Search results for the GEO ID: GSE48884  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1186322 | GPL1261 |
|
Mouse mammary gland Ccnd1+/+ Vehicle Rep1
|
mammary gland_Ccnd1+/+_Vehicle
|
strain background: C57BL/6
genotype/variation: Ccnd1+/+
treated with: placebo control
tissue: mouse mammary gland
|
|
| Sample_geo_accession | GSM1186322
| | Sample_status | Public on Jul 16 2013
| | Sample_submission_date | Jul 15 2013
| | Sample_last_update_date | Jul 16 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Virgin Ccnd1-/- and Ccnd1+/+ mice were overiectomized and allowed to recover for 2 after the surgery. Mice from each genotype split into 2 groups and treated with placebo control or estradiol releasing pelles (0.72mg, 60 day release). Mice were treated for 7 days and then sacrifised.
| | Sample_growth_protocol_ch1 | No specific growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix)
| | Sample_hyb_protocol | 15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module, followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.
| | Sample_data_processing | The data were analyzed and normalized by Robust Multi-array Average (RMA) algorithm using affylmGUI (1.14.0) running limma version 2.9.16 within the language and environment program R (2.4.1).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Mathew,Casimiro,Casimiro
| | Sample_contact_laboratory | Philadelphia
| | Sample_contact_department | 233 South 10th St, Rm 1035
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 South 10th St, Rm 1035
| | Sample_contact_city | 19107
| | Sample_contact_state | United States
| | Sample_contact_zip/postal_code | Mathew Casimiro
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1186nnn/GSM1186322/suppl/GSM1186322_333WTP.CEL.gz
| | Sample_series_id | GSE48884
| | Sample_data_row_count | 45101
| | |
|
GSM1186323 | GPL1261 |
|
Mouse mammary gland Ccnd1+/+ Vehicle Rep2
|
mammary gland_Ccnd1+/+_Vehicle
|
strain background: C57BL/6
genotype/variation: Ccnd1+/+
treated with: placebo control
tissue: mouse mammary gland
|
|
| Sample_geo_accession | GSM1186323
| | Sample_status | Public on Jul 16 2013
| | Sample_submission_date | Jul 15 2013
| | Sample_last_update_date | Jul 16 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Virgin Ccnd1-/- and Ccnd1+/+ mice were overiectomized and allowed to recover for 2 after the surgery. Mice from each genotype split into 2 groups and treated with placebo control or estradiol releasing pelles (0.72mg, 60 day release). Mice were treated for 7 days and then sacrifised.
| | Sample_growth_protocol_ch1 | No specific growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix)
| | Sample_hyb_protocol | 15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module, followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.
| | Sample_data_processing | The data were analyzed and normalized by Robust Multi-array Average (RMA) algorithm using affylmGUI (1.14.0) running limma version 2.9.16 within the language and environment program R (2.4.1).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Mathew,Casimiro,Casimiro
| | Sample_contact_laboratory | Philadelphia
| | Sample_contact_department | 233 South 10th St, Rm 1035
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 South 10th St, Rm 1035
| | Sample_contact_city | 19107
| | Sample_contact_state | United States
| | Sample_contact_zip/postal_code | Mathew Casimiro
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1186nnn/GSM1186323/suppl/GSM1186323_334WTP.CEL.gz
| | Sample_series_id | GSE48884
| | Sample_data_row_count | 45101
| | |
|
GSM1186324 | GPL1261 |
|
Mouse mammary gland Ccnd1+/+ Vehicle Rep3
|
mammary gland_Ccnd1+/+_Vehicle
|
strain background: C57BL/6
genotype/variation: Ccnd1+/+
treated with: placebo control
tissue: mouse mammary gland
|
|
| Sample_geo_accession | GSM1186324
| | Sample_status | Public on Jul 16 2013
| | Sample_submission_date | Jul 15 2013
| | Sample_last_update_date | Jul 16 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Virgin Ccnd1-/- and Ccnd1+/+ mice were overiectomized and allowed to recover for 2 after the surgery. Mice from each genotype split into 2 groups and treated with placebo control or estradiol releasing pelles (0.72mg, 60 day release). Mice were treated for 7 days and then sacrifised.
| | Sample_growth_protocol_ch1 | No specific growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix)
| | Sample_hyb_protocol | 15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module, followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.
| | Sample_data_processing | The data were analyzed and normalized by Robust Multi-array Average (RMA) algorithm using affylmGUI (1.14.0) running limma version 2.9.16 within the language and environment program R (2.4.1).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Mathew,Casimiro,Casimiro
| | Sample_contact_laboratory | Philadelphia
| | Sample_contact_department | 233 South 10th St, Rm 1035
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 South 10th St, Rm 1035
| | Sample_contact_city | 19107
| | Sample_contact_state | United States
| | Sample_contact_zip/postal_code | Mathew Casimiro
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1186nnn/GSM1186324/suppl/GSM1186324_54WTP.CEL.gz
| | Sample_series_id | GSE48884
| | Sample_data_row_count | 45101
| | |
|
GSM1186325 | GPL1261 |
|
Mouse mammary gland Ccnd1+/+ E2 Rep1
|
mammary gland_Ccnd1+/+_E2
|
strain background: C57BL/6
genotype/variation: Ccnd1+/+
treated with: estradiol releasing pellets
tissue: mouse mammary gland
|
|
| Sample_geo_accession | GSM1186325
| | Sample_status | Public on Jul 16 2013
| | Sample_submission_date | Jul 15 2013
| | Sample_last_update_date | Jul 16 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Virgin Ccnd1-/- and Ccnd1+/+ mice were overiectomized and allowed to recover for 2 after the surgery. Mice from each genotype split into 2 groups and treated with placebo control or estradiol releasing pelles (0.72mg, 60 day release). Mice were treated for 7 days and then sacrifised.
| | Sample_growth_protocol_ch1 | No specific growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix)
| | Sample_hyb_protocol | 15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module, followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.
| | Sample_data_processing | The data were analyzed and normalized by Robust Multi-array Average (RMA) algorithm using affylmGUI (1.14.0) running limma version 2.9.16 within the language and environment program R (2.4.1).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Mathew,Casimiro,Casimiro
| | Sample_contact_laboratory | Philadelphia
| | Sample_contact_department | 233 South 10th St, Rm 1035
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 South 10th St, Rm 1035
| | Sample_contact_city | 19107
| | Sample_contact_state | United States
| | Sample_contact_zip/postal_code | Mathew Casimiro
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1186nnn/GSM1186325/suppl/GSM1186325_99WTE.CEL.gz
| | Sample_series_id | GSE48884
| | Sample_data_row_count | 45101
| | |
|
GSM1186326 | GPL1261 |
|
Mouse mammary gland Ccnd1+/+ E2 Rep2
|
mammary gland_Ccnd1+/+_E2
|
strain background: C57BL/6
genotype/variation: Ccnd1+/+
treated with: estradiol releasing pellets
tissue: mouse mammary gland
|
|
| Sample_geo_accession | GSM1186326
| | Sample_status | Public on Jul 16 2013
| | Sample_submission_date | Jul 15 2013
| | Sample_last_update_date | Jul 16 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Virgin Ccnd1-/- and Ccnd1+/+ mice were overiectomized and allowed to recover for 2 after the surgery. Mice from each genotype split into 2 groups and treated with placebo control or estradiol releasing pelles (0.72mg, 60 day release). Mice were treated for 7 days and then sacrifised.
| | Sample_growth_protocol_ch1 | No specific growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix)
| | Sample_hyb_protocol | 15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module, followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.
| | Sample_data_processing | The data were analyzed and normalized by Robust Multi-array Average (RMA) algorithm using affylmGUI (1.14.0) running limma version 2.9.16 within the language and environment program R (2.4.1).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Mathew,Casimiro,Casimiro
| | Sample_contact_laboratory | Philadelphia
| | Sample_contact_department | 233 South 10th St, Rm 1035
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 South 10th St, Rm 1035
| | Sample_contact_city | 19107
| | Sample_contact_state | United States
| | Sample_contact_zip/postal_code | Mathew Casimiro
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1186nnn/GSM1186326/suppl/GSM1186326_57WTE.CEL.gz
| | Sample_series_id | GSE48884
| | Sample_data_row_count | 45101
| | |
|
GSM1186327 | GPL1261 |
|
Mouse mammary gland Ccnd1+/+ E2 Rep3
|
mammary gland_Ccnd1+/+_E2
|
strain background: C57BL/6
genotype/variation: Ccnd1+/+
treated with: estradiol releasing pellets
tissue: mouse mammary gland
|
|
| Sample_geo_accession | GSM1186327
| | Sample_status | Public on Jul 16 2013
| | Sample_submission_date | Jul 15 2013
| | Sample_last_update_date | Jul 16 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Virgin Ccnd1-/- and Ccnd1+/+ mice were overiectomized and allowed to recover for 2 after the surgery. Mice from each genotype split into 2 groups and treated with placebo control or estradiol releasing pelles (0.72mg, 60 day release). Mice were treated for 7 days and then sacrifised.
| | Sample_growth_protocol_ch1 | No specific growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix)
| | Sample_hyb_protocol | 15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module, followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.
| | Sample_data_processing | The data were analyzed and normalized by Robust Multi-array Average (RMA) algorithm using affylmGUI (1.14.0) running limma version 2.9.16 within the language and environment program R (2.4.1).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Mathew,Casimiro,Casimiro
| | Sample_contact_laboratory | Philadelphia
| | Sample_contact_department | 233 South 10th St, Rm 1035
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 South 10th St, Rm 1035
| | Sample_contact_city | 19107
| | Sample_contact_state | United States
| | Sample_contact_zip/postal_code | Mathew Casimiro
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1186nnn/GSM1186327/suppl/GSM1186327_336WTE.CEL.gz
| | Sample_series_id | GSE48884
| | Sample_data_row_count | 45101
| | |
|
GSM1186328 | GPL1261 |
|
Mouse mammary gland Ccnd1-/- Vehicle Rep1
|
mammary gland_Ccnd1-/-_Vehicle
|
strain background: C57BL/6
genotype/variation: Ccnd1-/-
treated with: placebo control
tissue: mouse mammary gland
|
|
| Sample_geo_accession | GSM1186328
| | Sample_status | Public on Jul 16 2013
| | Sample_submission_date | Jul 15 2013
| | Sample_last_update_date | Jul 16 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Virgin Ccnd1-/- and Ccnd1+/+ mice were overiectomized and allowed to recover for 2 after the surgery. Mice from each genotype split into 2 groups and treated with placebo control or estradiol releasing pelles (0.72mg, 60 day release). Mice were treated for 7 days and then sacrifised.
| | Sample_growth_protocol_ch1 | No specific growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix)
| | Sample_hyb_protocol | 15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module, followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.
| | Sample_data_processing | The data were analyzed and normalized by Robust Multi-array Average (RMA) algorithm using affylmGUI (1.14.0) running limma version 2.9.16 within the language and environment program R (2.4.1).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Mathew,Casimiro,Casimiro
| | Sample_contact_laboratory | Philadelphia
| | Sample_contact_department | 233 South 10th St, Rm 1035
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 South 10th St, Rm 1035
| | Sample_contact_city | 19107
| | Sample_contact_state | United States
| | Sample_contact_zip/postal_code | Mathew Casimiro
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1186nnn/GSM1186328/suppl/GSM1186328_5KOP.CEL.gz
| | Sample_series_id | GSE48884
| | Sample_data_row_count | 45101
| | |
|
GSM1186329 | GPL1261 |
|
Mouse mammary gland Ccnd1-/- Vehicle Rep2
|
mammary gland_Ccnd1-/-_Vehicle
|
strain background: C57BL/6
genotype/variation: Ccnd1-/-
treated with: placebo control
tissue: mouse mammary gland
|
|
| Sample_geo_accession | GSM1186329
| | Sample_status | Public on Jul 16 2013
| | Sample_submission_date | Jul 15 2013
| | Sample_last_update_date | Jul 16 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Virgin Ccnd1-/- and Ccnd1+/+ mice were overiectomized and allowed to recover for 2 after the surgery. Mice from each genotype split into 2 groups and treated with placebo control or estradiol releasing pelles (0.72mg, 60 day release). Mice were treated for 7 days and then sacrifised.
| | Sample_growth_protocol_ch1 | No specific growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix)
| | Sample_hyb_protocol | 15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module, followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.
| | Sample_data_processing | The data were analyzed and normalized by Robust Multi-array Average (RMA) algorithm using affylmGUI (1.14.0) running limma version 2.9.16 within the language and environment program R (2.4.1).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Mathew,Casimiro,Casimiro
| | Sample_contact_laboratory | Philadelphia
| | Sample_contact_department | 233 South 10th St, Rm 1035
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 South 10th St, Rm 1035
| | Sample_contact_city | 19107
| | Sample_contact_state | United States
| | Sample_contact_zip/postal_code | Mathew Casimiro
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1186nnn/GSM1186329/suppl/GSM1186329_69KOP.CEL.gz
| | Sample_series_id | GSE48884
| | Sample_data_row_count | 45101
| | |
|
GSM1186330 | GPL1261 |
|
Mouse mammary gland Ccnd1-/- Vehicle Rep3
|
mammary gland_Ccnd1-/-_Vehicle
|
strain background: C57BL/6
genotype/variation: Ccnd1-/-
treated with: placebo control
tissue: mouse mammary gland
|
|
| Sample_geo_accession | GSM1186330
| | Sample_status | Public on Jul 16 2013
| | Sample_submission_date | Jul 15 2013
| | Sample_last_update_date | Jul 16 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Virgin Ccnd1-/- and Ccnd1+/+ mice were overiectomized and allowed to recover for 2 after the surgery. Mice from each genotype split into 2 groups and treated with placebo control or estradiol releasing pelles (0.72mg, 60 day release). Mice were treated for 7 days and then sacrifised.
| | Sample_growth_protocol_ch1 | No specific growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix)
| | Sample_hyb_protocol | 15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module, followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.
| | Sample_data_processing | The data were analyzed and normalized by Robust Multi-array Average (RMA) algorithm using affylmGUI (1.14.0) running limma version 2.9.16 within the language and environment program R (2.4.1).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Mathew,Casimiro,Casimiro
| | Sample_contact_laboratory | Philadelphia
| | Sample_contact_department | 233 South 10th St, Rm 1035
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 South 10th St, Rm 1035
| | Sample_contact_city | 19107
| | Sample_contact_state | United States
| | Sample_contact_zip/postal_code | Mathew Casimiro
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1186nnn/GSM1186330/suppl/GSM1186330_322KOP.CEL.gz
| | Sample_series_id | GSE48884
| | Sample_data_row_count | 45101
| | |
|
GSM1186331 | GPL1261 |
|
Mouse mammary gland Ccnd1-/- E2 Rep1
|
mammary gland_Ccnd1-/-_E2
|
strain background: C57BL/6
genotype/variation: Ccnd1-/-
treated with: estradiol releasing pellets
tissue: mouse mammary gland
|
|
| Sample_geo_accession | GSM1186331
| | Sample_status | Public on Jul 16 2013
| | Sample_submission_date | Jul 15 2013
| | Sample_last_update_date | Jul 16 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Virgin Ccnd1-/- and Ccnd1+/+ mice were overiectomized and allowed to recover for 2 after the surgery. Mice from each genotype split into 2 groups and treated with placebo control or estradiol releasing pelles (0.72mg, 60 day release). Mice were treated for 7 days and then sacrifised.
| | Sample_growth_protocol_ch1 | No specific growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix)
| | Sample_hyb_protocol | 15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module, followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.
| | Sample_data_processing | The data were analyzed and normalized by Robust Multi-array Average (RMA) algorithm using affylmGUI (1.14.0) running limma version 2.9.16 within the language and environment program R (2.4.1).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Mathew,Casimiro,Casimiro
| | Sample_contact_laboratory | Philadelphia
| | Sample_contact_department | 233 South 10th St, Rm 1035
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 South 10th St, Rm 1035
| | Sample_contact_city | 19107
| | Sample_contact_state | United States
| | Sample_contact_zip/postal_code | Mathew Casimiro
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1186nnn/GSM1186331/suppl/GSM1186331_20KOE.CEL.gz
| | Sample_series_id | GSE48884
| | Sample_data_row_count | 45101
| | |
|
GSM1186332 | GPL1261 |
|
Mouse mammary gland Ccnd1-/- E2 Rep2
|
mammary gland_Ccnd1-/-_E2
|
strain background: C57BL/6
genotype/variation: Ccnd1-/-
treated with: estradiol releasing pellets
tissue: mouse mammary gland
|
|
| Sample_geo_accession | GSM1186332
| | Sample_status | Public on Jul 16 2013
| | Sample_submission_date | Jul 15 2013
| | Sample_last_update_date | Jul 16 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Virgin Ccnd1-/- and Ccnd1+/+ mice were overiectomized and allowed to recover for 2 after the surgery. Mice from each genotype split into 2 groups and treated with placebo control or estradiol releasing pelles (0.72mg, 60 day release). Mice were treated for 7 days and then sacrifised.
| | Sample_growth_protocol_ch1 | No specific growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix)
| | Sample_hyb_protocol | 15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module, followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.
| | Sample_data_processing | The data were analyzed and normalized by Robust Multi-array Average (RMA) algorithm using affylmGUI (1.14.0) running limma version 2.9.16 within the language and environment program R (2.4.1).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Mathew,Casimiro,Casimiro
| | Sample_contact_laboratory | Philadelphia
| | Sample_contact_department | 233 South 10th St, Rm 1035
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 South 10th St, Rm 1035
| | Sample_contact_city | 19107
| | Sample_contact_state | United States
| | Sample_contact_zip/postal_code | Mathew Casimiro
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1186nnn/GSM1186332/suppl/GSM1186332_21KOE.CEL.gz
| | Sample_series_id | GSE48884
| | Sample_data_row_count | 45101
| | |
|
GSM1186333 | GPL1261 |
|
Mouse mammary gland Ccnd1-/- E2 Rep3
|
mammary gland_Ccnd1-/-_E2
|
strain background: C57BL/6
genotype/variation: Ccnd1-/-
treated with: estradiol releasing pellets
tissue: mouse mammary gland
|
|
| Sample_geo_accession | GSM1186333
| | Sample_status | Public on Jul 16 2013
| | Sample_submission_date | Jul 15 2013
| | Sample_last_update_date | Jul 16 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Virgin Ccnd1-/- and Ccnd1+/+ mice were overiectomized and allowed to recover for 2 after the surgery. Mice from each genotype split into 2 groups and treated with placebo control or estradiol releasing pelles (0.72mg, 60 day release). Mice were treated for 7 days and then sacrifised.
| | Sample_growth_protocol_ch1 | No specific growth protocol
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix)
| | Sample_hyb_protocol | 15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module, followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).
| | Sample_scan_protocol | Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.
| | Sample_data_processing | The data were analyzed and normalized by Robust Multi-array Average (RMA) algorithm using affylmGUI (1.14.0) running limma version 2.9.16 within the language and environment program R (2.4.1).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Mathew,Casimiro,Casimiro
| | Sample_contact_laboratory | Philadelphia
| | Sample_contact_department | 233 South 10th St, Rm 1035
| | Sample_contact_institute | Thomas Jefferson University
| | Sample_contact_address | 233 South 10th St, Rm 1035
| | Sample_contact_city | 19107
| | Sample_contact_state | United States
| | Sample_contact_zip/postal_code | Mathew Casimiro
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1186nnn/GSM1186333/suppl/GSM1186333_53KOE.CEL.gz
| | Sample_series_id | GSE48884
| | Sample_data_row_count | 45101
| | |
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