Search results for the GEO ID: GSE33874  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM838230 | GPL570 |
|
Hoechst33342 dye sorted main population-1
|
Ovarian Cancer
|
cell type: high-grade advanced stage ovarian adenocarcinoma
sample: 1
cell population: MP
|
Gene expression data from high-grade advanced stage ovarian adenocarcinoma MP Cells
|
| Sample_geo_accession | GSM838230
| | Sample_status | Public on Nov 23 2011
| | Sample_submission_date | Nov 22 2011
| | Sample_last_update_date | Nov 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fresh ascites was obtained from 10 women with high-grade advanced stage ovarian adenocarcinoma at the time of primary cytoreductive surgery at Brigham and Women's Hospital, Boston, MA. All the specimens were collected under the protocols approved by the institutional review boards of the Brigham and Women’s Hospital and were obtained with informed written consent from the patients
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The ascites samples were centrifuged at 1400 RPM to isolate the cells. After lysis of the erythrocytes, the remaining cells were seeded and grown in culture dishes without passaging. Before sorting, cells were stained with CD45 to rule out contamination with blood cells and with CA125 antibody to confirm the ovarian origin of these cells. Between day 7 and 10 cells were stained with Hoechst33342 dye and sorted for side population and main population cells. The RNA was extracted from the SP and MP cells using the RNeasy kit (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from SP and MP 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/GSM838nnn/GSM838230/suppl/GSM838230.CEL.gz
| | Sample_series_id | GSE33874
| | Sample_data_row_count | 54675
| | |
|
GSM838231 | GPL570 |
|
Hoechst33342 dye sorted side population-1
|
Ovarian Cancer
|
cell type: high-grade advanced stage ovarian adenocarcinoma
sample: 1
cell population: SP
|
Gene expression data from high-grade advanced stage ovarian adenocarcinoma SP Cells
|
| Sample_geo_accession | GSM838231
| | Sample_status | Public on Nov 23 2011
| | Sample_submission_date | Nov 22 2011
| | Sample_last_update_date | Nov 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fresh ascites was obtained from 10 women with high-grade advanced stage ovarian adenocarcinoma at the time of primary cytoreductive surgery at Brigham and Women's Hospital, Boston, MA. All the specimens were collected under the protocols approved by the institutional review boards of the Brigham and Women’s Hospital and were obtained with informed written consent from the patients
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The ascites samples were centrifuged at 1400 RPM to isolate the cells. After lysis of the erythrocytes, the remaining cells were seeded and grown in culture dishes without passaging. Before sorting, cells were stained with CD45 to rule out contamination with blood cells and with CA125 antibody to confirm the ovarian origin of these cells. Between day 7 and 10 cells were stained with Hoechst33342 dye and sorted for side population and main population cells. The RNA was extracted from the SP and MP cells using the RNeasy kit (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from SP and MP 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/GSM838nnn/GSM838231/suppl/GSM838231.CEL.gz
| | Sample_series_id | GSE33874
| | Sample_data_row_count | 54675
| | |
|
GSM838232 | GPL570 |
|
Hoechst33342 dye sorted main population-2
|
Ovarian Cancer
|
cell type: high-grade advanced stage ovarian adenocarcinoma
sample: 2
cell population: MP
|
Gene expression data from high-grade advanced stage ovarian adenocarcinoma MP Cells
|
| Sample_geo_accession | GSM838232
| | Sample_status | Public on Nov 23 2011
| | Sample_submission_date | Nov 22 2011
| | Sample_last_update_date | Nov 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fresh ascites was obtained from 10 women with high-grade advanced stage ovarian adenocarcinoma at the time of primary cytoreductive surgery at Brigham and Women's Hospital, Boston, MA. All the specimens were collected under the protocols approved by the institutional review boards of the Brigham and Women’s Hospital and were obtained with informed written consent from the patients
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The ascites samples were centrifuged at 1400 RPM to isolate the cells. After lysis of the erythrocytes, the remaining cells were seeded and grown in culture dishes without passaging. Before sorting, cells were stained with CD45 to rule out contamination with blood cells and with CA125 antibody to confirm the ovarian origin of these cells. Between day 7 and 10 cells were stained with Hoechst33342 dye and sorted for side population and main population cells. The RNA was extracted from the SP and MP cells using the RNeasy kit (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from SP and MP 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/GSM838nnn/GSM838232/suppl/GSM838232.CEL.gz
| | Sample_series_id | GSE33874
| | Sample_data_row_count | 54675
| | |
|
GSM838233 | GPL570 |
|
Hoechst33342 dye sorted side population-2
|
Ovarian Cancer
|
cell type: high-grade advanced stage ovarian adenocarcinoma
sample: 2
cell population: SP
|
Gene expression data from high-grade advanced stage ovarian adenocarcinoma SP Cells
|
| Sample_geo_accession | GSM838233
| | Sample_status | Public on Nov 23 2011
| | Sample_submission_date | Nov 22 2011
| | Sample_last_update_date | Nov 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fresh ascites was obtained from 10 women with high-grade advanced stage ovarian adenocarcinoma at the time of primary cytoreductive surgery at Brigham and Women's Hospital, Boston, MA. All the specimens were collected under the protocols approved by the institutional review boards of the Brigham and Women’s Hospital and were obtained with informed written consent from the patients
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The ascites samples were centrifuged at 1400 RPM to isolate the cells. After lysis of the erythrocytes, the remaining cells were seeded and grown in culture dishes without passaging. Before sorting, cells were stained with CD45 to rule out contamination with blood cells and with CA125 antibody to confirm the ovarian origin of these cells. Between day 7 and 10 cells were stained with Hoechst33342 dye and sorted for side population and main population cells. The RNA was extracted from the SP and MP cells using the RNeasy kit (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from SP and MP 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/GSM838nnn/GSM838233/suppl/GSM838233.CEL.gz
| | Sample_series_id | GSE33874
| | Sample_data_row_count | 54675
| | |
|
GSM838234 | GPL570 |
|
Hoechst33342 dye sorted main population-3
|
Ovarian Cancer
|
cell type: high-grade advanced stage ovarian adenocarcinoma
sample: 3
cell population: MP
|
Gene expression data from high-grade advanced stage ovarian adenocarcinoma MP Cells
|
| Sample_geo_accession | GSM838234
| | Sample_status | Public on Nov 23 2011
| | Sample_submission_date | Nov 22 2011
| | Sample_last_update_date | Nov 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fresh ascites was obtained from 10 women with high-grade advanced stage ovarian adenocarcinoma at the time of primary cytoreductive surgery at Brigham and Women's Hospital, Boston, MA. All the specimens were collected under the protocols approved by the institutional review boards of the Brigham and Women’s Hospital and were obtained with informed written consent from the patients
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The ascites samples were centrifuged at 1400 RPM to isolate the cells. After lysis of the erythrocytes, the remaining cells were seeded and grown in culture dishes without passaging. Before sorting, cells were stained with CD45 to rule out contamination with blood cells and with CA125 antibody to confirm the ovarian origin of these cells. Between day 7 and 10 cells were stained with Hoechst33342 dye and sorted for side population and main population cells. The RNA was extracted from the SP and MP cells using the RNeasy kit (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from SP and MP 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/GSM838nnn/GSM838234/suppl/GSM838234.CEL.gz
| | Sample_series_id | GSE33874
| | Sample_data_row_count | 54675
| | |
|
GSM838235 | GPL570 |
|
Hoechst33342 dye sorted side population-3
|
Ovarian Cancer
|
cell type: high-grade advanced stage ovarian adenocarcinoma
sample: 3
cell population: SP
|
Gene expression data from high-grade advanced stage ovarian adenocarcinoma SP Cells
|
| Sample_geo_accession | GSM838235
| | Sample_status | Public on Nov 23 2011
| | Sample_submission_date | Nov 22 2011
| | Sample_last_update_date | Nov 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fresh ascites was obtained from 10 women with high-grade advanced stage ovarian adenocarcinoma at the time of primary cytoreductive surgery at Brigham and Women's Hospital, Boston, MA. All the specimens were collected under the protocols approved by the institutional review boards of the Brigham and Women’s Hospital and were obtained with informed written consent from the patients
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The ascites samples were centrifuged at 1400 RPM to isolate the cells. After lysis of the erythrocytes, the remaining cells were seeded and grown in culture dishes without passaging. Before sorting, cells were stained with CD45 to rule out contamination with blood cells and with CA125 antibody to confirm the ovarian origin of these cells. Between day 7 and 10 cells were stained with Hoechst33342 dye and sorted for side population and main population cells. The RNA was extracted from the SP and MP cells using the RNeasy kit (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from SP and MP 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/GSM838nnn/GSM838235/suppl/GSM838235.CEL.gz
| | Sample_series_id | GSE33874
| | Sample_data_row_count | 54675
| | |
|
GSM838236 | GPL570 |
|
Hoechst33342 dye sorted main population-4
|
Ovarian Cancer
|
cell type: high-grade advanced stage ovarian adenocarcinoma
sample: 4
cell population: MP
|
Gene expression data from high-grade advanced stage ovarian adenocarcinoma MP Cells
|
| Sample_geo_accession | GSM838236
| | Sample_status | Public on Nov 23 2011
| | Sample_submission_date | Nov 22 2011
| | Sample_last_update_date | Nov 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fresh ascites was obtained from 10 women with high-grade advanced stage ovarian adenocarcinoma at the time of primary cytoreductive surgery at Brigham and Women's Hospital, Boston, MA. All the specimens were collected under the protocols approved by the institutional review boards of the Brigham and Women’s Hospital and were obtained with informed written consent from the patients
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The ascites samples were centrifuged at 1400 RPM to isolate the cells. After lysis of the erythrocytes, the remaining cells were seeded and grown in culture dishes without passaging. Before sorting, cells were stained with CD45 to rule out contamination with blood cells and with CA125 antibody to confirm the ovarian origin of these cells. Between day 7 and 10 cells were stained with Hoechst33342 dye and sorted for side population and main population cells. The RNA was extracted from the SP and MP cells using the RNeasy kit (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from SP and MP 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/GSM838nnn/GSM838236/suppl/GSM838236.CEL.gz
| | Sample_series_id | GSE33874
| | Sample_data_row_count | 54675
| | |
|
GSM838237 | GPL570 |
|
Hoechst33342 dye sorted side population-4
|
Ovarian Cancer
|
cell type: high-grade advanced stage ovarian adenocarcinoma
sample: 4
cell population: SP
|
Gene expression data from high-grade advanced stage ovarian adenocarcinoma SP Cells
|
| Sample_geo_accession | GSM838237
| | Sample_status | Public on Nov 23 2011
| | Sample_submission_date | Nov 22 2011
| | Sample_last_update_date | Nov 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fresh ascites was obtained from 10 women with high-grade advanced stage ovarian adenocarcinoma at the time of primary cytoreductive surgery at Brigham and Women's Hospital, Boston, MA. All the specimens were collected under the protocols approved by the institutional review boards of the Brigham and Women’s Hospital and were obtained with informed written consent from the patients
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The ascites samples were centrifuged at 1400 RPM to isolate the cells. After lysis of the erythrocytes, the remaining cells were seeded and grown in culture dishes without passaging. Before sorting, cells were stained with CD45 to rule out contamination with blood cells and with CA125 antibody to confirm the ovarian origin of these cells. Between day 7 and 10 cells were stained with Hoechst33342 dye and sorted for side population and main population cells. The RNA was extracted from the SP and MP cells using the RNeasy kit (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from SP and MP 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/GSM838nnn/GSM838237/suppl/GSM838237.CEL.gz
| | Sample_series_id | GSE33874
| | Sample_data_row_count | 54675
| | |
|
GSM838238 | GPL570 |
|
Hoechst33342 dye sorted main population-5
|
Ovarian Cancer
|
cell type: high-grade advanced stage ovarian adenocarcinoma
sample: 5
cell population: MP
|
Gene expression data from high-grade advanced stage ovarian adenocarcinoma MP Cells
|
| Sample_geo_accession | GSM838238
| | Sample_status | Public on Nov 23 2011
| | Sample_submission_date | Nov 22 2011
| | Sample_last_update_date | Nov 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fresh ascites was obtained from 10 women with high-grade advanced stage ovarian adenocarcinoma at the time of primary cytoreductive surgery at Brigham and Women's Hospital, Boston, MA. All the specimens were collected under the protocols approved by the institutional review boards of the Brigham and Women’s Hospital and were obtained with informed written consent from the patients
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The ascites samples were centrifuged at 1400 RPM to isolate the cells. After lysis of the erythrocytes, the remaining cells were seeded and grown in culture dishes without passaging. Before sorting, cells were stained with CD45 to rule out contamination with blood cells and with CA125 antibody to confirm the ovarian origin of these cells. Between day 7 and 10 cells were stained with Hoechst33342 dye and sorted for side population and main population cells. The RNA was extracted from the SP and MP cells using the RNeasy kit (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from SP and MP 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/GSM838nnn/GSM838238/suppl/GSM838238.CEL.gz
| | Sample_series_id | GSE33874
| | Sample_data_row_count | 54675
| | |
|
GSM838239 | GPL570 |
|
Hoechst33342 dye sorted side population-5
|
Ovarian Cancer
|
cell type: high-grade advanced stage ovarian adenocarcinoma
sample: 5
cell population: SP
|
Gene expression data from high-grade advanced stage ovarian adenocarcinoma SP Cells
|
| Sample_geo_accession | GSM838239
| | Sample_status | Public on Nov 23 2011
| | Sample_submission_date | Nov 22 2011
| | Sample_last_update_date | Nov 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fresh ascites was obtained from 10 women with high-grade advanced stage ovarian adenocarcinoma at the time of primary cytoreductive surgery at Brigham and Women's Hospital, Boston, MA. All the specimens were collected under the protocols approved by the institutional review boards of the Brigham and Women’s Hospital and were obtained with informed written consent from the patients
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The ascites samples were centrifuged at 1400 RPM to isolate the cells. After lysis of the erythrocytes, the remaining cells were seeded and grown in culture dishes without passaging. Before sorting, cells were stained with CD45 to rule out contamination with blood cells and with CA125 antibody to confirm the ovarian origin of these cells. Between day 7 and 10 cells were stained with Hoechst33342 dye and sorted for side population and main population cells. The RNA was extracted from the SP and MP cells using the RNeasy kit (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from SP and MP 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/GSM838nnn/GSM838239/suppl/GSM838239.CEL.gz
| | Sample_series_id | GSE33874
| | Sample_data_row_count | 54675
| | |
|
GSM838240 | GPL570 |
|
Hoechst33342 dye sorted main population-6
|
Ovarian Cancer
|
cell type: high-grade advanced stage ovarian adenocarcinoma
sample: 6
cell population: MP
|
Gene expression data from high-grade advanced stage ovarian adenocarcinoma MP Cells
|
| Sample_geo_accession | GSM838240
| | Sample_status | Public on Nov 23 2011
| | Sample_submission_date | Nov 22 2011
| | Sample_last_update_date | Nov 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fresh ascites was obtained from 10 women with high-grade advanced stage ovarian adenocarcinoma at the time of primary cytoreductive surgery at Brigham and Women's Hospital, Boston, MA. All the specimens were collected under the protocols approved by the institutional review boards of the Brigham and Women’s Hospital and were obtained with informed written consent from the patients
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The ascites samples were centrifuged at 1400 RPM to isolate the cells. After lysis of the erythrocytes, the remaining cells were seeded and grown in culture dishes without passaging. Before sorting, cells were stained with CD45 to rule out contamination with blood cells and with CA125 antibody to confirm the ovarian origin of these cells. Between day 7 and 10 cells were stained with Hoechst33342 dye and sorted for side population and main population cells. The RNA was extracted from the SP and MP cells using the RNeasy kit (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from SP and MP 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/GSM838nnn/GSM838240/suppl/GSM838240.CEL.gz
| | Sample_series_id | GSE33874
| | Sample_data_row_count | 54675
| | |
|
GSM838241 | GPL570 |
|
Hoechst33342 dye sorted side population-6
|
Ovarian Cancer
|
cell type: high-grade advanced stage ovarian adenocarcinoma
sample: 6
cell population: SP
|
Gene expression data from high-grade advanced stage ovarian adenocarcinoma SP Cells
|
| Sample_geo_accession | GSM838241
| | Sample_status | Public on Nov 23 2011
| | Sample_submission_date | Nov 22 2011
| | Sample_last_update_date | Nov 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fresh ascites was obtained from 10 women with high-grade advanced stage ovarian adenocarcinoma at the time of primary cytoreductive surgery at Brigham and Women's Hospital, Boston, MA. All the specimens were collected under the protocols approved by the institutional review boards of the Brigham and Women’s Hospital and were obtained with informed written consent from the patients
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The ascites samples were centrifuged at 1400 RPM to isolate the cells. After lysis of the erythrocytes, the remaining cells were seeded and grown in culture dishes without passaging. Before sorting, cells were stained with CD45 to rule out contamination with blood cells and with CA125 antibody to confirm the ovarian origin of these cells. Between day 7 and 10 cells were stained with Hoechst33342 dye and sorted for side population and main population cells. The RNA was extracted from the SP and MP cells using the RNeasy kit (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from SP and MP 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/GSM838nnn/GSM838241/suppl/GSM838241.CEL.gz
| | Sample_series_id | GSE33874
| | Sample_data_row_count | 54675
| | |
|
GSM838242 | GPL570 |
|
Hoechst33342 dye sorted main population-7
|
Ovarian Cancer
|
cell type: high-grade advanced stage ovarian adenocarcinoma
sample: 7
cell population: MP
|
Gene expression data from high-grade advanced stage ovarian adenocarcinoma MP Cells
|
| Sample_geo_accession | GSM838242
| | Sample_status | Public on Nov 23 2011
| | Sample_submission_date | Nov 22 2011
| | Sample_last_update_date | Nov 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fresh ascites was obtained from 10 women with high-grade advanced stage ovarian adenocarcinoma at the time of primary cytoreductive surgery at Brigham and Women's Hospital, Boston, MA. All the specimens were collected under the protocols approved by the institutional review boards of the Brigham and Women’s Hospital and were obtained with informed written consent from the patients
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The ascites samples were centrifuged at 1400 RPM to isolate the cells. After lysis of the erythrocytes, the remaining cells were seeded and grown in culture dishes without passaging. Before sorting, cells were stained with CD45 to rule out contamination with blood cells and with CA125 antibody to confirm the ovarian origin of these cells. Between day 7 and 10 cells were stained with Hoechst33342 dye and sorted for side population and main population cells. The RNA was extracted from the SP and MP cells using the RNeasy kit (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from SP and MP 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/GSM838nnn/GSM838242/suppl/GSM838242.CEL.gz
| | Sample_series_id | GSE33874
| | Sample_data_row_count | 54675
| | |
|
GSM838243 | GPL570 |
|
Hoechst33342 dye sorted side population-7
|
Ovarian Cancer
|
cell type: high-grade advanced stage ovarian adenocarcinoma
sample: 7
cell population: SP
|
Gene expression data from high-grade advanced stage ovarian adenocarcinoma SP Cells
|
| Sample_geo_accession | GSM838243
| | Sample_status | Public on Nov 23 2011
| | Sample_submission_date | Nov 22 2011
| | Sample_last_update_date | Nov 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fresh ascites was obtained from 10 women with high-grade advanced stage ovarian adenocarcinoma at the time of primary cytoreductive surgery at Brigham and Women's Hospital, Boston, MA. All the specimens were collected under the protocols approved by the institutional review boards of the Brigham and Women’s Hospital and were obtained with informed written consent from the patients
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The ascites samples were centrifuged at 1400 RPM to isolate the cells. After lysis of the erythrocytes, the remaining cells were seeded and grown in culture dishes without passaging. Before sorting, cells were stained with CD45 to rule out contamination with blood cells and with CA125 antibody to confirm the ovarian origin of these cells. Between day 7 and 10 cells were stained with Hoechst33342 dye and sorted for side population and main population cells. The RNA was extracted from the SP and MP cells using the RNeasy kit (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from SP and MP 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/GSM838nnn/GSM838243/suppl/GSM838243.CEL.gz
| | Sample_series_id | GSE33874
| | Sample_data_row_count | 54675
| | |
|
GSM838244 | GPL570 |
|
Hoechst33342 dye sorted main population-8
|
Ovarian Cancer
|
cell type: high-grade advanced stage ovarian adenocarcinoma
sample: 8
cell population: MP
|
Gene expression data from high-grade advanced stage ovarian adenocarcinoma MP Cells
|
| Sample_geo_accession | GSM838244
| | Sample_status | Public on Nov 23 2011
| | Sample_submission_date | Nov 22 2011
| | Sample_last_update_date | Nov 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fresh ascites was obtained from 10 women with high-grade advanced stage ovarian adenocarcinoma at the time of primary cytoreductive surgery at Brigham and Women's Hospital, Boston, MA. All the specimens were collected under the protocols approved by the institutional review boards of the Brigham and Women’s Hospital and were obtained with informed written consent from the patients
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The ascites samples were centrifuged at 1400 RPM to isolate the cells. After lysis of the erythrocytes, the remaining cells were seeded and grown in culture dishes without passaging. Before sorting, cells were stained with CD45 to rule out contamination with blood cells and with CA125 antibody to confirm the ovarian origin of these cells. Between day 7 and 10 cells were stained with Hoechst33342 dye and sorted for side population and main population cells. The RNA was extracted from the SP and MP cells using the RNeasy kit (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from SP and MP 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/GSM838nnn/GSM838244/suppl/GSM838244.CEL.gz
| | Sample_series_id | GSE33874
| | Sample_data_row_count | 54675
| | |
|
GSM838245 | GPL570 |
|
Hoechst33342 dye sorted side population-8
|
Ovarian Cancer
|
cell type: high-grade advanced stage ovarian adenocarcinoma
sample: 8
cell population: SP
|
Gene expression data from high-grade advanced stage ovarian adenocarcinoma SP Cells
|
| Sample_geo_accession | GSM838245
| | Sample_status | Public on Nov 23 2011
| | Sample_submission_date | Nov 22 2011
| | Sample_last_update_date | Nov 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fresh ascites was obtained from 10 women with high-grade advanced stage ovarian adenocarcinoma at the time of primary cytoreductive surgery at Brigham and Women's Hospital, Boston, MA. All the specimens were collected under the protocols approved by the institutional review boards of the Brigham and Women’s Hospital and were obtained with informed written consent from the patients
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The ascites samples were centrifuged at 1400 RPM to isolate the cells. After lysis of the erythrocytes, the remaining cells were seeded and grown in culture dishes without passaging. Before sorting, cells were stained with CD45 to rule out contamination with blood cells and with CA125 antibody to confirm the ovarian origin of these cells. Between day 7 and 10 cells were stained with Hoechst33342 dye and sorted for side population and main population cells. The RNA was extracted from the SP and MP cells using the RNeasy kit (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from SP and MP 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/GSM838nnn/GSM838245/suppl/GSM838245.CEL.gz
| | Sample_series_id | GSE33874
| | Sample_data_row_count | 54675
| | |
|
GSM838246 | GPL570 |
|
Hoechst33342 dye sorted main population-9
|
Ovarian Cancer
|
cell type: high-grade advanced stage ovarian adenocarcinoma
sample: 9
cell population: MP
|
Gene expression data from high-grade advanced stage ovarian adenocarcinoma MP Cells
|
| Sample_geo_accession | GSM838246
| | Sample_status | Public on Nov 23 2011
| | Sample_submission_date | Nov 22 2011
| | Sample_last_update_date | Nov 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fresh ascites was obtained from 10 women with high-grade advanced stage ovarian adenocarcinoma at the time of primary cytoreductive surgery at Brigham and Women's Hospital, Boston, MA. All the specimens were collected under the protocols approved by the institutional review boards of the Brigham and Women’s Hospital and were obtained with informed written consent from the patients
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The ascites samples were centrifuged at 1400 RPM to isolate the cells. After lysis of the erythrocytes, the remaining cells were seeded and grown in culture dishes without passaging. Before sorting, cells were stained with CD45 to rule out contamination with blood cells and with CA125 antibody to confirm the ovarian origin of these cells. Between day 7 and 10 cells were stained with Hoechst33342 dye and sorted for side population and main population cells. The RNA was extracted from the SP and MP cells using the RNeasy kit (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from SP and MP 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/GSM838nnn/GSM838246/suppl/GSM838246.CEL.gz
| | Sample_series_id | GSE33874
| | Sample_data_row_count | 54675
| | |
|
GSM838247 | GPL570 |
|
Hoechst33342 dye sorted side population-9
|
Ovarian Cancer
|
cell type: high-grade advanced stage ovarian adenocarcinoma
sample: 9
cell population: SP
|
Gene expression data from high-grade advanced stage ovarian adenocarcinoma SP Cells
|
| Sample_geo_accession | GSM838247
| | Sample_status | Public on Nov 23 2011
| | Sample_submission_date | Nov 22 2011
| | Sample_last_update_date | Nov 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fresh ascites was obtained from 10 women with high-grade advanced stage ovarian adenocarcinoma at the time of primary cytoreductive surgery at Brigham and Women's Hospital, Boston, MA. All the specimens were collected under the protocols approved by the institutional review boards of the Brigham and Women’s Hospital and were obtained with informed written consent from the patients
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The ascites samples were centrifuged at 1400 RPM to isolate the cells. After lysis of the erythrocytes, the remaining cells were seeded and grown in culture dishes without passaging. Before sorting, cells were stained with CD45 to rule out contamination with blood cells and with CA125 antibody to confirm the ovarian origin of these cells. Between day 7 and 10 cells were stained with Hoechst33342 dye and sorted for side population and main population cells. The RNA was extracted from the SP and MP cells using the RNeasy kit (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from SP and MP 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/GSM838nnn/GSM838247/suppl/GSM838247.CEL.gz
| | Sample_series_id | GSE33874
| | Sample_data_row_count | 54675
| | |
|
GSM838248 | GPL570 |
|
Hoechst33342 dye sorted main population-10
|
Ovarian Cancer
|
cell type: high-grade advanced stage ovarian adenocarcinoma
sample: 10
cell population: MP
|
Gene expression data from high-grade advanced stage ovarian adenocarcinoma MP Cells
|
| Sample_geo_accession | GSM838248
| | Sample_status | Public on Nov 23 2011
| | Sample_submission_date | Nov 22 2011
| | Sample_last_update_date | Nov 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fresh ascites was obtained from 10 women with high-grade advanced stage ovarian adenocarcinoma at the time of primary cytoreductive surgery at Brigham and Women's Hospital, Boston, MA. All the specimens were collected under the protocols approved by the institutional review boards of the Brigham and Women’s Hospital and were obtained with informed written consent from the patients
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The ascites samples were centrifuged at 1400 RPM to isolate the cells. After lysis of the erythrocytes, the remaining cells were seeded and grown in culture dishes without passaging. Before sorting, cells were stained with CD45 to rule out contamination with blood cells and with CA125 antibody to confirm the ovarian origin of these cells. Between day 7 and 10 cells were stained with Hoechst33342 dye and sorted for side population and main population cells. The RNA was extracted from the SP and MP cells using the RNeasy kit (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from SP and MP 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/GSM838nnn/GSM838248/suppl/GSM838248.CEL.gz
| | Sample_series_id | GSE33874
| | Sample_data_row_count | 54675
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GSM838249 | GPL570 |
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Hoechst33342 dye sorted side population-10
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Ovarian Cancer
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cell type: high-grade advanced stage ovarian adenocarcinoma
sample: 10
cell population: SP
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Gene expression data from high-grade advanced stage ovarian adenocarcinoma SP Cells
|
| Sample_geo_accession | GSM838249
| | Sample_status | Public on Nov 23 2011
| | Sample_submission_date | Nov 22 2011
| | Sample_last_update_date | Nov 23 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Fresh ascites was obtained from 10 women with high-grade advanced stage ovarian adenocarcinoma at the time of primary cytoreductive surgery at Brigham and Women's Hospital, Boston, MA. All the specimens were collected under the protocols approved by the institutional review boards of the Brigham and Women’s Hospital and were obtained with informed written consent from the patients
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The ascites samples were centrifuged at 1400 RPM to isolate the cells. After lysis of the erythrocytes, the remaining cells were seeded and grown in culture dishes without passaging. Before sorting, cells were stained with CD45 to rule out contamination with blood cells and with CA125 antibody to confirm the ovarian origin of these cells. Between day 7 and 10 cells were stained with Hoechst33342 dye and sorted for side population and main population cells. The RNA was extracted from the SP and MP cells using the RNeasy kit (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeled amplified RNA (aRNA) for microarray analysis was generated from SP and MP 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/GSM838nnn/GSM838249/suppl/GSM838249.CEL.gz
| | Sample_series_id | GSE33874
| | Sample_data_row_count | 54675
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