Search results for the GEO ID: GSE29450  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM729034 | GPL570 |
|
CCOC-1411G
|
Ovarian Clear Cell Cancer
|
tissue: ovary
cell type: Primary tumors from clear cell ovarian cancer
|
Gene expression data from Ovarian Clear Cell Cancer
|
| Sample_geo_accession | GSM729034
| | Sample_status | Public on May 24 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | May 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Ten clear cell ovarian cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). A set of 10 normal ovarian surface epithelium (OSE) cytobrushing specimens was also obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen sections (7μm) were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol for 30 seconds, stained by 1% methyl green, rinsed in deionized water, and air-dried. Microdissection was performed using a MD LMD laser microdissecting microscope (Leica). Tumor cells (~ 5,000) were dissected for each case. Total RNA was isolated using the RNeasy Micro kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from tumor or OSE-derived total RNA using a two-cycle amplification protocol (Affymetrix)
| | Sample_hyb_protocol | A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Global normalization at a target value of 500 was applied to all 20 of the arrays under consideration using Gene Chip Operating Software. Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Drs. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis of the array data.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michael,,Birrer
| | Sample_contact_email | mbirrer@partners.org
| | Sample_contact_phone | 6177244800
| | Sample_contact_laboratory | Surgical Oncology Research Labs
| | Sample_contact_department | Medicine
| | Sample_contact_institute | MGH
| | Sample_contact_address | 70 Blossom Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729034/suppl/GSM729034.CEL.gz
| | Sample_series_id | GSE29450
| | Sample_data_row_count | 54675
| | |
|
GSM729035 | GPL570 |
|
CCOC-1609
|
Ovarian Clear Cell Cancer
|
tissue: ovary
cell type: Primary tumors from clear cell ovarian cancer
|
Gene expression data from Ovarian Clear Cell Cancer
|
| Sample_geo_accession | GSM729035
| | Sample_status | Public on May 24 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | May 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Ten clear cell ovarian cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). A set of 10 normal ovarian surface epithelium (OSE) cytobrushing specimens was also obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen sections (7μm) were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol for 30 seconds, stained by 1% methyl green, rinsed in deionized water, and air-dried. Microdissection was performed using a MD LMD laser microdissecting microscope (Leica). Tumor cells (~ 5,000) were dissected for each case. Total RNA was isolated using the RNeasy Micro kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from tumor or OSE-derived total RNA using a two-cycle amplification protocol (Affymetrix)
| | Sample_hyb_protocol | A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Global normalization at a target value of 500 was applied to all 20 of the arrays under consideration using Gene Chip Operating Software. Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Drs. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis of the array data.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michael,,Birrer
| | Sample_contact_email | mbirrer@partners.org
| | Sample_contact_phone | 6177244800
| | Sample_contact_laboratory | Surgical Oncology Research Labs
| | Sample_contact_department | Medicine
| | Sample_contact_institute | MGH
| | Sample_contact_address | 70 Blossom Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729035/suppl/GSM729035.CEL.gz
| | Sample_series_id | GSE29450
| | Sample_data_row_count | 54675
| | |
|
GSM729036 | GPL570 |
|
CCOC-1638
|
Ovarian Clear Cell Cancer
|
tissue: ovary
cell type: Primary tumors from clear cell ovarian cancer
|
Gene expression data from Ovarian Clear Cell Cancer
|
| Sample_geo_accession | GSM729036
| | Sample_status | Public on May 24 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | May 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Ten clear cell ovarian cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). A set of 10 normal ovarian surface epithelium (OSE) cytobrushing specimens was also obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen sections (7μm) were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol for 30 seconds, stained by 1% methyl green, rinsed in deionized water, and air-dried. Microdissection was performed using a MD LMD laser microdissecting microscope (Leica). Tumor cells (~ 5,000) were dissected for each case. Total RNA was isolated using the RNeasy Micro kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from tumor or OSE-derived total RNA using a two-cycle amplification protocol (Affymetrix)
| | Sample_hyb_protocol | A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Global normalization at a target value of 500 was applied to all 20 of the arrays under consideration using Gene Chip Operating Software. Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Drs. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis of the array data.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michael,,Birrer
| | Sample_contact_email | mbirrer@partners.org
| | Sample_contact_phone | 6177244800
| | Sample_contact_laboratory | Surgical Oncology Research Labs
| | Sample_contact_department | Medicine
| | Sample_contact_institute | MGH
| | Sample_contact_address | 70 Blossom Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729036/suppl/GSM729036.CEL.gz
| | Sample_series_id | GSE29450
| | Sample_data_row_count | 54675
| | |
|
GSM729037 | GPL570 |
|
CCOC-2316
|
Ovarian Clear Cell Cancer
|
tissue: ovary
cell type: Primary tumors from clear cell ovarian cancer
|
Gene expression data from Ovarian Clear Cell Cancer
|
| Sample_geo_accession | GSM729037
| | Sample_status | Public on May 24 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | May 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Ten clear cell ovarian cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). A set of 10 normal ovarian surface epithelium (OSE) cytobrushing specimens was also obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen sections (7μm) were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol for 30 seconds, stained by 1% methyl green, rinsed in deionized water, and air-dried. Microdissection was performed using a MD LMD laser microdissecting microscope (Leica). Tumor cells (~ 5,000) were dissected for each case. Total RNA was isolated using the RNeasy Micro kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from tumor or OSE-derived total RNA using a two-cycle amplification protocol (Affymetrix)
| | Sample_hyb_protocol | A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Global normalization at a target value of 500 was applied to all 20 of the arrays under consideration using Gene Chip Operating Software. Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Drs. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis of the array data.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michael,,Birrer
| | Sample_contact_email | mbirrer@partners.org
| | Sample_contact_phone | 6177244800
| | Sample_contact_laboratory | Surgical Oncology Research Labs
| | Sample_contact_department | Medicine
| | Sample_contact_institute | MGH
| | Sample_contact_address | 70 Blossom Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729037/suppl/GSM729037.CEL.gz
| | Sample_series_id | GSE29450
| | Sample_data_row_count | 54675
| | |
|
GSM729038 | GPL570 |
|
CCOC-2348G
|
Ovarian Clear Cell Cancer
|
tissue: ovary
cell type: Primary tumors from clear cell ovarian cancer
|
Gene expression data from Ovarian Clear Cell Cancer
|
| Sample_geo_accession | GSM729038
| | Sample_status | Public on May 24 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | May 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Ten clear cell ovarian cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). A set of 10 normal ovarian surface epithelium (OSE) cytobrushing specimens was also obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen sections (7μm) were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol for 30 seconds, stained by 1% methyl green, rinsed in deionized water, and air-dried. Microdissection was performed using a MD LMD laser microdissecting microscope (Leica). Tumor cells (~ 5,000) were dissected for each case. Total RNA was isolated using the RNeasy Micro kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from tumor or OSE-derived total RNA using a two-cycle amplification protocol (Affymetrix)
| | Sample_hyb_protocol | A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Global normalization at a target value of 500 was applied to all 20 of the arrays under consideration using Gene Chip Operating Software. Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Drs. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis of the array data.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michael,,Birrer
| | Sample_contact_email | mbirrer@partners.org
| | Sample_contact_phone | 6177244800
| | Sample_contact_laboratory | Surgical Oncology Research Labs
| | Sample_contact_department | Medicine
| | Sample_contact_institute | MGH
| | Sample_contact_address | 70 Blossom Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729038/suppl/GSM729038.CEL.gz
| | Sample_series_id | GSE29450
| | Sample_data_row_count | 54675
| | |
|
GSM729039 | GPL570 |
|
CCOC-2501
|
Ovarian Clear Cell Cancer
|
tissue: ovary
cell type: Primary tumors from clear cell ovarian cancer
|
Gene expression data from Ovarian Clear Cell Cancer
|
| Sample_geo_accession | GSM729039
| | Sample_status | Public on May 24 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | May 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Ten clear cell ovarian cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). A set of 10 normal ovarian surface epithelium (OSE) cytobrushing specimens was also obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen sections (7μm) were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol for 30 seconds, stained by 1% methyl green, rinsed in deionized water, and air-dried. Microdissection was performed using a MD LMD laser microdissecting microscope (Leica). Tumor cells (~ 5,000) were dissected for each case. Total RNA was isolated using the RNeasy Micro kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from tumor or OSE-derived total RNA using a two-cycle amplification protocol (Affymetrix)
| | Sample_hyb_protocol | A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Global normalization at a target value of 500 was applied to all 20 of the arrays under consideration using Gene Chip Operating Software. Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Drs. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis of the array data.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michael,,Birrer
| | Sample_contact_email | mbirrer@partners.org
| | Sample_contact_phone | 6177244800
| | Sample_contact_laboratory | Surgical Oncology Research Labs
| | Sample_contact_department | Medicine
| | Sample_contact_institute | MGH
| | Sample_contact_address | 70 Blossom Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729039/suppl/GSM729039.CEL.gz
| | Sample_series_id | GSE29450
| | Sample_data_row_count | 54675
| | |
|
GSM729040 | GPL570 |
|
CCOC-451G
|
Ovarian Clear Cell Cancer
|
tissue: ovary
cell type: Primary tumors from clear cell ovarian cancer
|
Gene expression data from Ovarian Clear Cell Cancer
|
| Sample_geo_accession | GSM729040
| | Sample_status | Public on May 24 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | May 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Ten clear cell ovarian cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). A set of 10 normal ovarian surface epithelium (OSE) cytobrushing specimens was also obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen sections (7μm) were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol for 30 seconds, stained by 1% methyl green, rinsed in deionized water, and air-dried. Microdissection was performed using a MD LMD laser microdissecting microscope (Leica). Tumor cells (~ 5,000) were dissected for each case. Total RNA was isolated using the RNeasy Micro kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from tumor or OSE-derived total RNA using a two-cycle amplification protocol (Affymetrix)
| | Sample_hyb_protocol | A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Global normalization at a target value of 500 was applied to all 20 of the arrays under consideration using Gene Chip Operating Software. Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Drs. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis of the array data.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michael,,Birrer
| | Sample_contact_email | mbirrer@partners.org
| | Sample_contact_phone | 6177244800
| | Sample_contact_laboratory | Surgical Oncology Research Labs
| | Sample_contact_department | Medicine
| | Sample_contact_institute | MGH
| | Sample_contact_address | 70 Blossom Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729040/suppl/GSM729040.CEL.gz
| | Sample_series_id | GSE29450
| | Sample_data_row_count | 54675
| | |
|
GSM729041 | GPL570 |
|
CCOC-671G
|
Ovarian Clear Cell Cancer
|
tissue: ovary
cell type: Primary tumors from clear cell ovarian cancer
|
Gene expression data from Ovarian Clear Cell Cancer
|
| Sample_geo_accession | GSM729041
| | Sample_status | Public on May 24 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | May 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Ten clear cell ovarian cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). A set of 10 normal ovarian surface epithelium (OSE) cytobrushing specimens was also obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen sections (7μm) were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol for 30 seconds, stained by 1% methyl green, rinsed in deionized water, and air-dried. Microdissection was performed using a MD LMD laser microdissecting microscope (Leica). Tumor cells (~ 5,000) were dissected for each case. Total RNA was isolated using the RNeasy Micro kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from tumor or OSE-derived total RNA using a two-cycle amplification protocol (Affymetrix)
| | Sample_hyb_protocol | A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Global normalization at a target value of 500 was applied to all 20 of the arrays under consideration using Gene Chip Operating Software. Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Drs. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis of the array data.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michael,,Birrer
| | Sample_contact_email | mbirrer@partners.org
| | Sample_contact_phone | 6177244800
| | Sample_contact_laboratory | Surgical Oncology Research Labs
| | Sample_contact_department | Medicine
| | Sample_contact_institute | MGH
| | Sample_contact_address | 70 Blossom Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729041/suppl/GSM729041.CEL.gz
| | Sample_series_id | GSE29450
| | Sample_data_row_count | 54675
| | |
|
GSM729042 | GPL570 |
|
CCOC-805G
|
Ovarian Clear Cell Cancer
|
tissue: ovary
cell type: Primary tumors from clear cell ovarian cancer
|
Gene expression data from Ovarian Clear Cell Cancer
|
| Sample_geo_accession | GSM729042
| | Sample_status | Public on May 24 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | May 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Ten clear cell ovarian cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). A set of 10 normal ovarian surface epithelium (OSE) cytobrushing specimens was also obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen sections (7μm) were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol for 30 seconds, stained by 1% methyl green, rinsed in deionized water, and air-dried. Microdissection was performed using a MD LMD laser microdissecting microscope (Leica). Tumor cells (~ 5,000) were dissected for each case. Total RNA was isolated using the RNeasy Micro kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from tumor or OSE-derived total RNA using a two-cycle amplification protocol (Affymetrix)
| | Sample_hyb_protocol | A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Global normalization at a target value of 500 was applied to all 20 of the arrays under consideration using Gene Chip Operating Software. Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Drs. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis of the array data.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michael,,Birrer
| | Sample_contact_email | mbirrer@partners.org
| | Sample_contact_phone | 6177244800
| | Sample_contact_laboratory | Surgical Oncology Research Labs
| | Sample_contact_department | Medicine
| | Sample_contact_institute | MGH
| | Sample_contact_address | 70 Blossom Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729042/suppl/GSM729042.CEL.gz
| | Sample_series_id | GSE29450
| | Sample_data_row_count | 54675
| | |
|
GSM729043 | GPL570 |
|
CCOC-810G
|
Ovarian Clear Cell Cancer
|
tissue: ovary
cell type: Primary tumors from clear cell ovarian cancer
|
Gene expression data from Ovarian Clear Cell Cancer
|
| Sample_geo_accession | GSM729043
| | Sample_status | Public on May 24 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | May 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Ten clear cell ovarian cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). A set of 10 normal ovarian surface epithelium (OSE) cytobrushing specimens was also obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen sections (7μm) were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol for 30 seconds, stained by 1% methyl green, rinsed in deionized water, and air-dried. Microdissection was performed using a MD LMD laser microdissecting microscope (Leica). Tumor cells (~ 5,000) were dissected for each case. Total RNA was isolated using the RNeasy Micro kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from tumor or OSE-derived total RNA using a two-cycle amplification protocol (Affymetrix)
| | Sample_hyb_protocol | A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Global normalization at a target value of 500 was applied to all 20 of the arrays under consideration using Gene Chip Operating Software. Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Drs. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis of the array data.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michael,,Birrer
| | Sample_contact_email | mbirrer@partners.org
| | Sample_contact_phone | 6177244800
| | Sample_contact_laboratory | Surgical Oncology Research Labs
| | Sample_contact_department | Medicine
| | Sample_contact_institute | MGH
| | Sample_contact_address | 70 Blossom Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729043/suppl/GSM729043.CEL.gz
| | Sample_series_id | GSE29450
| | Sample_data_row_count | 54675
| | |
|
GSM729044 | GPL570 |
|
HOSE2008
|
Normal
|
tissue: ovary
cell type: Normal ovarian surface epithelium
|
Gene expression data from ovarian surface epithelial cells
|
| Sample_geo_accession | GSM729044
| | Sample_status | Public on May 24 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | May 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Ten clear cell ovarian cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). A set of 10 normal ovarian surface epithelium (OSE) cytobrushing specimens was also obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen sections (7μm) were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol for 30 seconds, stained by 1% methyl green, rinsed in deionized water, and air-dried. Microdissection was performed using a MD LMD laser microdissecting microscope (Leica). Tumor cells (~ 5,000) were dissected for each case. Total RNA was isolated using the RNeasy Micro kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from tumor or OSE-derived total RNA using a two-cycle amplification protocol (Affymetrix)
| | Sample_hyb_protocol | A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Global normalization at a target value of 500 was applied to all 20 of the arrays under consideration using Gene Chip Operating Software. Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Drs. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis of the array data.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michael,,Birrer
| | Sample_contact_email | mbirrer@partners.org
| | Sample_contact_phone | 6177244800
| | Sample_contact_laboratory | Surgical Oncology Research Labs
| | Sample_contact_department | Medicine
| | Sample_contact_institute | MGH
| | Sample_contact_address | 70 Blossom Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729044/suppl/GSM729044.CEL.gz
| | Sample_series_id | GSE29450
| | Sample_data_row_count | 54675
| | |
|
GSM729045 | GPL570 |
|
HOSE2061
|
Normal
|
tissue: ovary
cell type: Normal ovarian surface epithelium
|
Gene expression data from ovarian surface epithelial cells
|
| Sample_geo_accession | GSM729045
| | Sample_status | Public on May 24 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | May 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Ten clear cell ovarian cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). A set of 10 normal ovarian surface epithelium (OSE) cytobrushing specimens was also obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen sections (7μm) were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol for 30 seconds, stained by 1% methyl green, rinsed in deionized water, and air-dried. Microdissection was performed using a MD LMD laser microdissecting microscope (Leica). Tumor cells (~ 5,000) were dissected for each case. Total RNA was isolated using the RNeasy Micro kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from tumor or OSE-derived total RNA using a two-cycle amplification protocol (Affymetrix)
| | Sample_hyb_protocol | A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Global normalization at a target value of 500 was applied to all 20 of the arrays under consideration using Gene Chip Operating Software. Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Drs. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis of the array data.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michael,,Birrer
| | Sample_contact_email | mbirrer@partners.org
| | Sample_contact_phone | 6177244800
| | Sample_contact_laboratory | Surgical Oncology Research Labs
| | Sample_contact_department | Medicine
| | Sample_contact_institute | MGH
| | Sample_contact_address | 70 Blossom Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729045/suppl/GSM729045.CEL.gz
| | Sample_series_id | GSE29450
| | Sample_data_row_count | 54675
| | |
|
GSM729046 | GPL570 |
|
HOSE2064
|
Normal
|
tissue: ovary
cell type: Normal ovarian surface epithelium
|
Gene expression data from ovarian surface epithelial cells
|
| Sample_geo_accession | GSM729046
| | Sample_status | Public on May 24 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | May 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Ten clear cell ovarian cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). A set of 10 normal ovarian surface epithelium (OSE) cytobrushing specimens was also obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen sections (7μm) were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol for 30 seconds, stained by 1% methyl green, rinsed in deionized water, and air-dried. Microdissection was performed using a MD LMD laser microdissecting microscope (Leica). Tumor cells (~ 5,000) were dissected for each case. Total RNA was isolated using the RNeasy Micro kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from tumor or OSE-derived total RNA using a two-cycle amplification protocol (Affymetrix)
| | Sample_hyb_protocol | A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Global normalization at a target value of 500 was applied to all 20 of the arrays under consideration using Gene Chip Operating Software. Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Drs. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis of the array data.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michael,,Birrer
| | Sample_contact_email | mbirrer@partners.org
| | Sample_contact_phone | 6177244800
| | Sample_contact_laboratory | Surgical Oncology Research Labs
| | Sample_contact_department | Medicine
| | Sample_contact_institute | MGH
| | Sample_contact_address | 70 Blossom Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729046/suppl/GSM729046.CEL.gz
| | Sample_series_id | GSE29450
| | Sample_data_row_count | 54675
| | |
|
GSM729047 | GPL570 |
|
HOSE2085
|
Normal
|
tissue: ovary
cell type: Normal ovarian surface epithelium
|
Gene expression data from ovarian surface epithelial cells
|
| Sample_geo_accession | GSM729047
| | Sample_status | Public on May 24 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | May 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Ten clear cell ovarian cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). A set of 10 normal ovarian surface epithelium (OSE) cytobrushing specimens was also obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen sections (7μm) were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol for 30 seconds, stained by 1% methyl green, rinsed in deionized water, and air-dried. Microdissection was performed using a MD LMD laser microdissecting microscope (Leica). Tumor cells (~ 5,000) were dissected for each case. Total RNA was isolated using the RNeasy Micro kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from tumor or OSE-derived total RNA using a two-cycle amplification protocol (Affymetrix)
| | Sample_hyb_protocol | A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Global normalization at a target value of 500 was applied to all 20 of the arrays under consideration using Gene Chip Operating Software. Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Drs. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis of the array data.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michael,,Birrer
| | Sample_contact_email | mbirrer@partners.org
| | Sample_contact_phone | 6177244800
| | Sample_contact_laboratory | Surgical Oncology Research Labs
| | Sample_contact_department | Medicine
| | Sample_contact_institute | MGH
| | Sample_contact_address | 70 Blossom Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729047/suppl/GSM729047.CEL.gz
| | Sample_series_id | GSE29450
| | Sample_data_row_count | 54675
| | |
|
GSM729048 | GPL570 |
|
HOSE2225
|
Normal
|
tissue: ovary
cell type: Normal ovarian surface epithelium
|
Gene expression data from ovarian surface epithelial cells
|
| Sample_geo_accession | GSM729048
| | Sample_status | Public on May 24 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | May 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Ten clear cell ovarian cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). A set of 10 normal ovarian surface epithelium (OSE) cytobrushing specimens was also obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen sections (7μm) were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol for 30 seconds, stained by 1% methyl green, rinsed in deionized water, and air-dried. Microdissection was performed using a MD LMD laser microdissecting microscope (Leica). Tumor cells (~ 5,000) were dissected for each case. Total RNA was isolated using the RNeasy Micro kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from tumor or OSE-derived total RNA using a two-cycle amplification protocol (Affymetrix)
| | Sample_hyb_protocol | A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Global normalization at a target value of 500 was applied to all 20 of the arrays under consideration using Gene Chip Operating Software. Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Drs. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis of the array data.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michael,,Birrer
| | Sample_contact_email | mbirrer@partners.org
| | Sample_contact_phone | 6177244800
| | Sample_contact_laboratory | Surgical Oncology Research Labs
| | Sample_contact_department | Medicine
| | Sample_contact_institute | MGH
| | Sample_contact_address | 70 Blossom Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729048/suppl/GSM729048.CEL.gz
| | Sample_series_id | GSE29450
| | Sample_data_row_count | 54675
| | |
|
GSM729049 | GPL570 |
|
HOSE2226
|
Normal
|
tissue: ovary
cell type: Normal ovarian surface epithelium
|
Gene expression data from ovarian surface epithelial cells
|
| Sample_geo_accession | GSM729049
| | Sample_status | Public on May 24 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | May 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Ten clear cell ovarian cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). A set of 10 normal ovarian surface epithelium (OSE) cytobrushing specimens was also obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen sections (7μm) were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol for 30 seconds, stained by 1% methyl green, rinsed in deionized water, and air-dried. Microdissection was performed using a MD LMD laser microdissecting microscope (Leica). Tumor cells (~ 5,000) were dissected for each case. Total RNA was isolated using the RNeasy Micro kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from tumor or OSE-derived total RNA using a two-cycle amplification protocol (Affymetrix)
| | Sample_hyb_protocol | A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Global normalization at a target value of 500 was applied to all 20 of the arrays under consideration using Gene Chip Operating Software. Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Drs. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis of the array data.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michael,,Birrer
| | Sample_contact_email | mbirrer@partners.org
| | Sample_contact_phone | 6177244800
| | Sample_contact_laboratory | Surgical Oncology Research Labs
| | Sample_contact_department | Medicine
| | Sample_contact_institute | MGH
| | Sample_contact_address | 70 Blossom Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729049/suppl/GSM729049.CEL.gz
| | Sample_series_id | GSE29450
| | Sample_data_row_count | 54675
| | |
|
GSM729050 | GPL570 |
|
HOSE2228
|
Normal
|
tissue: ovary
cell type: Normal ovarian surface epithelium
|
Gene expression data from ovarian surface epithelial cells
|
| Sample_geo_accession | GSM729050
| | Sample_status | Public on May 24 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | May 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Ten clear cell ovarian cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). A set of 10 normal ovarian surface epithelium (OSE) cytobrushing specimens was also obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen sections (7μm) were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol for 30 seconds, stained by 1% methyl green, rinsed in deionized water, and air-dried. Microdissection was performed using a MD LMD laser microdissecting microscope (Leica). Tumor cells (~ 5,000) were dissected for each case. Total RNA was isolated using the RNeasy Micro kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from tumor or OSE-derived total RNA using a two-cycle amplification protocol (Affymetrix)
| | Sample_hyb_protocol | A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Global normalization at a target value of 500 was applied to all 20 of the arrays under consideration using Gene Chip Operating Software. Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Drs. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis of the array data.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michael,,Birrer
| | Sample_contact_email | mbirrer@partners.org
| | Sample_contact_phone | 6177244800
| | Sample_contact_laboratory | Surgical Oncology Research Labs
| | Sample_contact_department | Medicine
| | Sample_contact_institute | MGH
| | Sample_contact_address | 70 Blossom Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729050/suppl/GSM729050.CEL.gz
| | Sample_series_id | GSE29450
| | Sample_data_row_count | 54675
| | |
|
GSM729051 | GPL570 |
|
HOSE2230
|
Normal
|
tissue: ovary
cell type: Normal ovarian surface epithelium
|
Gene expression data from ovarian surface epithelial cells
|
| Sample_geo_accession | GSM729051
| | Sample_status | Public on May 24 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | May 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Ten clear cell ovarian cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). A set of 10 normal ovarian surface epithelium (OSE) cytobrushing specimens was also obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen sections (7μm) were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol for 30 seconds, stained by 1% methyl green, rinsed in deionized water, and air-dried. Microdissection was performed using a MD LMD laser microdissecting microscope (Leica). Tumor cells (~ 5,000) were dissected for each case. Total RNA was isolated using the RNeasy Micro kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from tumor or OSE-derived total RNA using a two-cycle amplification protocol (Affymetrix)
| | Sample_hyb_protocol | A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Global normalization at a target value of 500 was applied to all 20 of the arrays under consideration using Gene Chip Operating Software. Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Drs. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis of the array data.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michael,,Birrer
| | Sample_contact_email | mbirrer@partners.org
| | Sample_contact_phone | 6177244800
| | Sample_contact_laboratory | Surgical Oncology Research Labs
| | Sample_contact_department | Medicine
| | Sample_contact_institute | MGH
| | Sample_contact_address | 70 Blossom Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729051/suppl/GSM729051.CEL.gz
| | Sample_series_id | GSE29450
| | Sample_data_row_count | 54675
| | |
|
GSM729052 | GPL570 |
|
HOSE2234
|
Normal
|
tissue: ovary
cell type: Normal ovarian surface epithelium
|
Gene expression data from ovarian surface epithelial cells
|
| Sample_geo_accession | GSM729052
| | Sample_status | Public on May 24 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | May 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Ten clear cell ovarian cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). A set of 10 normal ovarian surface epithelium (OSE) cytobrushing specimens was also obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen sections (7μm) were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol for 30 seconds, stained by 1% methyl green, rinsed in deionized water, and air-dried. Microdissection was performed using a MD LMD laser microdissecting microscope (Leica). Tumor cells (~ 5,000) were dissected for each case. Total RNA was isolated using the RNeasy Micro kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from tumor or OSE-derived total RNA using a two-cycle amplification protocol (Affymetrix)
| | Sample_hyb_protocol | A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Global normalization at a target value of 500 was applied to all 20 of the arrays under consideration using Gene Chip Operating Software. Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Drs. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis of the array data.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michael,,Birrer
| | Sample_contact_email | mbirrer@partners.org
| | Sample_contact_phone | 6177244800
| | Sample_contact_laboratory | Surgical Oncology Research Labs
| | Sample_contact_department | Medicine
| | Sample_contact_institute | MGH
| | Sample_contact_address | 70 Blossom Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729052/suppl/GSM729052.CEL.gz
| | Sample_series_id | GSE29450
| | Sample_data_row_count | 54675
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GSM729053 | GPL570 |
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HOSE2237
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Normal
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tissue: ovary
cell type: Normal ovarian surface epithelium
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Gene expression data from ovarian surface epithelial cells
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| Sample_geo_accession | GSM729053
| | Sample_status | Public on May 24 2011
| | Sample_submission_date | May 23 2011
| | Sample_last_update_date | May 24 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Ten clear cell ovarian cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). A set of 10 normal ovarian surface epithelium (OSE) cytobrushing specimens was also obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Frozen sections (7μm) were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol for 30 seconds, stained by 1% methyl green, rinsed in deionized water, and air-dried. Microdissection was performed using a MD LMD laser microdissecting microscope (Leica). Tumor cells (~ 5,000) were dissected for each case. Total RNA was isolated using the RNeasy Micro kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from tumor or OSE-derived total RNA using a two-cycle amplification protocol (Affymetrix)
| | Sample_hyb_protocol | A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Global normalization at a target value of 500 was applied to all 20 of the arrays under consideration using Gene Chip Operating Software. Biometric Research Branch (BRB) ArrayTools version 3.2.2 software developed by Drs. Richard Simon and Amy Peng Lam of the Biometrics Research Branch of the National Cancer Institute was used to filter and complete the statistical analysis of the array data.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Michael,,Birrer
| | Sample_contact_email | mbirrer@partners.org
| | Sample_contact_phone | 6177244800
| | Sample_contact_laboratory | Surgical Oncology Research Labs
| | Sample_contact_department | Medicine
| | Sample_contact_institute | MGH
| | Sample_contact_address | 70 Blossom Street
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM729nnn/GSM729053/suppl/GSM729053.CEL.gz
| | Sample_series_id | GSE29450
| | Sample_data_row_count | 54675
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