Search results for the GEO ID: GSE38060  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM933271 | GPL1355 |
|
Casein-pool1
|
postnatal day 64-rat mammary gland
|
diet: Casein
gender: female
strain: Sprague-Dawley
|
hepatic gene expression
|
| Sample_geo_accession | GSM933271
| | Sample_status | Public on May 22 2012
| | Sample_submission_date | May 20 2012
| | Sample_last_update_date | May 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Groups of female rats were fed casein or soy protein isolate from post-natal day (PND) 30 until PND 64. On PND 50 all rats were ovariectomized and half of each group underwent E2 replacement via a mini-osmotic pump. At sacrifice (PND 64) abdominal mammary gland pairs were collected and fresh frozen in liquid nitrogen..
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mammary gland pairs were collected and fresh frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total mammary glands RNA was isolated from the 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 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC 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 v 11.0.2.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM933nnn/GSM933271/suppl/GSM933271_Pool1.CEL.gz
| | Sample_series_id | GSE38060
| | Sample_data_row_count | 31099
| | |
|
GSM933272 | GPL1355 |
|
Casein-pool2
|
postnatal day 64-rat mammary gland
|
diet: Casein
gender: female
strain: Sprague-Dawley
|
hepatic gene expression
|
| Sample_geo_accession | GSM933272
| | Sample_status | Public on May 22 2012
| | Sample_submission_date | May 20 2012
| | Sample_last_update_date | May 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Groups of female rats were fed casein or soy protein isolate from post-natal day (PND) 30 until PND 64. On PND 50 all rats were ovariectomized and half of each group underwent E2 replacement via a mini-osmotic pump. At sacrifice (PND 64) abdominal mammary gland pairs were collected and fresh frozen in liquid nitrogen..
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mammary gland pairs were collected and fresh frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total mammary glands RNA was isolated from the 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 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC 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 v 11.0.2.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM933nnn/GSM933272/suppl/GSM933272_Pool2.CEL.gz
| | Sample_series_id | GSE38060
| | Sample_data_row_count | 31099
| | |
|
GSM933273 | GPL1355 |
|
Casein-pool3
|
postnatal day 64-rat mammary gland
|
diet: Casein
gender: female
strain: Sprague-Dawley
|
hepatic gene expression
|
| Sample_geo_accession | GSM933273
| | Sample_status | Public on May 22 2012
| | Sample_submission_date | May 20 2012
| | Sample_last_update_date | May 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Groups of female rats were fed casein or soy protein isolate from post-natal day (PND) 30 until PND 64. On PND 50 all rats were ovariectomized and half of each group underwent E2 replacement via a mini-osmotic pump. At sacrifice (PND 64) abdominal mammary gland pairs were collected and fresh frozen in liquid nitrogen..
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mammary gland pairs were collected and fresh frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total mammary glands RNA was isolated from the 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 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC 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 v 11.0.2.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM933nnn/GSM933273/suppl/GSM933273_Pool3.CEL.gz
| | Sample_series_id | GSE38060
| | Sample_data_row_count | 31099
| | |
|
GSM933274 | GPL1355 |
|
Estradiol-pool1
|
postnatal day 64-rat mammary gland
|
diet: 17-b estradiol
gender: female
strain: Sprague-Dawley
|
hepatic gene expression
|
| Sample_geo_accession | GSM933274
| | Sample_status | Public on May 22 2012
| | Sample_submission_date | May 20 2012
| | Sample_last_update_date | May 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Groups of female rats were fed casein or soy protein isolate from post-natal day (PND) 30 until PND 64. On PND 50 all rats were ovariectomized and half of each group underwent E2 replacement via a mini-osmotic pump. At sacrifice (PND 64) abdominal mammary gland pairs were collected and fresh frozen in liquid nitrogen..
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mammary gland pairs were collected and fresh frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total mammary glands RNA was isolated from the 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 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC 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 v 11.0.2.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM933nnn/GSM933274/suppl/GSM933274_Pool4.CEL.gz
| | Sample_series_id | GSE38060
| | Sample_data_row_count | 31099
| | |
|
GSM933275 | GPL1355 |
|
Estradiol-pool2
|
postnatal day 64-rat mammary gland
|
diet: 17-b estradiol
gender: female
strain: Sprague-Dawley
|
hepatic gene expression
|
| Sample_geo_accession | GSM933275
| | Sample_status | Public on May 22 2012
| | Sample_submission_date | May 20 2012
| | Sample_last_update_date | May 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Groups of female rats were fed casein or soy protein isolate from post-natal day (PND) 30 until PND 64. On PND 50 all rats were ovariectomized and half of each group underwent E2 replacement via a mini-osmotic pump. At sacrifice (PND 64) abdominal mammary gland pairs were collected and fresh frozen in liquid nitrogen..
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mammary gland pairs were collected and fresh frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total mammary glands RNA was isolated from the 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 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC 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 v 11.0.2.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM933nnn/GSM933275/suppl/GSM933275_Pool5.CEL.gz
| | Sample_series_id | GSE38060
| | Sample_data_row_count | 31099
| | |
|
GSM933276 | GPL1355 |
|
Estradiol-pool3
|
postnatal day 64-rat mammary gland
|
diet: 17-b estradiol
gender: female
strain: Sprague-Dawley
|
hepatic gene expression
|
| Sample_geo_accession | GSM933276
| | Sample_status | Public on May 22 2012
| | Sample_submission_date | May 20 2012
| | Sample_last_update_date | May 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Groups of female rats were fed casein or soy protein isolate from post-natal day (PND) 30 until PND 64. On PND 50 all rats were ovariectomized and half of each group underwent E2 replacement via a mini-osmotic pump. At sacrifice (PND 64) abdominal mammary gland pairs were collected and fresh frozen in liquid nitrogen..
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mammary gland pairs were collected and fresh frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total mammary glands RNA was isolated from the 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 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC 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 v 11.0.2.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM933nnn/GSM933276/suppl/GSM933276_Pool6.CEL.gz
| | Sample_series_id | GSE38060
| | Sample_data_row_count | 31099
| | |
|
GSM933277 | GPL1355 |
|
Soy-pool1
|
postnatal day 64-rat mammary gland
|
diet: Soy protein isolate
gender: female
strain: Sprague-Dawley
|
hepatic gene expression
|
| Sample_geo_accession | GSM933277
| | Sample_status | Public on May 22 2012
| | Sample_submission_date | May 20 2012
| | Sample_last_update_date | May 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Groups of female rats were fed casein or soy protein isolate from post-natal day (PND) 30 until PND 64. On PND 50 all rats were ovariectomized and half of each group underwent E2 replacement via a mini-osmotic pump. At sacrifice (PND 64) abdominal mammary gland pairs were collected and fresh frozen in liquid nitrogen..
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mammary gland pairs were collected and fresh frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total mammary glands RNA was isolated from the 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 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC 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 v 11.0.2.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM933nnn/GSM933277/suppl/GSM933277_Pool7.CEL.gz
| | Sample_series_id | GSE38060
| | Sample_data_row_count | 31099
| | |
|
GSM933278 | GPL1355 |
|
Soy-pool2
|
postnatal day 64-rat mammary gland
|
diet: Soy protein isolate
gender: female
strain: Sprague-Dawley
|
hepatic gene expression
|
| Sample_geo_accession | GSM933278
| | Sample_status | Public on May 22 2012
| | Sample_submission_date | May 20 2012
| | Sample_last_update_date | May 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Groups of female rats were fed casein or soy protein isolate from post-natal day (PND) 30 until PND 64. On PND 50 all rats were ovariectomized and half of each group underwent E2 replacement via a mini-osmotic pump. At sacrifice (PND 64) abdominal mammary gland pairs were collected and fresh frozen in liquid nitrogen..
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mammary gland pairs were collected and fresh frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total mammary glands RNA was isolated from the 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 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC 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 v 11.0.2.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM933nnn/GSM933278/suppl/GSM933278_Pool8.CEL.gz
| | Sample_series_id | GSE38060
| | Sample_data_row_count | 31099
| | |
|
GSM933279 | GPL1355 |
|
Soy-pool3
|
postnatal day 64-rat mammary gland
|
diet: Soy protein isolate
gender: female
strain: Sprague-Dawley
|
hepatic gene expression
|
| Sample_geo_accession | GSM933279
| | Sample_status | Public on May 22 2012
| | Sample_submission_date | May 20 2012
| | Sample_last_update_date | May 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Groups of female rats were fed casein or soy protein isolate from post-natal day (PND) 30 until PND 64. On PND 50 all rats were ovariectomized and half of each group underwent E2 replacement via a mini-osmotic pump. At sacrifice (PND 64) abdominal mammary gland pairs were collected and fresh frozen in liquid nitrogen..
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mammary gland pairs were collected and fresh frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total mammary glands RNA was isolated from the 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 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC 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 v 11.0.2.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM933nnn/GSM933279/suppl/GSM933279_Pool9.CEL.gz
| | Sample_series_id | GSE38060
| | Sample_data_row_count | 31099
| | |
|
GSM933280 | GPL1355 |
|
Estradiol-Soy-pool1
|
postnatal day 64-rat mammary gland
|
diet: 17-b estradiol and SPI
gender: female
strain: Sprague-Dawley
|
hepatic gene expression
|
| Sample_geo_accession | GSM933280
| | Sample_status | Public on May 22 2012
| | Sample_submission_date | May 20 2012
| | Sample_last_update_date | May 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Groups of female rats were fed casein or soy protein isolate from post-natal day (PND) 30 until PND 64. On PND 50 all rats were ovariectomized and half of each group underwent E2 replacement via a mini-osmotic pump. At sacrifice (PND 64) abdominal mammary gland pairs were collected and fresh frozen in liquid nitrogen..
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mammary gland pairs were collected and fresh frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total mammary glands RNA was isolated from the 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 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC 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 v 11.0.2.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM933nnn/GSM933280/suppl/GSM933280_Pool10.CEL.gz
| | Sample_series_id | GSE38060
| | Sample_data_row_count | 31099
| | |
|
GSM933281 | GPL1355 |
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Estradiol-Soy-pool2
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postnatal day 64-rat mammary gland
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diet: 17-b estradiol and SPI
gender: female
strain: Sprague-Dawley
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hepatic gene expression
|
| Sample_geo_accession | GSM933281
| | Sample_status | Public on May 22 2012
| | Sample_submission_date | May 20 2012
| | Sample_last_update_date | May 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Groups of female rats were fed casein or soy protein isolate from post-natal day (PND) 30 until PND 64. On PND 50 all rats were ovariectomized and half of each group underwent E2 replacement via a mini-osmotic pump. At sacrifice (PND 64) abdominal mammary gland pairs were collected and fresh frozen in liquid nitrogen..
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mammary gland pairs were collected and fresh frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total mammary glands RNA was isolated from the 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 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC 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 v 11.0.2.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM933nnn/GSM933281/suppl/GSM933281_Pool11.CEL.gz
| | Sample_series_id | GSE38060
| | Sample_data_row_count | 31099
| | |
|
GSM933282 | GPL1355 |
|
Estradiol-Soy-pool3
|
postnatal day 64-rat mammary gland
|
diet: 17-b estradiol and SPI
gender: female
strain: Sprague-Dawley
|
hepatic gene expression
|
| Sample_geo_accession | GSM933282
| | Sample_status | Public on May 22 2012
| | Sample_submission_date | May 20 2012
| | Sample_last_update_date | May 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Groups of female rats were fed casein or soy protein isolate from post-natal day (PND) 30 until PND 64. On PND 50 all rats were ovariectomized and half of each group underwent E2 replacement via a mini-osmotic pump. At sacrifice (PND 64) abdominal mammary gland pairs were collected and fresh frozen in liquid nitrogen..
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mammary gland pairs were collected and fresh frozen in liquid nitrogen.
| | Sample_extract_protocol_ch1 | Total mammary glands RNA was isolated from the 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 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat arrays (N | 3/treatment) for 16 h at 45ºC 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 v 11.0.2.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Horacio,,Gomez-Acevedo
| | Sample_contact_email | gomezacevedohoracio@uams.edu
| | Sample_contact_institute | Arkansas Children's Nutrition Center
| | Sample_contact_address | 15 Children's Way
| | Sample_contact_city | Little Rock
| | Sample_contact_state | Arkansas
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM933nnn/GSM933282/suppl/GSM933282_Pool12.CEL.gz
| | Sample_series_id | GSE38060
| | Sample_data_row_count | 31099
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