
| | Sample_contact_institute | Uppsala Array Platform
| | Sample_contact_address | Akademiska sjukhuset ing61 3tr
| | Sample_contact_city | Uppsala
| | Sample_contact_zip/postal_code | 75185
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM739nnn/GSM739654/suppl/GSM739654.CEL.gz
| | Sample_series_id | GSE29859
| | Sample_data_row_count | 31099
| | |
|
GSM739655 | GPL1355 |
|
CorticalBone+Marrow_ExcessVitA_rep4
|
CorticalBone+Marrow_ExcessVitA
|
breed: Sprague-Dawley
gender: male
age: 8 week
disease status: Hypervitaminosis A
tissue: Humerus, Diaphyseal Cortical Bone including Marrow
|
a24
|
| Sample_geo_accession | GSM739655
| | Sample_status | Public on Dec 21 2011
| | Sample_submission_date | Jun 09 2011
| | Sample_last_update_date | Dec 21 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The rats were divided into two groups, each with 12 animals. They were fed a standard diet containing 12 IU vitamin A/g pellet (“cont”), or a standard diet supplemented with 1700 IU (“Ex. vitA”) vitamin A/g pellet. The vitamin A was added to the pellets in the form of retinyl palmitate and retinyl acetate. After eight days, the rats were euthanized by exsanguinations from the abdominal aorta under Eqvitesin anesthesia (chloral hydrate 182 mg/kg, pentobarbital 41.7 g/kg).
| | Sample_growth_protocol_ch1 | They were acclimatized for one week and kept in groups of three animals and had free access to water and commercial pellet diet (Lactamin R36, Stockholm, Sweden).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Bones were snap-frozen in liquid nitrogen and quickly crushed into a fine powder using a mortar and pestle followed by total RNA extraction with TRI Reagent® (Sigma-Aldrich). For cortical bone without marrow, diaphyseal bones were cut into pieces, vortexed in ice-cold PBS three times for 10 s to remove marrow cells followed by snap-freezing in liquid nitrogen, crushing into a fine powder and RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Sample preparation and processing were performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_hyb_protocol | Hybridization was performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_scan_protocol | The arrays were washed using Affymetrix fluidics stations, and scanned using the GeneChip® Scanner 3000 7G.
| | Sample_data_processing | Gene expression data were processed in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project. The raw data was normalized using the robust multi-array average (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anders,,Isaksson
| | Sample_contact_email | anders.isaksson@medsci.uu.se
| | Sample_contact_institute | Uppsala Array Platform
| | Sample_contact_address | Akademiska sjukhuset ing61 3tr
| | Sample_contact_city | Uppsala
| | Sample_contact_zip/postal_code | 75185
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM739nnn/GSM739655/suppl/GSM739655.CEL.gz
| | Sample_series_id | GSE29859
| | Sample_data_row_count | 31099
| | |
|
GSM739656 | GPL1355 |
|
CorticalBone_Control_rep3
|
CorticalBone_Control
|
breed: Sprague-Dawley
gender: male
age: 8 week
disease status: Control
tissue: Humerus, Diaphyseal Cortical Bone
|
c10
|
| Sample_geo_accession | GSM739656
| | Sample_status | Public on Dec 21 2011
| | Sample_submission_date | Jun 09 2011
| | Sample_last_update_date | Dec 21 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The rats were divided into two groups, each with 12 animals. They were fed a standard diet containing 12 IU vitamin A/g pellet (“cont”), or a standard diet supplemented with 1700 IU (“Ex. vitA”) vitamin A/g pellet. The vitamin A was added to the pellets in the form of retinyl palmitate and retinyl acetate. After eight days, the rats were euthanized by exsanguinations from the abdominal aorta under Eqvitesin anesthesia (chloral hydrate 182 mg/kg, pentobarbital 41.7 g/kg).
| | Sample_growth_protocol_ch1 | They were acclimatized for one week and kept in groups of three animals and had free access to water and commercial pellet diet (Lactamin R36, Stockholm, Sweden).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Bones were snap-frozen in liquid nitrogen and quickly crushed into a fine powder using a mortar and pestle followed by total RNA extraction with TRI Reagent® (Sigma-Aldrich). For cortical bone without marrow, diaphyseal bones were cut into pieces, vortexed in ice-cold PBS three times for 10 s to remove marrow cells followed by snap-freezing in liquid nitrogen, crushing into a fine powder and RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Sample preparation and processing were performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_hyb_protocol | Hybridization was performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_scan_protocol | The arrays were washed using Affymetrix fluidics stations, and scanned using the GeneChip® Scanner 3000 7G.
| | Sample_data_processing | Gene expression data were processed in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project. The raw data was normalized using the robust multi-array average (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anders,,Isaksson
| | Sample_contact_email | anders.isaksson@medsci.uu.se
| | Sample_contact_institute | Uppsala Array Platform
| | Sample_contact_address | Akademiska sjukhuset ing61 3tr
| | Sample_contact_city | Uppsala
| | Sample_contact_zip/postal_code | 75185
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM739nnn/GSM739656/suppl/GSM739656.CEL.gz
| | Sample_series_id | GSE29859
| | Sample_data_row_count | 31099
| | |
|
GSM739657 | GPL1355 |
|
CorticalBone_Control_rep4
|
CorticalBone_Control
|
breed: Sprague-Dawley
gender: male
age: 8 week
disease status: Control
tissue: Humerus, Diaphyseal Cortical Bone
|
c11
|
| Sample_geo_accession | GSM739657
| | Sample_status | Public on Dec 21 2011
| | Sample_submission_date | Jun 09 2011
| | Sample_last_update_date | Dec 21 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The rats were divided into two groups, each with 12 animals. They were fed a standard diet containing 12 IU vitamin A/g pellet (“cont”), or a standard diet supplemented with 1700 IU (“Ex. vitA”) vitamin A/g pellet. The vitamin A was added to the pellets in the form of retinyl palmitate and retinyl acetate. After eight days, the rats were euthanized by exsanguinations from the abdominal aorta under Eqvitesin anesthesia (chloral hydrate 182 mg/kg, pentobarbital 41.7 g/kg).
| | Sample_growth_protocol_ch1 | They were acclimatized for one week and kept in groups of three animals and had free access to water and commercial pellet diet (Lactamin R36, Stockholm, Sweden).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Bones were snap-frozen in liquid nitrogen and quickly crushed into a fine powder using a mortar and pestle followed by total RNA extraction with TRI Reagent® (Sigma-Aldrich). For cortical bone without marrow, diaphyseal bones were cut into pieces, vortexed in ice-cold PBS three times for 10 s to remove marrow cells followed by snap-freezing in liquid nitrogen, crushing into a fine powder and RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Sample preparation and processing were performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_hyb_protocol | Hybridization was performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_scan_protocol | The arrays were washed using Affymetrix fluidics stations, and scanned using the GeneChip® Scanner 3000 7G.
| | Sample_data_processing | Gene expression data were processed in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project. The raw data was normalized using the robust multi-array average (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anders,,Isaksson
| | Sample_contact_email | anders.isaksson@medsci.uu.se
| | Sample_contact_institute | Uppsala Array Platform
| | Sample_contact_address | Akademiska sjukhuset ing61 3tr
| | Sample_contact_city | Uppsala
| | Sample_contact_zip/postal_code | 75185
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM739nnn/GSM739657/suppl/GSM739657.CEL.gz
| | Sample_series_id | GSE29859
| | Sample_data_row_count | 31099
| | |
|
GSM739658 | GPL1355 |
|
CorticalBone+Marrow_Control_rep4
|
CorticalBone+Marrow_Control
|
breed: Sprague-Dawley
gender: male
age: 8 week
disease status: Control
tissue: Humerus, Diaphyseal Cortical Bone including Marrow
|
c12
|
| Sample_geo_accession | GSM739658
| | Sample_status | Public on Dec 21 2011
| | Sample_submission_date | Jun 09 2011
| | Sample_last_update_date | Dec 21 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The rats were divided into two groups, each with 12 animals. They were fed a standard diet containing 12 IU vitamin A/g pellet (“cont”), or a standard diet supplemented with 1700 IU (“Ex. vitA”) vitamin A/g pellet. The vitamin A was added to the pellets in the form of retinyl palmitate and retinyl acetate. After eight days, the rats were euthanized by exsanguinations from the abdominal aorta under Eqvitesin anesthesia (chloral hydrate 182 mg/kg, pentobarbital 41.7 g/kg).
| | Sample_growth_protocol_ch1 | They were acclimatized for one week and kept in groups of three animals and had free access to water and commercial pellet diet (Lactamin R36, Stockholm, Sweden).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Bones were snap-frozen in liquid nitrogen and quickly crushed into a fine powder using a mortar and pestle followed by total RNA extraction with TRI Reagent® (Sigma-Aldrich). For cortical bone without marrow, diaphyseal bones were cut into pieces, vortexed in ice-cold PBS three times for 10 s to remove marrow cells followed by snap-freezing in liquid nitrogen, crushing into a fine powder and RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Sample preparation and processing were performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_hyb_protocol | Hybridization was performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_scan_protocol | The arrays were washed using Affymetrix fluidics stations, and scanned using the GeneChip® Scanner 3000 7G.
| | Sample_data_processing | Gene expression data were processed in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project. The raw data was normalized using the robust multi-array average (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anders,,Isaksson
| | Sample_contact_email | anders.isaksson@medsci.uu.se
| | Sample_contact_institute | Uppsala Array Platform
| | Sample_contact_address | Akademiska sjukhuset ing61 3tr
| | Sample_contact_city | Uppsala
| | Sample_contact_zip/postal_code | 75185
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM739nnn/GSM739658/suppl/GSM739658.CEL.gz
| | Sample_series_id | GSE29859
| | Sample_data_row_count | 31099
| | |
|
GSM739659 | GPL1355 |
|
CorticalBone_Control_rep1
|
CorticalBone_Control
|
breed: Sprague-Dawley
gender: male
age: 8 week
disease status: Control
tissue: Humerus, Diaphyseal Cortical Bone including Marrow
|
c2
|
| Sample_geo_accession | GSM739659
| | Sample_status | Public on Dec 21 2011
| | Sample_submission_date | Jun 09 2011
| | Sample_last_update_date | Dec 21 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The rats were divided into two groups, each with 12 animals. They were fed a standard diet containing 12 IU vitamin A/g pellet (“cont”), or a standard diet supplemented with 1700 IU (“Ex. vitA”) vitamin A/g pellet. The vitamin A was added to the pellets in the form of retinyl palmitate and retinyl acetate. After eight days, the rats were euthanized by exsanguinations from the abdominal aorta under Eqvitesin anesthesia (chloral hydrate 182 mg/kg, pentobarbital 41.7 g/kg).
| | Sample_growth_protocol_ch1 | They were acclimatized for one week and kept in groups of three animals and had free access to water and commercial pellet diet (Lactamin R36, Stockholm, Sweden).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Bones were snap-frozen in liquid nitrogen and quickly crushed into a fine powder using a mortar and pestle followed by total RNA extraction with TRI Reagent® (Sigma-Aldrich). For cortical bone without marrow, diaphyseal bones were cut into pieces, vortexed in ice-cold PBS three times for 10 s to remove marrow cells followed by snap-freezing in liquid nitrogen, crushing into a fine powder and RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Sample preparation and processing were performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_hyb_protocol | Hybridization was performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_scan_protocol | The arrays were washed using Affymetrix fluidics stations, and scanned using the GeneChip® Scanner 3000 7G.
| | Sample_data_processing | Gene expression data were processed in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project. The raw data was normalized using the robust multi-array average (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anders,,Isaksson
| | Sample_contact_email | anders.isaksson@medsci.uu.se
| | Sample_contact_institute | Uppsala Array Platform
| | Sample_contact_address | Akademiska sjukhuset ing61 3tr
| | Sample_contact_city | Uppsala
| | Sample_contact_zip/postal_code | 75185
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM739nnn/GSM739659/suppl/GSM739659.CEL.gz
| | Sample_series_id | GSE29859
| | Sample_data_row_count | 31099
| | |
|
GSM739660 | GPL1355 |
|
CorticalBone+Marrow_Control_rep1
|
CorticalBone+Marrow_Control
|
breed: Sprague-Dawley
gender: male
age: 8 week
disease status: Control
tissue: Humerus, Diaphyseal Cortical Bone
|
c3
|
| Sample_geo_accession | GSM739660
| | Sample_status | Public on Dec 21 2011
| | Sample_submission_date | Jun 09 2011
| | Sample_last_update_date | Dec 21 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The rats were divided into two groups, each with 12 animals. They were fed a standard diet containing 12 IU vitamin A/g pellet (“cont”), or a standard diet supplemented with 1700 IU (“Ex. vitA”) vitamin A/g pellet. The vitamin A was added to the pellets in the form of retinyl palmitate and retinyl acetate. After eight days, the rats were euthanized by exsanguinations from the abdominal aorta under Eqvitesin anesthesia (chloral hydrate 182 mg/kg, pentobarbital 41.7 g/kg).
| | Sample_growth_protocol_ch1 | They were acclimatized for one week and kept in groups of three animals and had free access to water and commercial pellet diet (Lactamin R36, Stockholm, Sweden).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Bones were snap-frozen in liquid nitrogen and quickly crushed into a fine powder using a mortar and pestle followed by total RNA extraction with TRI Reagent® (Sigma-Aldrich). For cortical bone without marrow, diaphyseal bones were cut into pieces, vortexed in ice-cold PBS three times for 10 s to remove marrow cells followed by snap-freezing in liquid nitrogen, crushing into a fine powder and RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Sample preparation and processing were performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_hyb_protocol | Hybridization was performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_scan_protocol | The arrays were washed using Affymetrix fluidics stations, and scanned using the GeneChip® Scanner 3000 7G.
| | Sample_data_processing | Gene expression data were processed in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project. The raw data was normalized using the robust multi-array average (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anders,,Isaksson
| | Sample_contact_email | anders.isaksson@medsci.uu.se
| | Sample_contact_institute | Uppsala Array Platform
| | Sample_contact_address | Akademiska sjukhuset ing61 3tr
| | Sample_contact_city | Uppsala
| | Sample_contact_zip/postal_code | 75185
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM739nnn/GSM739660/suppl/GSM739660.CEL.gz
| | Sample_series_id | GSE29859
| | Sample_data_row_count | 31099
| | |
|
GSM739661 | GPL1355 |
|
CorticalBone+Marrow_Control_rep2
|
CorticalBone+Marrow_Control
|
breed: Sprague-Dawley
gender: male
age: 8 week
disease status: Control
tissue: Humerus, Diaphyseal Cortical Bone including Marrow
|
c4
|
| Sample_geo_accession | GSM739661
| | Sample_status | Public on Dec 21 2011
| | Sample_submission_date | Jun 09 2011
| | Sample_last_update_date | Dec 21 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The rats were divided into two groups, each with 12 animals. They were fed a standard diet containing 12 IU vitamin A/g pellet (“cont”), or a standard diet supplemented with 1700 IU (“Ex. vitA”) vitamin A/g pellet. The vitamin A was added to the pellets in the form of retinyl palmitate and retinyl acetate. After eight days, the rats were euthanized by exsanguinations from the abdominal aorta under Eqvitesin anesthesia (chloral hydrate 182 mg/kg, pentobarbital 41.7 g/kg).
| | Sample_growth_protocol_ch1 | They were acclimatized for one week and kept in groups of three animals and had free access to water and commercial pellet diet (Lactamin R36, Stockholm, Sweden).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Bones were snap-frozen in liquid nitrogen and quickly crushed into a fine powder using a mortar and pestle followed by total RNA extraction with TRI Reagent® (Sigma-Aldrich). For cortical bone without marrow, diaphyseal bones were cut into pieces, vortexed in ice-cold PBS three times for 10 s to remove marrow cells followed by snap-freezing in liquid nitrogen, crushing into a fine powder and RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Sample preparation and processing were performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_hyb_protocol | Hybridization was performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_scan_protocol | The arrays were washed using Affymetrix fluidics stations, and scanned using the GeneChip® Scanner 3000 7G.
| | Sample_data_processing | Gene expression data were processed in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project. The raw data was normalized using the robust multi-array average (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anders,,Isaksson
| | Sample_contact_email | anders.isaksson@medsci.uu.se
| | Sample_contact_institute | Uppsala Array Platform
| | Sample_contact_address | Akademiska sjukhuset ing61 3tr
| | Sample_contact_city | Uppsala
| | Sample_contact_zip/postal_code | 75185
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM739nnn/GSM739661/suppl/GSM739661.CEL.gz
| | Sample_series_id | GSE29859
| | Sample_data_row_count | 31099
| | |
|
GSM739662 | GPL1355 |
|
CorticalBone_Control_rep2
|
CorticalBone_Control
|
breed: Sprague-Dawley
gender: male
age: 8 week
disease status: Control
tissue: Humerus, Diaphyseal Cortical Bone
|
c6
|
| Sample_geo_accession | GSM739662
| | Sample_status | Public on Dec 21 2011
| | Sample_submission_date | Jun 09 2011
| | Sample_last_update_date | Dec 21 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The rats were divided into two groups, each with 12 animals. They were fed a standard diet containing 12 IU vitamin A/g pellet (“cont”), or a standard diet supplemented with 1700 IU (“Ex. vitA”) vitamin A/g pellet. The vitamin A was added to the pellets in the form of retinyl palmitate and retinyl acetate. After eight days, the rats were euthanized by exsanguinations from the abdominal aorta under Eqvitesin anesthesia (chloral hydrate 182 mg/kg, pentobarbital 41.7 g/kg).
| | Sample_growth_protocol_ch1 | They were acclimatized for one week and kept in groups of three animals and had free access to water and commercial pellet diet (Lactamin R36, Stockholm, Sweden).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Bones were snap-frozen in liquid nitrogen and quickly crushed into a fine powder using a mortar and pestle followed by total RNA extraction with TRI Reagent® (Sigma-Aldrich). For cortical bone without marrow, diaphyseal bones were cut into pieces, vortexed in ice-cold PBS three times for 10 s to remove marrow cells followed by snap-freezing in liquid nitrogen, crushing into a fine powder and RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Sample preparation and processing were performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_hyb_protocol | Hybridization was performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_scan_protocol | The arrays were washed using Affymetrix fluidics stations, and scanned using the GeneChip® Scanner 3000 7G.
| | Sample_data_processing | Gene expression data were processed in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project. The raw data was normalized using the robust multi-array average (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anders,,Isaksson
| | Sample_contact_email | anders.isaksson@medsci.uu.se
| | Sample_contact_institute | Uppsala Array Platform
| | Sample_contact_address | Akademiska sjukhuset ing61 3tr
| | Sample_contact_city | Uppsala
| | Sample_contact_zip/postal_code | 75185
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM739nnn/GSM739662/suppl/GSM739662.CEL.gz
| | Sample_series_id | GSE29859
| | Sample_data_row_count | 31099
| | |
|
GSM739663 | GPL1355 |
|
CorticalBone+Marrow_Control_rep3
|
CorticalBone+Marrow_Control
|
breed: Sprague-Dawley
gender: male
age: 8 week
disease status: Control
tissue: Humerus, Diaphyseal Cortical Bone including Marrow
|
c7
|
| Sample_geo_accession | GSM739663
| | Sample_status | Public on Dec 21 2011
| | Sample_submission_date | Jun 09 2011
| | Sample_last_update_date | Dec 21 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The rats were divided into two groups, each with 12 animals. They were fed a standard diet containing 12 IU vitamin A/g pellet (“cont”), or a standard diet supplemented with 1700 IU (“Ex. vitA”) vitamin A/g pellet. The vitamin A was added to the pellets in the form of retinyl palmitate and retinyl acetate. After eight days, the rats were euthanized by exsanguinations from the abdominal aorta under Eqvitesin anesthesia (chloral hydrate 182 mg/kg, pentobarbital 41.7 g/kg).
| | Sample_growth_protocol_ch1 | They were acclimatized for one week and kept in groups of three animals and had free access to water and commercial pellet diet (Lactamin R36, Stockholm, Sweden).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Bones were snap-frozen in liquid nitrogen and quickly crushed into a fine powder using a mortar and pestle followed by total RNA extraction with TRI Reagent® (Sigma-Aldrich). For cortical bone without marrow, diaphyseal bones were cut into pieces, vortexed in ice-cold PBS three times for 10 s to remove marrow cells followed by snap-freezing in liquid nitrogen, crushing into a fine powder and RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Sample preparation and processing were performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_hyb_protocol | Hybridization was performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 1).
| | Sample_scan_protocol | The arrays were washed using Affymetrix fluidics stations, and scanned using the GeneChip® Scanner 3000 7G.
| | Sample_data_processing | Gene expression data were processed in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project. The raw data was normalized using the robust multi-array average (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anders,,Isaksson
| | Sample_contact_email | anders.isaksson@medsci.uu.se
| | Sample_contact_institute | Uppsala Array Platform
| | Sample_contact_address | Akademiska sjukhuset ing61 3tr
| | Sample_contact_city | Uppsala
| | Sample_contact_zip/postal_code | 75185
| | Sample_contact_country | Sweden
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM739nnn/GSM739663/suppl/GSM739663.CEL.gz
| | Sample_series_id | GSE29859
| | Sample_data_row_count | 31099
| | |
|
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