Search results for the GEO ID: GSE21947  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM512560 | GPL96 |
|
histologically normal breast epithelium from ER+ breast cancer patient sample 4
|
Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
specimen: ER+ Breast Cancer
disease state: breast cancer
tissue: breast epithelium
|
Gene Expression data from case 304BH:Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
| Sample_geo_accession | GSM512560
| | Sample_status | Public on Jun 01 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | May 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most HN samples were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells. Some HN lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | .cel files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512560/suppl/GSM512560_304BH.CEL.gz
| | Sample_relation | Reanalyzed by: GSE47561
| | Sample_series_id | GSE20437
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM512564 | GPL96 |
|
histologically normal breast epithelium from ER+ breast cancer patient sample 8
|
Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
specimen: ER+ Breast Cancer
disease state: breast cancer
tissue: breast epithelium
|
Gene Expression data from case 388AH:Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
| Sample_geo_accession | GSM512564
| | Sample_status | Public on Jun 01 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | May 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most HN samples were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells. Some HN lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | .cel files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512564/suppl/GSM512564_388AH.CEL.gz
| | Sample_relation | Reanalyzed by: GSE47561
| | Sample_series_id | GSE20437
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM512565 | GPL96 |
|
histologically normal breast epithelium from ER+ breast cancer patient sample 9
|
Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
specimen: ER+ Breast Cancer
disease state: breast cancer
tissue: breast epithelium
|
Gene Expression data from case 232H:Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
| Sample_geo_accession | GSM512565
| | Sample_status | Public on Jun 01 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | May 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most HN samples were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells. Some HN lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | .cel files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512565/suppl/GSM512565_232H.CEL.gz
| | Sample_relation | Reanalyzed by: GSE47561
| | Sample_series_id | GSE20437
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM512566 | GPL96 |
|
histologically normal breast epithelium from ER- breast cancer patient sample 1
|
Histologically Normal Epithelium from ER- Breast Cancer Patient
|
specimen: ER- Breast Cancer
disease state: breast cancer
tissue: breast epithelium
|
Gene Expression data from case 319H:Histologically Normal Epithelium from ER- Breast Cancer Patient
|
| Sample_geo_accession | GSM512566
| | Sample_status | Public on Jun 01 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | May 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most HN samples were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells. Some HN lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | .cel files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512566/suppl/GSM512566_319H.CEL.gz
| | Sample_relation | Reanalyzed by: GSE47561
| | Sample_series_id | GSE20437
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM512567 | GPL96 |
|
histologically normal breast epithelium from ER- breast cancer patient sample 2
|
Histologically Normal Epithelium from ER- Breast Cancer Patient
|
specimen: ER- Breast Cancer
disease state: breast cancer
tissue: breast epithelium
|
Gene Expression data from case 289H:Histologically Normal Epithelium from ER- Breast Cancer Patient
|
| Sample_geo_accession | GSM512567
| | Sample_status | Public on Jun 01 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | May 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most HN samples were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells. Some HN lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | .cel files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512567/suppl/GSM512567_289H.CEL.gz
| | Sample_relation | Reanalyzed by: GSE47561
| | Sample_series_id | GSE20437
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM512568 | GPL96 |
|
histologically normal breast epithelium from ER- breast cancer patient sample 3
|
Histologically Normal Epithelium from ER- Breast Cancer Patient
|
specimen: ER- Breast Cancer
disease state: breast cancer
tissue: breast epithelium
|
Gene Expression data from case 364H:Histologically Normal Epithelium from ER- Breast Cancer Patient
|
| Sample_geo_accession | GSM512568
| | Sample_status | Public on Jun 01 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | May 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most HN samples were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells. Some HN lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | .cel files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512568/suppl/GSM512568_364H.CEL.gz
| | Sample_relation | Reanalyzed by: GSE47561
| | Sample_series_id | GSE20437
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM512569 | GPL96 |
|
histologically normal breast epithelium from ER- breast cancer patient sample 4
|
Histologically Normal Epithelium from ER- Breast Cancer Patient
|
specimen: ER- Breast Cancer
disease state: breast cancer
tissue: breast epithelium
|
Gene Expression data from case 342H:Histologically Normal Epithelium from ER- Breast Cancer Patient
|
| Sample_geo_accession | GSM512569
| | Sample_status | Public on Jun 01 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | May 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most HN samples were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells. Some HN lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | .cel files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512569/suppl/GSM512569_342H.CEL.gz
| | Sample_relation | Reanalyzed by: GSE47561
| | Sample_series_id | GSE20437
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM512570 | GPL96 |
|
histologically normal breast epithelium from ER- breast cancer patient sample 5
|
Histologically Normal Epithelium from ER- Breast Cancer Patient
|
specimen: ER- Breast Cancer
disease state: breast cancer
tissue: breast epithelium
|
Gene Expression data from case 273H:Histologically Normal Epithelium from ER- Breast Cancer Patient
|
| Sample_geo_accession | GSM512570
| | Sample_status | Public on Jun 01 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | May 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most HN samples were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells. Some HN lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | .cel files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512570/suppl/GSM512570_273H.CEL.gz
| | Sample_relation | Reanalyzed by: GSE47561
| | Sample_series_id | GSE20437
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM512571 | GPL96 |
|
histologically normal breast epithelium from ER- breast cancer patient sample 6
|
Histologically Normal Epithelium from ER- Breast Cancer Patient
|
specimen: ER- Breast Cancer
disease state: breast cancer
tissue: breast epithelium
|
Gene Expression data from case 322H:Histologically Normal Epithelium from ER- Breast Cancer Patient
|
| Sample_geo_accession | GSM512571
| | Sample_status | Public on Jun 01 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | May 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most HN samples were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells. Some HN lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | .cel files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512571/suppl/GSM512571_322H.CEL.gz
| | Sample_relation | Reanalyzed by: GSE47561
| | Sample_series_id | GSE20437
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM512572 | GPL96 |
|
histologically normal breast epithelium from ER- breast cancer patient sample 7
|
Histologically Normal Epithelium from ER- Breast Cancer Patient
|
specimen: ER- Breast Cancer
disease state: breast cancer
tissue: breast epithelium
|
Gene Expression data from case 272H:Histologically Normal Epithelium from ER- Breast Cancer Patient
|
| Sample_geo_accession | GSM512572
| | Sample_status | Public on Jun 01 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | May 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most HN samples were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells. Some HN lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | .cel files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512572/suppl/GSM512572_272H.CEL.gz
| | Sample_relation | Reanalyzed by: GSE47561
| | Sample_series_id | GSE20437
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM512573 | GPL96 |
|
histologically normal breast epithelium from ER- breast cancer patient sample 8
|
Histologically Normal Epithelium from ER- Breast Cancer Patient
|
specimen: ER- Breast Cancer
disease state: breast cancer
tissue: breast epithelium
|
Gene Expression data from case 226H:Histologically Normal Epithelium from ER- Breast Cancer Patient
|
| Sample_geo_accession | GSM512573
| | Sample_status | Public on Jun 01 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | May 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most HN samples were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells. Some HN lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | .cel files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512573/suppl/GSM512573_226H.CEL.gz
| | Sample_relation | Reanalyzed by: GSE47561
| | Sample_series_id | GSE20437
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM512574 | GPL96 |
|
histologically normal breast epithelium from ER- breast cancer patient sample 9
|
Histologically Normal Epithelium from ER- Breast Cancer Patient
|
specimen: ER- Breast Cancer
disease state: breast cancer
tissue: breast epithelium
|
Gene Expression data from case 333H:Histologically Normal Epithelium from ER- Breast Cancer Patient
|
| Sample_geo_accession | GSM512574
| | Sample_status | Public on Jun 01 2010
| | Sample_submission_date | Feb 19 2010
| | Sample_last_update_date | May 31 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most HN samples were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells. Some HN lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | .cel files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM512nnn/GSM512574/suppl/GSM512574_333H.CEL.gz
| | Sample_relation | Reanalyzed by: GSE47561
| | Sample_series_id | GSE20437
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM546465 | GPL96 |
|
histologically normal breast epithelium from ER+ breast cancer patient sample 1 (351H)
|
Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
breast cancer patient id: 351H
er status: ER+
tissue: normal breast epithelium (laser capture microdissected)
|
Gene Expression data from case 351H:Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
| Sample_geo_accession | GSM546465
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | May 24 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most NlEpi samples (n=20) were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells). Some NlEpi samples (n=10) lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions. Most NlEpi samples consisted only of TDLUs, but about 20% of samples (mainly from older patients) contained some ducts, as well.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | The .CEL files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM546nnn/GSM546465/suppl/GSM546465_351H.CEL.gz
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM546466 | GPL96 |
|
histologically normal breast epithelium from ER+ breast cancer patient sample 2 (297BH)
|
Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
breast cancer patient id: 297BH
er status: ER+
tissue: normal breast epithelium (laser capture microdissected)
|
Gene Expression data from case 297BH:Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
| Sample_geo_accession | GSM546466
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | May 24 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most NlEpi samples (n=20) were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells). Some NlEpi samples (n=10) lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions. Most NlEpi samples consisted only of TDLUs, but about 20% of samples (mainly from older patients) contained some ducts, as well.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | The .CEL files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM546nnn/GSM546466/suppl/GSM546466_297BH.CEL.gz
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM546467 | GPL96 |
|
histologically normal breast epithelium from ER+ breast cancer patient sample 3 (359H)
|
Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
breast cancer patient id: 359H
er status: ER+
tissue: normal breast epithelium (laser capture microdissected)
|
Gene Expression data from case 359H:Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
| Sample_geo_accession | GSM546467
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | May 24 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most NlEpi samples (n=20) were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells). Some NlEpi samples (n=10) lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions. Most NlEpi samples consisted only of TDLUs, but about 20% of samples (mainly from older patients) contained some ducts, as well.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | The .CEL files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM546nnn/GSM546467/suppl/GSM546467_359H.CEL.gz
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM546468 | GPL96 |
|
histologically normal breast epithelium from ER+ breast cancer patient sample 5 (248H)
|
Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
breast cancer patient id: 248H
er status: ER+
tissue: normal breast epithelium (laser capture microdissected)
|
Gene Expression data from case 248H:Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
| Sample_geo_accession | GSM546468
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | May 24 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most NlEpi samples (n=20) were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells). Some NlEpi samples (n=10) lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions. Most NlEpi samples consisted only of TDLUs, but about 20% of samples (mainly from older patients) contained some ducts, as well.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | The .CEL files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM546nnn/GSM546468/suppl/GSM546468_248H.CEL.gz
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM546469 | GPL96 |
|
histologically normal breast epithelium from ER+ breast cancer patient sample 6 (345H)
|
Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
breast cancer patient id: 345H
er status: ER+
tissue: normal breast epithelium (laser capture microdissected)
|
Gene Expression data from case 345H:Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
| Sample_geo_accession | GSM546469
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | May 24 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most NlEpi samples (n=20) were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells). Some NlEpi samples (n=10) lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions. Most NlEpi samples consisted only of TDLUs, but about 20% of samples (mainly from older patients) contained some ducts, as well.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | The .CEL files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM546nnn/GSM546469/suppl/GSM546469_345H.CEL.gz
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM546470 | GPL96 |
|
histologically normal breast epithelium from ER+ breast cancer patient sample 9 (258H)
|
Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
breast cancer patient id: 258H
er status: ER+
tissue: normal breast epithelium (laser capture microdissected)
|
Gene Expression data from case 258H:Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
| Sample_geo_accession | GSM546470
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | May 24 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most NlEpi samples (n=20) were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells). Some NlEpi samples (n=10) lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions. Most NlEpi samples consisted only of TDLUs, but about 20% of samples (mainly from older patients) contained some ducts, as well.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | The .CEL files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM546nnn/GSM546470/suppl/GSM546470_258H.CEL.gz
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM546471 | GPL96 |
|
histologically normal breast epithelium from ER+ breast cancer patient sample 10 (405H)
|
Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
breast cancer patient id: 405H
er status: ER+
tissue: normal breast epithelium (laser capture microdissected)
|
Gene Expression data from case 405H:Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
| Sample_geo_accession | GSM546471
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | May 24 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most NlEpi samples (n=20) were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells). Some NlEpi samples (n=10) lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions. Most NlEpi samples consisted only of TDLUs, but about 20% of samples (mainly from older patients) contained some ducts, as well.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | The .CEL files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM546nnn/GSM546471/suppl/GSM546471_405H.CEL.gz
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM546472 | GPL96 |
|
histologically normal breast epithelium from ER+ breast cancer patient sample 11 (311H)
|
Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
breast cancer patient id: 311H
er status: ER+
tissue: normal breast epithelium (laser capture microdissected)
|
Gene Expression data from case 311H:Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
| Sample_geo_accession | GSM546472
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | May 24 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most NlEpi samples (n=20) were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells). Some NlEpi samples (n=10) lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions. Most NlEpi samples consisted only of TDLUs, but about 20% of samples (mainly from older patients) contained some ducts, as well.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | The .CEL files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM546nnn/GSM546472/suppl/GSM546472_311H.CEL.gz
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM546473 | GPL96 |
|
histologically normal breast epithelium from ER+ breast cancer patient sample 12 (453H)
|
Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
breast cancer patient id: 453H
er status: ER+
tissue: normal breast epithelium (laser capture microdissected)
|
Gene Expression data from case 453H:Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
| Sample_geo_accession | GSM546473
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | May 24 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most NlEpi samples (n=20) were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells). Some NlEpi samples (n=10) lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions. Most NlEpi samples consisted only of TDLUs, but about 20% of samples (mainly from older patients) contained some ducts, as well.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | The .CEL files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM546nnn/GSM546473/suppl/GSM546473_453H.CEL.gz
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM546474 | GPL96 |
|
histologically normal breast epithelium from ER+ breast cancer patient sample 13 (394H)
|
Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
breast cancer patient id: 394H
er status: ER+
tissue: normal breast epithelium (laser capture microdissected)
|
Gene Expression data from case 394H:Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
| Sample_geo_accession | GSM546474
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | May 24 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most NlEpi samples (n=20) were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells). Some NlEpi samples (n=10) lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions. Most NlEpi samples consisted only of TDLUs, but about 20% of samples (mainly from older patients) contained some ducts, as well.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | The .CEL files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM546nnn/GSM546474/suppl/GSM546474_394H.CEL.gz
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM546475 | GPL96 |
|
histologically normal breast epithelium from ER+ breast cancer patient sample 14 (275H)
|
Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
breast cancer patient id: 275H
er status: ER+
tissue: normal breast epithelium (laser capture microdissected)
|
Gene Expression data from case 275H:Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
| Sample_geo_accession | GSM546475
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | May 24 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most NlEpi samples (n=20) were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells). Some NlEpi samples (n=10) lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions. Most NlEpi samples consisted only of TDLUs, but about 20% of samples (mainly from older patients) contained some ducts, as well.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | The .CEL files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM546nnn/GSM546475/suppl/GSM546475_275H.CEL.gz
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM546476 | GPL96 |
|
histologically normal breast epithelium from ER+ breast cancer patient sample 15 (228H)
|
Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
breast cancer patient id: 228H
er status: ER+
tissue: normal breast epithelium (laser capture microdissected)
|
Gene Expression data from case 228H:Histologically Normal Epithelium from ER+ Breast Cancer Patient
|
| Sample_geo_accession | GSM546476
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | May 24 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most NlEpi samples (n=20) were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells). Some NlEpi samples (n=10) lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions. Most NlEpi samples consisted only of TDLUs, but about 20% of samples (mainly from older patients) contained some ducts, as well.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | The .CEL files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM546nnn/GSM546476/suppl/GSM546476_228H.CEL.gz
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM546477 | GPL96 |
|
histologically normal breast epithelium from ER- breast cancer patient sample 9 (452H)
|
Histologically Normal Epithelium from ER- Breast Cancer Patient
|
breast cancer patient id: 452H
er status: ER-
tissue: normal breast epithelium (laser capture microdissected)
|
Gene Expression data from case 452H:Histologically Normal Epithelium from ER- Breast Cancer Patient
|
| Sample_geo_accession | GSM546477
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | May 24 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most NlEpi samples (n=20) were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells). Some NlEpi samples (n=10) lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions. Most NlEpi samples consisted only of TDLUs, but about 20% of samples (mainly from older patients) contained some ducts, as well.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | The .CEL files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM546nnn/GSM546477/suppl/GSM546477_452H.CEL.gz
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM546478 | GPL96 |
|
histologically normal breast epithelium from ER- breast cancer patient sample 10 (298H)
|
Histologically Normal Epithelium from ER- Breast Cancer Patient
|
breast cancer patient id: 298H
er status: ER-
tissue: normal breast epithelium (laser capture microdissected)
|
Gene Expression data from case 298H:Histologically Normal Epithelium from ER- Breast Cancer Patient
|
| Sample_geo_accession | GSM546478
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | May 24 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most NlEpi samples (n=20) were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells). Some NlEpi samples (n=10) lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions. Most NlEpi samples consisted only of TDLUs, but about 20% of samples (mainly from older patients) contained some ducts, as well.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | The .CEL files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM546nnn/GSM546478/suppl/GSM546478_298H.CEL.gz
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM546479 | GPL96 |
|
histologically normal breast epithelium from ER- breast cancer patient sample 11 (429H)
|
Histologically Normal Epithelium from ER- Breast Cancer Patient
|
breast cancer patient id: 429H
er status: ER-
tissue: normal breast epithelium (laser capture microdissected)
|
Gene Expression data from case 429H:Histologically Normal Epithelium from ER- Breast Cancer Patient
|
| Sample_geo_accession | GSM546479
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | May 24 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most NlEpi samples (n=20) were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells). Some NlEpi samples (n=10) lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions. Most NlEpi samples consisted only of TDLUs, but about 20% of samples (mainly from older patients) contained some ducts, as well.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | The .CEL files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM546nnn/GSM546479/suppl/GSM546479_429H.CEL.gz
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM546480 | GPL96 |
|
histologically normal breast epithelium from ER- breast cancer patient sample 13 (413H)
|
Histologically Normal Epithelium from ER- Breast Cancer Patient
|
breast cancer patient id: 413H
er status: ER-
tissue: normal breast epithelium (laser capture microdissected)
|
Gene Expression data from case 413H:Histologically Normal Epithelium from ER- Breast Cancer Patient
|
| Sample_geo_accession | GSM546480
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | May 24 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most NlEpi samples (n=20) were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells). Some NlEpi samples (n=10) lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions. Most NlEpi samples consisted only of TDLUs, but about 20% of samples (mainly from older patients) contained some ducts, as well.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | The .CEL files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM546nnn/GSM546480/suppl/GSM546480_413H.CEL.gz
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM546481 | GPL96 |
|
histologically normal breast epithelium from ER- breast cancer patient sample 14 (296H)
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Histologically Normal Epithelium from ER- Breast Cancer Patient
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breast cancer patient id: 296H
er status: ER-
tissue: normal breast epithelium (laser capture microdissected)
|
Gene Expression data from case 296H:Histologically Normal Epithelium from ER- Breast Cancer Patient
|
| Sample_geo_accession | GSM546481
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | May 24 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most NlEpi samples (n=20) were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells). Some NlEpi samples (n=10) lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions. Most NlEpi samples consisted only of TDLUs, but about 20% of samples (mainly from older patients) contained some ducts, as well.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | The .CEL files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM546nnn/GSM546481/suppl/GSM546481_296H.CEL.gz
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
| | |
|
GSM546482 | GPL96 |
|
histologically normal breast epithelium from ER- breast cancer patient sample 15 (401H)
|
Histologically Normal Epithelium from ER- Breast Cancer Patient
|
breast cancer patient id: 401H
er status: ER-
tissue: normal breast epithelium (laser capture microdissected)
|
Gene Expression data from case 401H:Histologically Normal Epithelium from ER- Breast Cancer Patient
|
| Sample_geo_accession | GSM546482
| | Sample_status | Public on Dec 07 2010
| | Sample_submission_date | May 24 2010
| | Sample_last_update_date | Dec 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most NlEpi samples (n=20) were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells). Some NlEpi samples (n=10) lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions. Most NlEpi samples consisted only of TDLUs, but about 20% of samples (mainly from older patients) contained some ducts, as well.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
| | Sample_scan_protocol | The stained arrays were scanned using a G2500 Scanner (Agilent)
| | Sample_data_processing | The .CEL files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kelly,,Graham
| | Sample_contact_laboratory | Rosenberg
| | Sample_contact_department | Hematology/Oncology
| | Sample_contact_institute | Boston University School of Medicine
| | Sample_contact_address | 650 Albany Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02118
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM546nnn/GSM546482/suppl/GSM546482_401H.CEL.gz
| | Sample_series_id | GSE21947
| | Sample_data_row_count | 22283
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