Search results for the GEO ID: GSE19697  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM491610 | GPL570 |
|
Pre-Treatment breast tumor 7411
|
Pre-Treatment breast tumor
|
gender: Female
percent: -89.19
er: 0
pr: 0
her2: 1
grade: 3
histology: IDC
positive nodes: 0
nodes examined: 13
recur: 0
race: Caucasian
t stage: 2
|
Stage II or III breast cancer Patient 1
|
| Sample_geo_accession | GSM491610
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491610/suppl/GSM491610.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
GSM491611 | GPL570 |
|
Pre-Treatment breast tumor 7412
|
Pre-Treatment breast tumor
|
gender: Female
percent: -100
er: 0
pr: 0
her2: 0
grade: 3
histology: IDC
positive nodes: 0
nodes examined: 14
recur: 1
race: African American
t stage: 2
|
Stage II or III breast cancer Patient 2
|
| Sample_geo_accession | GSM491611
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491611/suppl/GSM491611.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
GSM491612 | GPL570 |
|
Pre-Treatment breast tumor 7415
|
Pre-Treatment breast tumor
|
gender: Female
percent: -20
er: 0
pr: 0
her2: 0
grade: 3
histology: IDC
positive nodes: 3
nodes examined: 6
recur: 1
race: African American
t stage: 2
|
Stage II or III breast cancer Patient 3
|
| Sample_geo_accession | GSM491612
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491612/suppl/GSM491612.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
GSM491613 | GPL570 |
|
Pre-Treatment breast tumor 7421
|
Pre-Treatment breast tumor
|
gender: Female
percent: -33.33
er: 0
pr: 0
her2: 0
grade: 2
histology: IDC
positive nodes: 0
nodes examined: 16
recur: 0
race: Caucasian
t stage: 2
|
Stage II or III breast cancer Patient 4
|
| Sample_geo_accession | GSM491613
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491613/suppl/GSM491613.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
GSM491614 | GPL570 |
|
Pre-Treatment breast tumor 7422
|
Pre-Treatment breast tumor
|
gender: Female
percent: -100
er: 0
pr: 0
her2: 0
grade: 3
histology: IDC
positive nodes: 0
nodes examined: 8
recur: 0
race: African American
t stage: 3
|
Stage II or III breast cancer Patient 5
|
| Sample_geo_accession | GSM491614
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491614/suppl/GSM491614.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
GSM491615 | GPL570 |
|
Pre-Treatment breast tumor 8159
|
Pre-Treatment breast tumor
|
gender: Female
percent: -28.57
er: 0
pr: 0
her2: 0
grade: 3
histology: IDC
positive nodes: 5
nodes examined: 16
recur: 0
race: Caucasian
t stage: 2
|
Stage II or III breast cancer Patient 6
|
| Sample_geo_accession | GSM491615
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491615/suppl/GSM491615.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
GSM491616 | GPL570 |
|
Pre-Treatment breast tumor 8170
|
Pre-Treatment breast tumor
|
gender: Female
percent: -1000
er: 0
pr: 0
her2: 0
grade: 3
histology: IDC
positive nodes: 0
nodes examined: 19
recur: 0
race: African American
t stage: 2
|
Stage II or III breast cancer Patient 7
|
| Sample_geo_accession | GSM491616
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491616/suppl/GSM491616.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
GSM491617 | GPL570 |
|
Pre-Treatment breast tumor 8189
|
Pre-Treatment breast tumor
|
gender: Female
percent: -100
er: 0
pr: 0
her2: 0
grade: 3
histology: IDC
positive nodes: 0
nodes examined: 9
recur: 0
race: African American
t stage: 2
|
Stage II or III breast cancer Patient 8
|
| Sample_geo_accession | GSM491617
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491617/suppl/GSM491617.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
GSM491618 | GPL570 |
|
Pre-Treatment breast tumor 8190
|
Pre-Treatment breast tumor
|
gender: Female
percent: -68.75
er: 0
pr: 0
her2: 0
grade: 3
histology: IDC
positive nodes: 1
nodes examined: 29
recur: 0
race: African American
t stage: 2
|
Stage II or III breast cancer Patient 9
|
| Sample_geo_accession | GSM491618
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491618/suppl/GSM491618.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
GSM491619 | GPL570 |
|
Pre-Treatment breast tumor 8191
|
Pre-Treatment breast tumor
|
gender: Female
percent: 11.11
er: 0
pr: 0
her2: 0
grade: 3
histology: IDC
positive nodes: 0
nodes examined: 9
recur: 1
race: Caucasian
t stage: 2
|
Stage II or III breast cancer Patient 10
|
| Sample_geo_accession | GSM491619
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491619/suppl/GSM491619.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
GSM491620 | GPL570 |
|
Pre-Treatment breast tumor 8199
|
Pre-Treatment breast tumor
|
gender: Female
percent: -100
er: 0
pr: 0
her2: 0
grade: 3
histology: IDC
positive nodes: 0
nodes examined: 20
recur: 0
race: African American
t stage: 1
|
Stage II or III breast cancer Patient 11
|
| Sample_geo_accession | GSM491620
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491620/suppl/GSM491620.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
GSM491621 | GPL570 |
|
Pre-Treatment breast tumor 8200
|
Pre-Treatment breast tumor
|
gender: Female
percent: -51.61
er: 0
pr: 0
her2: 0
grade: 3
histology: IDC
positive nodes: 1
nodes examined: 26
recur: 0
race: Caucasian
t stage: 2
|
Stage II or III breast cancer Patient 12
|
| Sample_geo_accession | GSM491621
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491621/suppl/GSM491621.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
GSM491622 | GPL570 |
|
Pre-Treatment breast tumor 8209
|
Pre-Treatment breast tumor
|
gender: Female
percent: -10
er: 0
pr: 0
her2: 1
grade: 3
histology: IDC
positive nodes: 1
nodes examined: 15
recur: 1
race: Caucasian
t stage: 2
|
Stage II or III breast cancer Patient 13
|
| Sample_geo_accession | GSM491622
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491622/suppl/GSM491622.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
GSM491623 | GPL570 |
|
Pre-Treatment breast tumor 8210
|
Pre-Treatment breast tumor
|
gender: Female
percent: 53.85
er: 1
pr: 0
her2: 0
grade: 3
histology: IDC
positive nodes: 0
nodes examined: 17
recur: 0
race: Caucasian
t stage: 2
|
Stage II or III breast cancer Patient 14
|
| Sample_geo_accession | GSM491623
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491623/suppl/GSM491623.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
GSM491624 | GPL570 |
|
Pre-Treatment breast tumor 8413
|
Pre-Treatment breast tumor
|
gender: Female
percent: 39.34
er: 0
pr: 0
her2: 0
grade: 2
histology: IDC
positive nodes: 10
nodes examined: 10
recur: 1
race: Caucasian
t stage: 3
|
Stage II or III breast cancer Patient 15
|
| Sample_geo_accession | GSM491624
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491624/suppl/GSM491624.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
GSM491625 | GPL570 |
|
Pre-Treatment breast tumor 11519
|
Pre-Treatment breast tumor
|
gender: Female
percent: -45.65
er: 0
pr: 0
her2: 0
grade: 3
histology: IDC
positive nodes: 0
nodes examined: 16
recur: 0
race: African American
t stage: 2
|
Stage II or III breast cancer Patient 16
|
| Sample_geo_accession | GSM491625
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491625/suppl/GSM491625.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
GSM491626 | GPL570 |
|
Pre-Treatment breast tumor 11524
|
Pre-Treatment breast tumor
|
gender: Female
percent: -51.61
er: 0
pr: 0
her2: 0
grade: 3
histology: IDC
positive nodes: 14
nodes examined: 15
recur: 1
race: Caucasian
t stage: 3
|
Stage II or III breast cancer Patient 17
|
| Sample_geo_accession | GSM491626
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491626/suppl/GSM491626.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
GSM491627 | GPL570 |
|
Pre-Treatment breast tumor 11526
|
Pre-Treatment breast tumor
|
gender: Female
percent: -100
er: 0
pr: 0
her2: 0
grade: 3
histology: IDC
positive nodes: 0
nodes examined: 1
recur: 0
race: Caucasian
t stage: 2
|
Stage II or III breast cancer Patient 18
|
| Sample_geo_accession | GSM491627
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491627/suppl/GSM491627.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
GSM491628 | GPL570 |
|
Pre-Treatment breast tumor 11529
|
Pre-Treatment breast tumor
|
gender: Female
percent: -70.83
er: 0
pr: 0
her2: 0
grade: 3
histology: IDC
positive nodes: 1
nodes examined: 19
recur: 0
race: Caucasian
t stage: 2
|
Stage II or III breast cancer Patient 19
|
| Sample_geo_accession | GSM491628
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491628/suppl/GSM491628.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
GSM491629 | GPL570 |
|
Pre-Treatment breast tumor 11530
|
Pre-Treatment breast tumor
|
gender: Female
percent: 0
er: 0
pr: 0
her2: 0
grade: 3
histology: IDC
positive nodes: 0
nodes examined: 16
recur: 0
race: Caucasian
t stage: 2
|
Stage II or III breast cancer Patient 20
|
| Sample_geo_accession | GSM491629
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491629/suppl/GSM491629.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
GSM491630 | GPL570 |
|
Pre-Treatment breast tumor 11532
|
Pre-Treatment breast tumor
|
gender: Female
percent: -58.97
er: 0
pr: 0
her2: 0
grade: 3
histology: IDC
positive nodes: 0
nodes examined: 1
recur: 0
race: Caucasian
t stage: 2
|
Stage II or III breast cancer Patient 21
|
| Sample_geo_accession | GSM491630
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491630/suppl/GSM491630.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
GSM491631 | GPL570 |
|
Pre-Treatment breast tumor 11571
|
Pre-Treatment breast tumor
|
gender: Female
percent: -97.75
er: 0
pr: 0
her2: 0
grade: 3
histology: IDC
positive nodes: 0
nodes examined: 12
recur: 0
race: Caucasian
t stage: 2
|
Stage II or III breast cancer Patient 22
|
| Sample_geo_accession | GSM491631
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491631/suppl/GSM491631.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
GSM491632 | GPL570 |
|
Pre-Treatment breast tumor 11582
|
Pre-Treatment breast tumor
|
gender: Female
percent: 50
er: 0
pr: 0
her2: 0
grade: 3
histology: IDC
positive nodes: 0
nodes examined: 12
recur: 0
race: African American
t stage: 2
|
Stage II or III breast cancer Patient 23
|
| Sample_geo_accession | GSM491632
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491632/suppl/GSM491632.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
GSM491633 | GPL570 |
|
Pre-Treatment breast tumor 11585
|
Pre-Treatment breast tumor
|
gender: Female
percent: 16.67
er: 0
pr: 0
her2: 0
grade: 3
histology: IDC
positive nodes: 2
nodes examined: 29
recur: 0
race: African American
t stage: 2
|
Stage II or III breast cancer Patient 24
|
| Sample_geo_accession | GSM491633
| | Sample_status | Public on Dec 30 2009
| | Sample_submission_date | Dec 29 2009
| | Sample_last_update_date | Dec 29 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).
| | Sample_hyb_protocol | 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2 GeneChipTM oligonucleotide arrays.
| | Sample_scan_protocol | Gene chips were scanned using GS3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rekha,,Meyer
| | Sample_contact_email | rmeyer@pathbox.wustl.edu
| | Sample_contact_phone | 314 362 8853
| | Sample_contact_institute | Washington University School of Medicine
| | Sample_contact_address | 4320 Forest Park Av
| | Sample_contact_city | St Louis
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 63128
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM491nnn/GSM491633/suppl/GSM491633.CEL.gz
| | Sample_series_id | GSE19697
| | Sample_data_row_count | 54675
| | |
|
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