Search results for the GEO ID: GSE6879  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM158579 | GPL341 |
|
CAS-2
|
rat mammary epithelial cells
|
Female Sprague-Dawley rat, postnatal day 50, life-time ingestion of casein based diet (CAS)
|
Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.
|
| Sample_geo_accession | GSM158579
| | Sample_status | Public on Jan 31 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Jan 30 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Pooled RNA (equal amounts of RNA from #4 mammry gland of two animals; 8 ug total) was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool
| | Sample_hyb_protocol | 10 ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat RAE230A GeneChip (3-4 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.
| | Sample_scan_protocol | GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.
| | Sample_data_processing | Value column are raw signal intensity generated from MAS 5.0.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Ying,,Su
| | Sample_contact_email | suying@uams.edu
| | Sample_contact_phone | 501-364-2033
| | Sample_contact_fax | 501-364-3161
| | Sample_contact_department | physiology
| | Sample_contact_institute | UAMS
| | Sample_contact_address | 1120 Marshall St. South Campus
| | 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/GSM158nnn/GSM158579/suppl/GSM158579.CEL.gz
| | Sample_series_id | GSE6879
| | Sample_data_row_count | 15923
| | |
|
GSM158580 | GPL341 |
|
CAS-1
|
rat mammary epithelial cells
|
Female Sprague-Dawley rat, postnatal day 50, life-time ingestion of casein based diet (CAS )
|
Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.
|
| Sample_geo_accession | GSM158580
| | Sample_status | Public on Jan 31 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Jan 30 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Pooled RNA (equal amounts of RNA from #4 mammary gland from 2 animals; 8 ug total) was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool
| | Sample_hyb_protocol | 10 ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat RAE230A GeneChip (3-4chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.
| | Sample_scan_protocol | GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.
| | Sample_data_processing | Value column are raw signal intensity generated from MAS 5.0.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Ying,,Su
| | Sample_contact_email | suying@uams.edu
| | Sample_contact_phone | 501-364-2033
| | Sample_contact_fax | 501-364-3161
| | Sample_contact_department | physiology
| | Sample_contact_institute | UAMS
| | Sample_contact_address | 1120 Marshall St. South Campus
| | 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/GSM158nnn/GSM158580/suppl/GSM158580.CEL.gz
| | Sample_series_id | GSE6879
| | Sample_data_row_count | 15923
| | |
|
GSM158581 | GPL341 |
|
CAS-3
|
rat mammary epithelial cells
|
Female Sprague-Dawley rat, postnatal day 50, life-time ingestion of casein based diet (CAS ) or SPI diet.
|
Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.
|
| Sample_geo_accession | GSM158581
| | Sample_status | Public on Jan 31 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Jan 30 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Pooled RNA (equal amounts of RNA from each of 7 animals; 8 ug total) was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool
| | Sample_hyb_protocol | 10 ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat RAE230 GeneChip (3 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.
| | Sample_scan_protocol | GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.
| | Sample_data_processing | Value column are raw signal intensity generated from MAS 5.0.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Ying,,Su
| | Sample_contact_email | suying@uams.edu
| | Sample_contact_phone | 501-364-2033
| | Sample_contact_fax | 501-364-3161
| | Sample_contact_department | physiology
| | Sample_contact_institute | UAMS
| | Sample_contact_address | 1120 Marshall St. South Campus
| | 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/GSM158nnn/GSM158581/suppl/GSM158581.CEL.gz
| | Sample_series_id | GSE6879
| | Sample_data_row_count | 15923
| | |
|
GSM158582 | GPL341 |
|
SPI-2
|
rat mammary epithelial cells
|
Female Sprague-Dawley rat, postnatal day 50, life-time ingestion of SPI diet.
|
Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.
|
| Sample_geo_accession | GSM158582
| | Sample_status | Public on Jan 31 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Jan 30 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Pooled RNA (equal amounts of RNA from #4 mammary gland from 2 animals; 8 ug total) was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool
| | Sample_hyb_protocol | 10 ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat RAE230 GeneChip (3-4 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.
| | Sample_scan_protocol | GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.
| | Sample_data_processing | Value column are raw signal intensity generated from MAS 5.0.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Ying,,Su
| | Sample_contact_email | suying@uams.edu
| | Sample_contact_phone | 501-364-2033
| | Sample_contact_fax | 501-364-3161
| | Sample_contact_department | physiology
| | Sample_contact_institute | UAMS
| | Sample_contact_address | 1120 Marshall St. South Campus
| | 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/GSM158nnn/GSM158582/suppl/GSM158582.CEL.gz
| | Sample_series_id | GSE6879
| | Sample_data_row_count | 15923
| | |
|
GSM158583 | GPL341 |
|
SPI-3
|
rat mammary epithelial cells
|
Female Sprague-Dawley rat, postnatal day 50, life-time ingestion of casein based SPI diet
|
Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.
|
| Sample_geo_accession | GSM158583
| | Sample_status | Public on Jan 31 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Jan 30 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Pooled RNA (equal amounts of RNA from #4 mammary gland from 2 animals; 8 ug total) was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool
| | Sample_hyb_protocol | 10 ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat RAE230 GeneChip ( 3-4 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.
| | Sample_scan_protocol | GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.
| | Sample_data_processing | Value column are raw signal intensity generated from MAS 5.0.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Ying,,Su
| | Sample_contact_email | suying@uams.edu
| | Sample_contact_phone | 501-364-2033
| | Sample_contact_fax | 501-364-3161
| | Sample_contact_department | physiology
| | Sample_contact_institute | UAMS
| | Sample_contact_address | 1120 Marshall St. South Campus
| | 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/GSM158nnn/GSM158583/suppl/GSM158583.CEL.gz
| | Sample_series_id | GSE6879
| | Sample_data_row_count | 15923
| | |
|
GSM158584 | GPL341 |
|
SPI-4
|
rat mammary epithelial cells
|
Female Sprague-Dawley rat, postnatal day 50, life-time ingestion of casein based diet SPI diet
|
Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.
|
| Sample_geo_accession | GSM158584
| | Sample_status | Public on Jan 31 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Jan 30 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Pooled RNA (equal amounts of RNA from #4 mammary gland of two animals; 8 ug total) was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool.
| | Sample_hyb_protocol | 10 ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat RAE230A GeneChip (3-4 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.
| | Sample_scan_protocol | GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.
| | Sample_data_processing | Value column are raw signal intensity generated from MAS 5.0.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Ying,,Su
| | Sample_contact_email | suying@uams.edu
| | Sample_contact_phone | 501-364-2033
| | Sample_contact_fax | 501-364-3161
| | Sample_contact_department | physiology
| | Sample_contact_institute | UAMS
| | Sample_contact_address | 1120 Marshall St. South Campus
| | 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/GSM158nnn/GSM158584/suppl/GSM158584.CEL.gz
| | Sample_series_id | GSE6879
| | Sample_data_row_count | 15923
| | |
|
GSM158585 | GPL341 |
|
SPI-5
|
rat mammary epithelial cells
|
Female Sprague-Dawley rat, postnatal day 50, life-time ingestion of SPI diet.
|
Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.
|
| Sample_geo_accession | GSM158585
| | Sample_status | Public on Jan 31 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Jan 30 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Pooled RNA (equal amounts of RNA from #4 mammary gland of two animals; 8 ug total) was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool.
| | Sample_hyb_protocol | 10 ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat RAE230A GeneChip (3-4 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.
| | Sample_scan_protocol | GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.
| | Sample_data_processing | Value column are raw signal intensity generated from MAS 5.0.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Ying,,Su
| | Sample_contact_email | suying@uams.edu
| | Sample_contact_phone | 501-364-2033
| | Sample_contact_fax | 501-364-3161
| | Sample_contact_department | physiology
| | Sample_contact_institute | UAMS
| | Sample_contact_address | 1120 Marshall St. South Campus
| | 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/GSM158nnn/GSM158585/suppl/GSM158585.CEL.gz
| | Sample_series_id | GSE6879
| | Sample_data_row_count | 15923
| | |
|
GSM158586 | GPL341 |
|
GEN-1
|
rat mammary epithelial cells
|
Female Sprague-Dawley rat, postnatal day 50, life-time ingestion of casein based diet with addition of Genistein (250mg/kg).
|
Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.
|
| Sample_geo_accession | GSM158586
| | Sample_status | Public on Jan 31 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Jan 30 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Pooled RNA (equal amounts of RNA from #4 mammary gland of two animals; 8 ug total) was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool.
| | Sample_hyb_protocol | 10 ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat RAE230A GeneChip (3-4 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.
| | Sample_scan_protocol | GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.
| | Sample_data_processing | Value column are raw signal intensity generated from MAS 5.0.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Ying,,Su
| | Sample_contact_email | suying@uams.edu
| | Sample_contact_phone | 501-364-2033
| | Sample_contact_fax | 501-364-3161
| | Sample_contact_department | physiology
| | Sample_contact_institute | UAMS
| | Sample_contact_address | 1120 Marshall St. South Campus
| | 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/GSM158nnn/GSM158586/suppl/GSM158586.CEL.gz
| | Sample_series_id | GSE6879
| | Sample_data_row_count | 15923
| | |
|
GSM158587 | GPL341 |
|
GEN-3
|
rat mammary epithelial cells
|
Female Sprague-Dawley rat, postnatal day 50, life-time ingestion of casein based diet with addition of Genistein(250mg/kg).
|
Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.
|
| Sample_geo_accession | GSM158587
| | Sample_status | Public on Jan 31 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Jan 30 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Pooled RNA (equal amounts of RNA from #4 mammary gland of two animals; 8 ug total) was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool.
| | Sample_hyb_protocol | 10 ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat RAE230A GeneChip (3-4 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.
| | Sample_scan_protocol | GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.
| | Sample_data_processing | Value column are raw signal intensity generated from MAS 5.0.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Ying,,Su
| | Sample_contact_email | suying@uams.edu
| | Sample_contact_phone | 501-364-2033
| | Sample_contact_fax | 501-364-3161
| | Sample_contact_department | physiology
| | Sample_contact_institute | UAMS
| | Sample_contact_address | 1120 Marshall St. South Campus
| | 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/GSM158nnn/GSM158587/suppl/GSM158587.CEL.gz
| | Sample_series_id | GSE6879
| | Sample_data_row_count | 15923
| | |
|
GSM158588 | GPL341 |
|
Gen-5
|
rat mammary epithelial cells
|
Female Sprague-Dawley rat, postnatal day 50, life-time ingestion of casein based diet with addition of Genistein (250mg/kg)
|
Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.
|
| Sample_geo_accession | GSM158588
| | Sample_status | Public on Jan 31 2007
| | Sample_submission_date | Jan 26 2007
| | Sample_last_update_date | Jan 30 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Pooled RNA (equal amounts of RNA from #4 mammary gland of two animals; 8 ug total) was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool.
| | Sample_hyb_protocol | 10 ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat RAE230A GeneChip (3-4 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.
| | Sample_scan_protocol | GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.
| | Sample_data_processing | Value column are raw signal intensity generated from MAS 5.0.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Ying,,Su
| | Sample_contact_email | suying@uams.edu
| | Sample_contact_phone | 501-364-2033
| | Sample_contact_fax | 501-364-3161
| | Sample_contact_department | physiology
| | Sample_contact_institute | UAMS
| | Sample_contact_address | 1120 Marshall St. South Campus
| | 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/GSM158nnn/GSM158588/suppl/GSM158588.CEL.gz
| | Sample_series_id | GSE6879
| | Sample_data_row_count | 15923
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Make groups for comparisons |
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| Select GSMs and click on "Add groups" |
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