Search results for the GEO ID: GSE27083  |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM668528 | GPL1261 |
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mammary tissue_Wt control_untreated
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Wild-type group maintained on standard rodent chow
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tissue: mammary gland
genetic background: FVB
genotype: wild type
treatment: untreated
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Gene expression data from FVB wild type mice
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| Sample_geo_accession | GSM668528
| | Sample_status | Public on Feb 05 2011
| | Sample_submission_date | Feb 04 2011
| | Sample_last_update_date | Feb 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice were maintained on standard rodent chow or a diet supplemented with 0.005% GW501516 for 7 days. GW501516 was provided by the Chemoprevention Branch, National Cancer Institute.
| | Sample_growth_protocol_ch1 | All animal studies were conducted under protocols 07-017 and 09-061. Female nulliparious FVB/MMTV-PDK1 mice and age-matched FVB/wild-type littermates used in this study. Numbers of animals per groups were as follows: WT, n=10, WT+GW, n=8, MMTV-PDK1, n=8, MTV-PDK1, n=6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mammary gland tissue was excised and preserved in RNAlater (Ambion) at -20◦C until RNA extraction using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA purity was assessed by an A260/A280 ratio of >1.9, and RNA quality was monitored using a microfluidic nanochip (Agilent). Each cRNA was prepared from equal amounts of RNA (1ug) pooled from 5 mice per group according to the manufacturers protocol (Invitrogen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labelled cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Biotin-labeled cRNA was fragmented at 94°C for 35 min and used for hybridization overnight to an Affymetrix mouse 430A2.0 GeneChip® by the Genomics and Epigenomics Shared Resource, LCCC, Georgetown University.
| | Sample_scan_protocol | The GeneChip® was scanned using an Agilent Gene Array scanner.
| | Sample_data_processing | Raw data generation was performed with the Affymetrix GeneChip® Operating software 1.1. A noise value (Q) based on the variance of low-intensity probe cells was used to calculate a minimum threshold for each GeneChip. Data generated after scanning was subjected to comparison analysis to select change calls at 100% increase or decrease compared with control for each gene. Genes with a signal of <300 in all experimental groups were excluded from analysis.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Robert,I,Glazer
| | Sample_contact_email | glazerr@georgetown.edu
| | Sample_contact_phone | 202-687-8324
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Georgetown University
| | Sample_contact_address | 3970 Reservoir Rd, NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20007
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://explore.georgetown.edu/people/glazerr/?PageTemplateID=208
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM668nnn/GSM668528/suppl/GSM668528_CP1.CEL.gz
| | Sample_series_id | GSE27083
| | Sample_data_row_count | 15833
| | |
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GSM668529 | GPL1261 |
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mammary tissue_Wt treated with GW501516_7 days
|
Wild-type group, maintained on GW501516 supplemented diet
|
tissue: mammary gland
genetic background: FVB
genotype: wild type
treatment: GW501516
|
Gene expression data from FVB wild type mice maintained on a GW501516 supplemented diet for 7 days
|
| Sample_geo_accession | GSM668529
| | Sample_status | Public on Feb 05 2011
| | Sample_submission_date | Feb 04 2011
| | Sample_last_update_date | Feb 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice were maintained on standard rodent chow or a diet supplemented with 0.005% GW501516 for 7 days. GW501516 was provided by the Chemoprevention Branch, National Cancer Institute.
| | Sample_growth_protocol_ch1 | All animal studies were conducted under protocols 07-017 and 09-061. Female nulliparious FVB/MMTV-PDK1 mice and age-matched FVB/wild-type littermates used in this study. Numbers of animals per groups were as follows: WT, n=10, WT+GW, n=8, MMTV-PDK1, n=8, MTV-PDK1, n=6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mammary gland tissue was excised and preserved in RNAlater (Ambion) at -20◦C until RNA extraction using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA purity was assessed by an A260/A280 ratio of >1.9, and RNA quality was monitored using a microfluidic nanochip (Agilent). Each cRNA was prepared from equal amounts of RNA (1ug) pooled from 5 mice per group according to the manufacturers protocol (Invitrogen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labelled cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Biotin-labeled cRNA was fragmented at 94°C for 35 min and used for hybridization overnight to an Affymetrix mouse 430A2.0 GeneChip® by the Genomics and Epigenomics Shared Resource, LCCC, Georgetown University.
| | Sample_scan_protocol | The GeneChip® was scanned using an Agilent Gene Array scanner.
| | Sample_data_processing | Raw data generation was performed with the Affymetrix GeneChip® Operating software 1.1. A noise value (Q) based on the variance of low-intensity probe cells was used to calculate a minimum threshold for each GeneChip. Data generated after scanning was subjected to comparison analysis to select change calls at 100% increase or decrease compared with control for each gene. Genes with a signal of <300 in all experimental groups were excluded from analysis.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Robert,I,Glazer
| | Sample_contact_email | glazerr@georgetown.edu
| | Sample_contact_phone | 202-687-8324
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Georgetown University
| | Sample_contact_address | 3970 Reservoir Rd, NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20007
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://explore.georgetown.edu/people/glazerr/?PageTemplateID=208
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM668nnn/GSM668529/suppl/GSM668529_CP2.CEL.gz
| | Sample_series_id | GSE27083
| | Sample_data_row_count | 15833
| | |
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GSM668530 | GPL1261 |
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mammary tissue_MMTV-PDK1_untreated
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Transgenic group, maintained on standard rodent chow
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tissue: mammary gland
genetic background: FVB
genotype: MMTV-PDK1 transgenic
treatment: untreated
|
Gene expression data from MMTV-PDK1 transgenic mice
|
| Sample_geo_accession | GSM668530
| | Sample_status | Public on Feb 05 2011
| | Sample_submission_date | Feb 04 2011
| | Sample_last_update_date | Feb 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice were maintained on standard rodent chow or a diet supplemented with 0.005% GW501516 for 7 days. GW501516 was provided by the Chemoprevention Branch, National Cancer Institute.
| | Sample_growth_protocol_ch1 | All animal studies were conducted under protocols 07-017 and 09-061. Female nulliparious FVB/MMTV-PDK1 mice and age-matched FVB/wild-type littermates used in this study. Numbers of animals per groups were as follows: WT, n=10, WT+GW, n=8, MMTV-PDK1, n=8, MTV-PDK1, n=6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mammary gland tissue was excised and preserved in RNAlater (Ambion) at -20◦C until RNA extraction using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA purity was assessed by an A260/A280 ratio of >1.9, and RNA quality was monitored using a microfluidic nanochip (Agilent). Each cRNA was prepared from equal amounts of RNA (1ug) pooled from 5 mice per group according to the manufacturers protocol (Invitrogen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labelled cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Biotin-labeled cRNA was fragmented at 94°C for 35 min and used for hybridization overnight to an Affymetrix mouse 430A2.0 GeneChip® by the Genomics and Epigenomics Shared Resource, LCCC, Georgetown University.
| | Sample_scan_protocol | The GeneChip® was scanned using an Agilent Gene Array scanner.
| | Sample_data_processing | Raw data generation was performed with the Affymetrix GeneChip® Operating software 1.1. A noise value (Q) based on the variance of low-intensity probe cells was used to calculate a minimum threshold for each GeneChip. Data generated after scanning was subjected to comparison analysis to select change calls at 100% increase or decrease compared with control for each gene. Genes with a signal of <300 in all experimental groups were excluded from analysis.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Robert,I,Glazer
| | Sample_contact_email | glazerr@georgetown.edu
| | Sample_contact_phone | 202-687-8324
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Georgetown University
| | Sample_contact_address | 3970 Reservoir Rd, NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20007
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://explore.georgetown.edu/people/glazerr/?PageTemplateID=208
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM668nnn/GSM668530/suppl/GSM668530_CP3.CEL.gz
| | Sample_series_id | GSE27083
| | Sample_data_row_count | 15833
| | |
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GSM668531 | GPL1261 |
|
mammary tissue_ MMTV-PDK1 treated with GW501516_7days
|
Transgenic group, maintained on GW501516 supplemented diet
|
tissue: mammary gland
genetic background: FVB
genotype: MMTV-PDK1 transgenic
treatment: GW501516
|
Gene expression data from MMTV-PDK1 transgenic mice maintained on a GW501516 supplemented diet for 7 days
|
| Sample_geo_accession | GSM668531
| | Sample_status | Public on Feb 05 2011
| | Sample_submission_date | Feb 04 2011
| | Sample_last_update_date | Feb 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice were maintained on standard rodent chow or a diet supplemented with 0.005% GW501516 for 7 days. GW501516 was provided by the Chemoprevention Branch, National Cancer Institute.
| | Sample_growth_protocol_ch1 | All animal studies were conducted under protocols 07-017 and 09-061. Female nulliparious FVB/MMTV-PDK1 mice and age-matched FVB/wild-type littermates used in this study. Numbers of animals per groups were as follows: WT, n=10, WT+GW, n=8, MMTV-PDK1, n=8, MTV-PDK1, n=6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Mammary gland tissue was excised and preserved in RNAlater (Ambion) at -20◦C until RNA extraction using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA purity was assessed by an A260/A280 ratio of >1.9, and RNA quality was monitored using a microfluidic nanochip (Agilent). Each cRNA was prepared from equal amounts of RNA (1ug) pooled from 5 mice per group according to the manufacturers protocol (Invitrogen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labelled cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Biotin-labeled cRNA was fragmented at 94°C for 35 min and used for hybridization overnight to an Affymetrix mouse 430A2.0 GeneChip® by the Genomics and Epigenomics Shared Resource, LCCC, Georgetown University.
| | Sample_scan_protocol | The GeneChip® was scanned using an Agilent Gene Array scanner.
| | Sample_data_processing | Raw data generation was performed with the Affymetrix GeneChip® Operating software 1.1. A noise value (Q) based on the variance of low-intensity probe cells was used to calculate a minimum threshold for each GeneChip. Data generated after scanning was subjected to comparison analysis to select change calls at 100% increase or decrease compared with control for each gene. Genes with a signal of <300 in all experimental groups were excluded from analysis.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Robert,I,Glazer
| | Sample_contact_email | glazerr@georgetown.edu
| | Sample_contact_phone | 202-687-8324
| | Sample_contact_department | Oncology
| | Sample_contact_institute | Georgetown University
| | Sample_contact_address | 3970 Reservoir Rd, NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20007
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://explore.georgetown.edu/people/glazerr/?PageTemplateID=208
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM668nnn/GSM668531/suppl/GSM668531_CP4.CEL.gz
| | Sample_series_id | GSE27083
| | Sample_data_row_count | 15833
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