Search results for the GEO ID: GSE30862  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM765613 | GPL1355 |
|
Female-CAS-fed-pool1
|
Female-CAS-fed
|
gender: female
age: postnatal day 34
tissue: bone
diet: casein diet control (CAS)
|
osteogenic gene expression
|
| Sample_geo_accession | GSM765613
| | Sample_status | Public on Jul 15 2012
| | Sample_submission_date | Jul 21 2011
| | Sample_last_update_date | Jul 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Bone tissues after aspiration of bone marrow were collected from rats at sacrifice and flash frozen in liquid nitrogen
| | Sample_growth_protocol_ch1 | Female casein control diet fed rats compared rats fed control diet with 17 beta estrodial, soy protein isolate diet and combination of 17 beta estrodial with soy protein isolate from PND21 to PND34
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total bone RNA was isolated from the casein diet control, control diet with 17 beta estrodial, soy protein isolate and combination 17 beta estrodial with soy protein isolate fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94C. aRNAs were hybridized to an individual Affymetrix GeneChip Porcine arrays (N | 3/treatment) for 16 h at 45C in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring Gx v 7.3. RMA normalization was utilized to generated values using GeneSpring v 7.3.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Kartik,,Shankar
| | Sample_contact_email | shankarkartik@uams.edu
| | Sample_contact_phone | 501 364 2847
| | Sample_contact_fax | 501 364 3161
| | Sample_contact_department | Pharmacology and Toxicology
| | Sample_contact_institute | University of Arkansas for Medical Sciences/Arkansas Childrens Nutrition Center
| | Sample_contact_address | 1120 Marshall Street, Slot 512-20B
| | Sample_contact_city | Little rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM765nnn/GSM765613/suppl/GSM765613.CEL.gz
| | Sample_series_id | GSE30862
| | Sample_data_row_count | 31099
| | |
|
GSM765614 | GPL1355 |
|
Female-CAS-fed-pool2
|
Female-CAS-fed
|
gender: female
age: postnatal day 34
tissue: bone
diet: casein diet control (CAS)
|
osteogenic gene expression
|
| Sample_geo_accession | GSM765614
| | Sample_status | Public on Jul 15 2012
| | Sample_submission_date | Jul 21 2011
| | Sample_last_update_date | Jul 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Bone tissues after aspiration of bone marrow were collected from rats at sacrifice and flash frozen in liquid nitrogen
| | Sample_growth_protocol_ch1 | Female casein control diet fed rats compared rats fed control diet with 17 beta estrodial, soy protein isolate diet and combination of 17 beta estrodial with soy protein isolate from PND21 to PND34
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total bone RNA was isolated from the casein diet control, control diet with 17 beta estrodial, soy protein isolate and combination 17 beta estrodial with soy protein isolate fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94C. aRNAs were hybridized to an individual Affymetrix GeneChip Porcine arrays (N | 3/treatment) for 16 h at 45C in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring Gx v 7.3. RMA normalization was utilized to generated values using GeneSpring v 7.3.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Kartik,,Shankar
| | Sample_contact_email | shankarkartik@uams.edu
| | Sample_contact_phone | 501 364 2847
| | Sample_contact_fax | 501 364 3161
| | Sample_contact_department | Pharmacology and Toxicology
| | Sample_contact_institute | University of Arkansas for Medical Sciences/Arkansas Childrens Nutrition Center
| | Sample_contact_address | 1120 Marshall Street, Slot 512-20B
| | Sample_contact_city | Little rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM765nnn/GSM765614/suppl/GSM765614.CEL.gz
| | Sample_series_id | GSE30862
| | Sample_data_row_count | 31099
| | |
|
GSM765615 | GPL1355 |
|
Female-CAS-fed-pool3
|
Female-CAS-fed
|
gender: female
age: postnatal day 34
tissue: bone
diet: casein diet control (CAS)
|
osteogenic gene expression
|
| Sample_geo_accession | GSM765615
| | Sample_status | Public on Jul 15 2012
| | Sample_submission_date | Jul 21 2011
| | Sample_last_update_date | Jul 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Bone tissues after aspiration of bone marrow were collected from rats at sacrifice and flash frozen in liquid nitrogen
| | Sample_growth_protocol_ch1 | Female casein control diet fed rats compared rats fed control diet with 17 beta estrodial, soy protein isolate diet and combination of 17 beta estrodial with soy protein isolate from PND21 to PND34
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total bone RNA was isolated from the casein diet control, control diet with 17 beta estrodial, soy protein isolate and combination 17 beta estrodial with soy protein isolate fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94C. aRNAs were hybridized to an individual Affymetrix GeneChip Porcine arrays (N | 3/treatment) for 16 h at 45C in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring Gx v 7.3. RMA normalization was utilized to generated values using GeneSpring v 7.3.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Kartik,,Shankar
| | Sample_contact_email | shankarkartik@uams.edu
| | Sample_contact_phone | 501 364 2847
| | Sample_contact_fax | 501 364 3161
| | Sample_contact_department | Pharmacology and Toxicology
| | Sample_contact_institute | University of Arkansas for Medical Sciences/Arkansas Childrens Nutrition Center
| | Sample_contact_address | 1120 Marshall Street, Slot 512-20B
| | Sample_contact_city | Little rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM765nnn/GSM765615/suppl/GSM765615.CEL.gz
| | Sample_series_id | GSE30862
| | Sample_data_row_count | 31099
| | |
|
GSM765616 | GPL1355 |
|
Female-SPI-fed-pool1
|
Female-SPI-fed
|
gender: female
age: postnatal day 34
tissue: bone
diet: soy protein isolate (SPI)
|
osteogenic gene expression
|
| Sample_geo_accession | GSM765616
| | Sample_status | Public on Jul 15 2012
| | Sample_submission_date | Jul 21 2011
| | Sample_last_update_date | Jul 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Bone tissues after aspiration of bone marrow were collected from rats at sacrifice and flash frozen in liquid nitrogen
| | Sample_growth_protocol_ch1 | Female casein control diet fed rats compared rats fed control diet with 17 beta estrodial, soy protein isolate diet and combination of 17 beta estrodial with soy protein isolate from PND21 to PND34
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total bone RNA was isolated from the casein diet control, control diet with 17 beta estrodial, soy protein isolate and combination 17 beta estrodial with soy protein isolate fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94C. aRNAs were hybridized to an individual Affymetrix GeneChip Porcine arrays (N | 3/treatment) for 16 h at 45C in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring Gx v 7.3. RMA normalization was utilized to generated values using GeneSpring v 7.3.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Kartik,,Shankar
| | Sample_contact_email | shankarkartik@uams.edu
| | Sample_contact_phone | 501 364 2847
| | Sample_contact_fax | 501 364 3161
| | Sample_contact_department | Pharmacology and Toxicology
| | Sample_contact_institute | University of Arkansas for Medical Sciences/Arkansas Childrens Nutrition Center
| | Sample_contact_address | 1120 Marshall Street, Slot 512-20B
| | Sample_contact_city | Little rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM765nnn/GSM765616/suppl/GSM765616.CEL.gz
| | Sample_series_id | GSE30862
| | Sample_data_row_count | 31099
| | |
|
GSM765617 | GPL1355 |
|
Female-SPI-fed-pool2
|
Female-SPI-fed
|
gender: female
age: postnatal day 34
tissue: bone
diet: soy protein isolate (SPI)
|
osteogenic gene expression
|
| Sample_geo_accession | GSM765617
| | Sample_status | Public on Jul 15 2012
| | Sample_submission_date | Jul 21 2011
| | Sample_last_update_date | Jul 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Bone tissues after aspiration of bone marrow were collected from rats at sacrifice and flash frozen in liquid nitrogen
| | Sample_growth_protocol_ch1 | Female casein control diet fed rats compared rats fed control diet with 17 beta estrodial, soy protein isolate diet and combination of 17 beta estrodial with soy protein isolate from PND21 to PND34
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total bone RNA was isolated from the casein diet control, control diet with 17 beta estrodial, soy protein isolate and combination 17 beta estrodial with soy protein isolate fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94C. aRNAs were hybridized to an individual Affymetrix GeneChip Porcine arrays (N | 3/treatment) for 16 h at 45C in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring Gx v 7.3. RMA normalization was utilized to generated values using GeneSpring v 7.3.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Kartik,,Shankar
| | Sample_contact_email | shankarkartik@uams.edu
| | Sample_contact_phone | 501 364 2847
| | Sample_contact_fax | 501 364 3161
| | Sample_contact_department | Pharmacology and Toxicology
| | Sample_contact_institute | University of Arkansas for Medical Sciences/Arkansas Childrens Nutrition Center
| | Sample_contact_address | 1120 Marshall Street, Slot 512-20B
| | Sample_contact_city | Little rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM765nnn/GSM765617/suppl/GSM765617.CEL.gz
| | Sample_series_id | GSE30862
| | Sample_data_row_count | 31099
| | |
|
GSM765618 | GPL1355 |
|
Female-SPI-fed-pool3
|
Female-SPI-fed
|
gender: female
age: postnatal day 34
tissue: bone
diet: soy protein isolate (SPI)
|
osteogenic gene expression
|
| Sample_geo_accession | GSM765618
| | Sample_status | Public on Jul 15 2012
| | Sample_submission_date | Jul 21 2011
| | Sample_last_update_date | Jul 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Bone tissues after aspiration of bone marrow were collected from rats at sacrifice and flash frozen in liquid nitrogen
| | Sample_growth_protocol_ch1 | Female casein control diet fed rats compared rats fed control diet with 17 beta estrodial, soy protein isolate diet and combination of 17 beta estrodial with soy protein isolate from PND21 to PND34
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total bone RNA was isolated from the casein diet control, control diet with 17 beta estrodial, soy protein isolate and combination 17 beta estrodial with soy protein isolate fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94C. aRNAs were hybridized to an individual Affymetrix GeneChip Porcine arrays (N | 3/treatment) for 16 h at 45C in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring Gx v 7.3. RMA normalization was utilized to generated values using GeneSpring v 7.3.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Kartik,,Shankar
| | Sample_contact_email | shankarkartik@uams.edu
| | Sample_contact_phone | 501 364 2847
| | Sample_contact_fax | 501 364 3161
| | Sample_contact_department | Pharmacology and Toxicology
| | Sample_contact_institute | University of Arkansas for Medical Sciences/Arkansas Childrens Nutrition Center
| | Sample_contact_address | 1120 Marshall Street, Slot 512-20B
| | Sample_contact_city | Little rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM765nnn/GSM765618/suppl/GSM765618.CEL.gz
| | Sample_series_id | GSE30862
| | Sample_data_row_count | 31099
| | |
|
GSM765619 | GPL1355 |
|
Female-E2-fed-pool1
|
Female-E2-fed
|
gender: female
age: postnatal day 34
tissue: bone
diet: 17 beta estrodial (E2)
|
osteogenic gene expression
|
| Sample_geo_accession | GSM765619
| | Sample_status | Public on Jul 15 2012
| | Sample_submission_date | Jul 21 2011
| | Sample_last_update_date | Jul 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Bone tissues after aspiration of bone marrow were collected from rats at sacrifice and flash frozen in liquid nitrogen
| | Sample_growth_protocol_ch1 | Female casein control diet fed rats compared rats fed control diet with 17 beta estrodial, soy protein isolate diet and combination of 17 beta estrodial with soy protein isolate from PND21 to PND34
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total bone RNA was isolated from the casein diet control, control diet with 17 beta estrodial, soy protein isolate and combination 17 beta estrodial with soy protein isolate fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94C. aRNAs were hybridized to an individual Affymetrix GeneChip Porcine arrays (N | 3/treatment) for 16 h at 45C in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring Gx v 7.3. RMA normalization was utilized to generated values using GeneSpring v 7.3.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Kartik,,Shankar
| | Sample_contact_email | shankarkartik@uams.edu
| | Sample_contact_phone | 501 364 2847
| | Sample_contact_fax | 501 364 3161
| | Sample_contact_department | Pharmacology and Toxicology
| | Sample_contact_institute | University of Arkansas for Medical Sciences/Arkansas Childrens Nutrition Center
| | Sample_contact_address | 1120 Marshall Street, Slot 512-20B
| | Sample_contact_city | Little rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM765nnn/GSM765619/suppl/GSM765619.CEL.gz
| | Sample_series_id | GSE30862
| | Sample_data_row_count | 31099
| | |
|
GSM765620 | GPL1355 |
|
Female-E2-fed-pool2
|
Female-E2-fed
|
gender: female
age: postnatal day 34
tissue: bone
diet: 17 beta estrodial (E2)
|
osteogenic gene expression
|
| Sample_geo_accession | GSM765620
| | Sample_status | Public on Jul 15 2012
| | Sample_submission_date | Jul 21 2011
| | Sample_last_update_date | Jul 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Bone tissues after aspiration of bone marrow were collected from rats at sacrifice and flash frozen in liquid nitrogen
| | Sample_growth_protocol_ch1 | Female casein control diet fed rats compared rats fed control diet with 17 beta estrodial, soy protein isolate diet and combination of 17 beta estrodial with soy protein isolate from PND21 to PND34
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total bone RNA was isolated from the casein diet control, control diet with 17 beta estrodial, soy protein isolate and combination 17 beta estrodial with soy protein isolate fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94C. aRNAs were hybridized to an individual Affymetrix GeneChip Porcine arrays (N | 3/treatment) for 16 h at 45C in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring Gx v 7.3. RMA normalization was utilized to generated values using GeneSpring v 7.3.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Kartik,,Shankar
| | Sample_contact_email | shankarkartik@uams.edu
| | Sample_contact_phone | 501 364 2847
| | Sample_contact_fax | 501 364 3161
| | Sample_contact_department | Pharmacology and Toxicology
| | Sample_contact_institute | University of Arkansas for Medical Sciences/Arkansas Childrens Nutrition Center
| | Sample_contact_address | 1120 Marshall Street, Slot 512-20B
| | Sample_contact_city | Little rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM765nnn/GSM765620/suppl/GSM765620.CEL.gz
| | Sample_series_id | GSE30862
| | Sample_data_row_count | 31099
| | |
|
GSM765621 | GPL1355 |
|
Female-E2-fed-pool3
|
Female-E2-fed
|
gender: female
age: postnatal day 34
tissue: bone
diet: 17 beta estrodial (E2)
|
osteogenic gene expression
|
| Sample_geo_accession | GSM765621
| | Sample_status | Public on Jul 15 2012
| | Sample_submission_date | Jul 21 2011
| | Sample_last_update_date | Jul 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Bone tissues after aspiration of bone marrow were collected from rats at sacrifice and flash frozen in liquid nitrogen
| | Sample_growth_protocol_ch1 | Female casein control diet fed rats compared rats fed control diet with 17 beta estrodial, soy protein isolate diet and combination of 17 beta estrodial with soy protein isolate from PND21 to PND34
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total bone RNA was isolated from the casein diet control, control diet with 17 beta estrodial, soy protein isolate and combination 17 beta estrodial with soy protein isolate fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94C. aRNAs were hybridized to an individual Affymetrix GeneChip Porcine arrays (N | 3/treatment) for 16 h at 45C in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring Gx v 7.3. RMA normalization was utilized to generated values using GeneSpring v 7.3.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Kartik,,Shankar
| | Sample_contact_email | shankarkartik@uams.edu
| | Sample_contact_phone | 501 364 2847
| | Sample_contact_fax | 501 364 3161
| | Sample_contact_department | Pharmacology and Toxicology
| | Sample_contact_institute | University of Arkansas for Medical Sciences/Arkansas Childrens Nutrition Center
| | Sample_contact_address | 1120 Marshall Street, Slot 512-20B
| | Sample_contact_city | Little rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM765nnn/GSM765621/suppl/GSM765621.CEL.gz
| | Sample_series_id | GSE30862
| | Sample_data_row_count | 31099
| | |
|
GSM765622 | GPL1355 |
|
Female-SPI+E2-fed-pool1
|
Female-SPI+E2-fed
|
gender: female
age: postnatal day 34
tissue: bone
diet: combination of 17 beta estrodial with soy protein isolate (SPI+E2)
|
osteogenic gene expression
|
| Sample_geo_accession | GSM765622
| | Sample_status | Public on Jul 15 2012
| | Sample_submission_date | Jul 21 2011
| | Sample_last_update_date | Jul 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Bone tissues after aspiration of bone marrow were collected from rats at sacrifice and flash frozen in liquid nitrogen
| | Sample_growth_protocol_ch1 | Female casein control diet fed rats compared rats fed control diet with 17 beta estrodial, soy protein isolate diet and combination of 17 beta estrodial with soy protein isolate from PND21 to PND34
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total bone RNA was isolated from the casein diet control, control diet with 17 beta estrodial, soy protein isolate and combination 17 beta estrodial with soy protein isolate fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94C. aRNAs were hybridized to an individual Affymetrix GeneChip Porcine arrays (N | 3/treatment) for 16 h at 45C in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring Gx v 7.3. RMA normalization was utilized to generated values using GeneSpring v 7.3.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Kartik,,Shankar
| | Sample_contact_email | shankarkartik@uams.edu
| | Sample_contact_phone | 501 364 2847
| | Sample_contact_fax | 501 364 3161
| | Sample_contact_department | Pharmacology and Toxicology
| | Sample_contact_institute | University of Arkansas for Medical Sciences/Arkansas Childrens Nutrition Center
| | Sample_contact_address | 1120 Marshall Street, Slot 512-20B
| | Sample_contact_city | Little rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM765nnn/GSM765622/suppl/GSM765622.CEL.gz
| | Sample_series_id | GSE30862
| | Sample_data_row_count | 31099
| | |
|
GSM765623 | GPL1355 |
|
Female-SPI+E2-fed-pool2
|
Female-SPI+E2-fed
|
gender: female
age: postnatal day 34
tissue: bone
diet: combination of 17 beta estrodial with soy protein isolate (SPI+E2)
|
osteogenic gene expression
|
| Sample_geo_accession | GSM765623
| | Sample_status | Public on Jul 15 2012
| | Sample_submission_date | Jul 21 2011
| | Sample_last_update_date | Jul 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Bone tissues after aspiration of bone marrow were collected from rats at sacrifice and flash frozen in liquid nitrogen
| | Sample_growth_protocol_ch1 | Female casein control diet fed rats compared rats fed control diet with 17 beta estrodial, soy protein isolate diet and combination of 17 beta estrodial with soy protein isolate from PND21 to PND34
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total bone RNA was isolated from the casein diet control, control diet with 17 beta estrodial, soy protein isolate and combination 17 beta estrodial with soy protein isolate fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94C. aRNAs were hybridized to an individual Affymetrix GeneChip Porcine arrays (N | 3/treatment) for 16 h at 45C in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring Gx v 7.3. RMA normalization was utilized to generated values using GeneSpring v 7.3.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Kartik,,Shankar
| | Sample_contact_email | shankarkartik@uams.edu
| | Sample_contact_phone | 501 364 2847
| | Sample_contact_fax | 501 364 3161
| | Sample_contact_department | Pharmacology and Toxicology
| | Sample_contact_institute | University of Arkansas for Medical Sciences/Arkansas Childrens Nutrition Center
| | Sample_contact_address | 1120 Marshall Street, Slot 512-20B
| | Sample_contact_city | Little rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM765nnn/GSM765623/suppl/GSM765623.CEL.gz
| | Sample_series_id | GSE30862
| | Sample_data_row_count | 31099
| | |
|
GSM765624 | GPL1355 |
|
Female-SPI+E2-fed-pool3
|
Female-SPI+E2-fed
|
gender: female
age: postnatal day 34
tissue: bone
diet: combination of 17 beta estrodial with soy protein isolate (SPI+E2)
|
osteogenic gene expression
|
| Sample_geo_accession | GSM765624
| | Sample_status | Public on Jul 15 2012
| | Sample_submission_date | Jul 21 2011
| | Sample_last_update_date | Jul 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Bone tissues after aspiration of bone marrow were collected from rats at sacrifice and flash frozen in liquid nitrogen
| | Sample_growth_protocol_ch1 | Female casein control diet fed rats compared rats fed control diet with 17 beta estrodial, soy protein isolate diet and combination of 17 beta estrodial with soy protein isolate from PND21 to PND34
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total bone RNA was isolated from the casein diet control, control diet with 17 beta estrodial, soy protein isolate and combination 17 beta estrodial with soy protein isolate fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First- and second- strand cDNA synthesis (from 8 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions
| | Sample_hyb_protocol = Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94C. aRNAs were hybridized to an individual Affymetrix GeneChip Porcine arrays (N | 3/treatment) for 16 h at 45C in the hybridization oven set at 60 rpm.
| | Sample_scan_protocol | The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were generated using GCOS and utilized for analysis using GeneSpring Gx v 7.3. RMA normalization was utilized to generated values using GeneSpring v 7.3.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Kartik,,Shankar
| | Sample_contact_email | shankarkartik@uams.edu
| | Sample_contact_phone | 501 364 2847
| | Sample_contact_fax | 501 364 3161
| | Sample_contact_department | Pharmacology and Toxicology
| | Sample_contact_institute | University of Arkansas for Medical Sciences/Arkansas Childrens Nutrition Center
| | Sample_contact_address | 1120 Marshall Street, Slot 512-20B
| | Sample_contact_city | Little rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM765nnn/GSM765624/suppl/GSM765624.CEL.gz
| | Sample_series_id | GSE30862
| | Sample_data_row_count | 31099
| | |
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