Search results for the GEO ID: GSE32375  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM801483 | GPL570 |
|
MSK0366 SP
|
Soft tissue sarcoma
|
cells: Primary Malignant Fibrous Histiocytoma
phenotype: pleomorphic undifferentiated sarcoma
subpopulation: SP
|
|
| Sample_geo_accession | GSM801483
| | Sample_status | Public on Jan 17 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | Jan 17 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For SP assays, cells that were recovered from cryopreservation are treated either alone with 2.5 μg/mL of Hoechst 33342 dye (Sigma) for 90 min at 37°C, or in combination with 50 μmol/L verapamil (Sigma), an inhibitor of ABC transporters. Cells are counterstained with 1 μg/mL of propidium iodide (Molecular Probes), and nonviable cells were excluded from both analysis and sorting assays. To detect for SP, cells are analyzed by using a dual wavelength analysis (blue, 424–444 nm; red, 675 nm) after excitation with 350 nm UV light (MoFlow, Cytomation).
| | Sample_growth_protocol_ch1 | Primary tumour sample is manually minced, and all visible clumps removed. Enzymatic digestion follows at 37°C for 45 min with constant rotation using 10 mg/mL of collagenase IV (Worthington), 2.4 units/mL Dispase (Becton Dickinson), 0.05% trypsin (Wisent). Further manual dissociation is done by passing the cell slurry through an 18-gauge needle. Cells are then centrifuged at 1400 rpm for 5 min and washed thrice in PBS. After washing, cells are strained through 70-μm filters to remove remaining clumps. Collected cells were then cyropreserved for later analysis by fluorescence-activated cell sorting (FACS).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For microarray analysis, 500 SP or non-SP cells are sorted into 50 μl of direct lysis buffer which is included in Nugen WT-Ovation One-direct RNA amplification system.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 5-6 μg of cDNA was labeled using NuGEN Encore™ Biotin Module
| | Sample_hyb_protocol | EukGE-WS2v4
| | Sample_scan_protocol | Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data were normalized using robust multi-array average (RMA) algorithm15
| | Sample_platform_id | GPL570
| | Sample_contact_name | Qingxia,,Wei
| | Sample_contact_email | wqingxia@hotmail.com
| | Sample_contact_phone | 416-813-7231
| | Sample_contact_laboratory | Alman Lab
| | Sample_contact_department | Development Biology
| | Sample_contact_institute | Hospital for Sick Children
| | Sample_contact_address | 101 College Street
| | Sample_contact_city | Toronto
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | M5G 1L7
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801483/suppl/GSM801483BA1_MSK0366_SP.CEL.gz
| | Sample_series_id | GSE32375
| | Sample_data_row_count | 54675
| | |
|
GSM801484 | GPL570 |
|
MSK0366 NSP
|
Soft tissue sarcoma
|
cells: Primary Malignant Fibrous Histiocytoma
phenotype: pleomorphic undifferentiated sarcoma
subpopulation: non-SP
|
|
| Sample_geo_accession | GSM801484
| | Sample_status | Public on Jan 17 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | Jan 17 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For SP assays, cells that were recovered from cryopreservation are treated either alone with 2.5 μg/mL of Hoechst 33342 dye (Sigma) for 90 min at 37°C, or in combination with 50 μmol/L verapamil (Sigma), an inhibitor of ABC transporters. Cells are counterstained with 1 μg/mL of propidium iodide (Molecular Probes), and nonviable cells were excluded from both analysis and sorting assays. To detect for SP, cells are analyzed by using a dual wavelength analysis (blue, 424–444 nm; red, 675 nm) after excitation with 350 nm UV light (MoFlow, Cytomation).
| | Sample_growth_protocol_ch1 | Primary tumour sample is manually minced, and all visible clumps removed. Enzymatic digestion follows at 37°C for 45 min with constant rotation using 10 mg/mL of collagenase IV (Worthington), 2.4 units/mL Dispase (Becton Dickinson), 0.05% trypsin (Wisent). Further manual dissociation is done by passing the cell slurry through an 18-gauge needle. Cells are then centrifuged at 1400 rpm for 5 min and washed thrice in PBS. After washing, cells are strained through 70-μm filters to remove remaining clumps. Collected cells were then cyropreserved for later analysis by fluorescence-activated cell sorting (FACS).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For microarray analysis, 500 SP or non-SP cells are sorted into 50 μl of direct lysis buffer which is included in Nugen WT-Ovation One-direct RNA amplification system.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 5-6 μg of cDNA was labeled using NuGEN Encore™ Biotin Module
| | Sample_hyb_protocol | EukGE-WS2v4
| | Sample_scan_protocol | Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data were normalized using robust multi-array average (RMA) algorithm15
| | Sample_platform_id | GPL570
| | Sample_contact_name | Qingxia,,Wei
| | Sample_contact_email | wqingxia@hotmail.com
| | Sample_contact_phone | 416-813-7231
| | Sample_contact_laboratory | Alman Lab
| | Sample_contact_department | Development Biology
| | Sample_contact_institute | Hospital for Sick Children
| | Sample_contact_address | 101 College Street
| | Sample_contact_city | Toronto
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | M5G 1L7
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801484/suppl/GSM801484BA2_MSK0366_NSP.CEL.gz
| | Sample_series_id | GSE32375
| | Sample_data_row_count | 54675
| | |
|
GSM801485 | GPL570 |
|
MSK0227 SP
|
Soft tissue sarcoma
|
cells: Primary Malignant Fibrous Histiocytoma
phenotype: MFH (myofibrosarcoma) III/III
subpopulation: SP
|
|
| Sample_geo_accession | GSM801485
| | Sample_status | Public on Jan 17 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | Jan 17 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For SP assays, cells that were recovered from cryopreservation are treated either alone with 2.5 μg/mL of Hoechst 33342 dye (Sigma) for 90 min at 37°C, or in combination with 50 μmol/L verapamil (Sigma), an inhibitor of ABC transporters. Cells are counterstained with 1 μg/mL of propidium iodide (Molecular Probes), and nonviable cells were excluded from both analysis and sorting assays. To detect for SP, cells are analyzed by using a dual wavelength analysis (blue, 424–444 nm; red, 675 nm) after excitation with 350 nm UV light (MoFlow, Cytomation).
| | Sample_growth_protocol_ch1 | Primary tumour sample is manually minced, and all visible clumps removed. Enzymatic digestion follows at 37°C for 45 min with constant rotation using 10 mg/mL of collagenase IV (Worthington), 2.4 units/mL Dispase (Becton Dickinson), 0.05% trypsin (Wisent). Further manual dissociation is done by passing the cell slurry through an 18-gauge needle. Cells are then centrifuged at 1400 rpm for 5 min and washed thrice in PBS. After washing, cells are strained through 70-μm filters to remove remaining clumps. Collected cells were then cyropreserved for later analysis by fluorescence-activated cell sorting (FACS).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For microarray analysis, 500 SP or non-SP cells are sorted into 50 μl of direct lysis buffer which is included in Nugen WT-Ovation One-direct RNA amplification system.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 5-6 μg of cDNA was labeled using NuGEN Encore™ Biotin Module
| | Sample_hyb_protocol | EukGE-WS2v4
| | Sample_scan_protocol | Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data were normalized using robust multi-array average (RMA) algorithm15
| | Sample_platform_id | GPL570
| | Sample_contact_name | Qingxia,,Wei
| | Sample_contact_email | wqingxia@hotmail.com
| | Sample_contact_phone | 416-813-7231
| | Sample_contact_laboratory | Alman Lab
| | Sample_contact_department | Development Biology
| | Sample_contact_institute | Hospital for Sick Children
| | Sample_contact_address | 101 College Street
| | Sample_contact_city | Toronto
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | M5G 1L7
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801485/suppl/GSM801485BA3_MSK0227_SP.CEL.gz
| | Sample_series_id | GSE32375
| | Sample_data_row_count | 54675
| | |
|
GSM801486 | GPL570 |
|
MSK0227 NSP
|
Soft tissue sarcoma
|
cells: Primary Malignant Fibrous Histiocytoma
phenotype: MFH (myofibrosarcoma) III/III
subpopulation: non-SP
|
|
| Sample_geo_accession | GSM801486
| | Sample_status | Public on Jan 17 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | Jan 17 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For SP assays, cells that were recovered from cryopreservation are treated either alone with 2.5 μg/mL of Hoechst 33342 dye (Sigma) for 90 min at 37°C, or in combination with 50 μmol/L verapamil (Sigma), an inhibitor of ABC transporters. Cells are counterstained with 1 μg/mL of propidium iodide (Molecular Probes), and nonviable cells were excluded from both analysis and sorting assays. To detect for SP, cells are analyzed by using a dual wavelength analysis (blue, 424–444 nm; red, 675 nm) after excitation with 350 nm UV light (MoFlow, Cytomation).
| | Sample_growth_protocol_ch1 | Primary tumour sample is manually minced, and all visible clumps removed. Enzymatic digestion follows at 37°C for 45 min with constant rotation using 10 mg/mL of collagenase IV (Worthington), 2.4 units/mL Dispase (Becton Dickinson), 0.05% trypsin (Wisent). Further manual dissociation is done by passing the cell slurry through an 18-gauge needle. Cells are then centrifuged at 1400 rpm for 5 min and washed thrice in PBS. After washing, cells are strained through 70-μm filters to remove remaining clumps. Collected cells were then cyropreserved for later analysis by fluorescence-activated cell sorting (FACS).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For microarray analysis, 500 SP or non-SP cells are sorted into 50 μl of direct lysis buffer which is included in Nugen WT-Ovation One-direct RNA amplification system.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 5-6 μg of cDNA was labeled using NuGEN Encore™ Biotin Module
| | Sample_hyb_protocol | EukGE-WS2v4
| | Sample_scan_protocol | Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data were normalized using robust multi-array average (RMA) algorithm15
| | Sample_platform_id | GPL570
| | Sample_contact_name | Qingxia,,Wei
| | Sample_contact_email | wqingxia@hotmail.com
| | Sample_contact_phone | 416-813-7231
| | Sample_contact_laboratory | Alman Lab
| | Sample_contact_department | Development Biology
| | Sample_contact_institute | Hospital for Sick Children
| | Sample_contact_address | 101 College Street
| | Sample_contact_city | Toronto
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | M5G 1L7
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801486/suppl/GSM801486BA4_MSK0227_NSP.CEL.gz
| | Sample_series_id | GSE32375
| | Sample_data_row_count | 54675
| | |
|
GSM801487 | GPL570 |
|
MSK0282 SP
|
Soft tissue sarcoma
|
cells: Primary Malignant Fibrous Histiocytoma
phenotype: STS(soft tissue sarcoma)-MFH (myofibrosarcoma), GRD.3
subpopulation: SP
|
|
| Sample_geo_accession | GSM801487
| | Sample_status | Public on Jan 17 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | Jan 17 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For SP assays, cells that were recovered from cryopreservation are treated either alone with 2.5 μg/mL of Hoechst 33342 dye (Sigma) for 90 min at 37°C, or in combination with 50 μmol/L verapamil (Sigma), an inhibitor of ABC transporters. Cells are counterstained with 1 μg/mL of propidium iodide (Molecular Probes), and nonviable cells were excluded from both analysis and sorting assays. To detect for SP, cells are analyzed by using a dual wavelength analysis (blue, 424–444 nm; red, 675 nm) after excitation with 350 nm UV light (MoFlow, Cytomation).
| | Sample_growth_protocol_ch1 | Primary tumour sample is manually minced, and all visible clumps removed. Enzymatic digestion follows at 37°C for 45 min with constant rotation using 10 mg/mL of collagenase IV (Worthington), 2.4 units/mL Dispase (Becton Dickinson), 0.05% trypsin (Wisent). Further manual dissociation is done by passing the cell slurry through an 18-gauge needle. Cells are then centrifuged at 1400 rpm for 5 min and washed thrice in PBS. After washing, cells are strained through 70-μm filters to remove remaining clumps. Collected cells were then cyropreserved for later analysis by fluorescence-activated cell sorting (FACS).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For microarray analysis, 500 SP or non-SP cells are sorted into 50 μl of direct lysis buffer which is included in Nugen WT-Ovation One-direct RNA amplification system.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 5-6 μg of cDNA was labeled using NuGEN Encore™ Biotin Module
| | Sample_hyb_protocol | EukGE-WS2v4
| | Sample_scan_protocol | Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data were normalized using robust multi-array average (RMA) algorithm15
| | Sample_platform_id | GPL570
| | Sample_contact_name | Qingxia,,Wei
| | Sample_contact_email | wqingxia@hotmail.com
| | Sample_contact_phone | 416-813-7231
| | Sample_contact_laboratory | Alman Lab
| | Sample_contact_department | Development Biology
| | Sample_contact_institute | Hospital for Sick Children
| | Sample_contact_address | 101 College Street
| | Sample_contact_city | Toronto
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | M5G 1L7
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801487/suppl/GSM801487BA5_MSK0282_SP.CEL.gz
| | Sample_series_id | GSE32375
| | Sample_data_row_count | 54675
| | |
|
GSM801488 | GPL570 |
|
MSK0282 NSP
|
Soft tissue sarcoma
|
cells: Primary Malignant Fibrous Histiocytoma
phenotype: STS(soft tissue sarcoma)-MFH (myofibrosarcoma), GRD.3
subpopulation: non-SP
|
|
| Sample_geo_accession | GSM801488
| | Sample_status | Public on Jan 17 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | Jan 17 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For SP assays, cells that were recovered from cryopreservation are treated either alone with 2.5 μg/mL of Hoechst 33342 dye (Sigma) for 90 min at 37°C, or in combination with 50 μmol/L verapamil (Sigma), an inhibitor of ABC transporters. Cells are counterstained with 1 μg/mL of propidium iodide (Molecular Probes), and nonviable cells were excluded from both analysis and sorting assays. To detect for SP, cells are analyzed by using a dual wavelength analysis (blue, 424–444 nm; red, 675 nm) after excitation with 350 nm UV light (MoFlow, Cytomation).
| | Sample_growth_protocol_ch1 | Primary tumour sample is manually minced, and all visible clumps removed. Enzymatic digestion follows at 37°C for 45 min with constant rotation using 10 mg/mL of collagenase IV (Worthington), 2.4 units/mL Dispase (Becton Dickinson), 0.05% trypsin (Wisent). Further manual dissociation is done by passing the cell slurry through an 18-gauge needle. Cells are then centrifuged at 1400 rpm for 5 min and washed thrice in PBS. After washing, cells are strained through 70-μm filters to remove remaining clumps. Collected cells were then cyropreserved for later analysis by fluorescence-activated cell sorting (FACS).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For microarray analysis, 500 SP or non-SP cells are sorted into 50 μl of direct lysis buffer which is included in Nugen WT-Ovation One-direct RNA amplification system.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 5-6 μg of cDNA was labeled using NuGEN Encore™ Biotin Module
| | Sample_hyb_protocol | EukGE-WS2v4
| | Sample_scan_protocol | Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data were normalized using robust multi-array average (RMA) algorithm15
| | Sample_platform_id | GPL570
| | Sample_contact_name | Qingxia,,Wei
| | Sample_contact_email | wqingxia@hotmail.com
| | Sample_contact_phone | 416-813-7231
| | Sample_contact_laboratory | Alman Lab
| | Sample_contact_department | Development Biology
| | Sample_contact_institute | Hospital for Sick Children
| | Sample_contact_address | 101 College Street
| | Sample_contact_city | Toronto
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | M5G 1L7
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801488/suppl/GSM801488BA6_MSK0282_NSP.CEL.gz
| | Sample_series_id | GSE32375
| | Sample_data_row_count | 54675
| | |
|
GSM801489 | GPL570 |
|
MSK0306 SP
|
Soft tissue sarcoma
|
cells: Primary Malignant Fibrous Histiocytoma
phenotype: STS(soft tissue sarcoma)-MFH (myofibrosarcoma)
subpopulation: SP
|
|
| Sample_geo_accession | GSM801489
| | Sample_status | Public on Jan 17 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | Jan 17 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For SP assays, cells that were recovered from cryopreservation are treated either alone with 2.5 μg/mL of Hoechst 33342 dye (Sigma) for 90 min at 37°C, or in combination with 50 μmol/L verapamil (Sigma), an inhibitor of ABC transporters. Cells are counterstained with 1 μg/mL of propidium iodide (Molecular Probes), and nonviable cells were excluded from both analysis and sorting assays. To detect for SP, cells are analyzed by using a dual wavelength analysis (blue, 424–444 nm; red, 675 nm) after excitation with 350 nm UV light (MoFlow, Cytomation).
| | Sample_growth_protocol_ch1 | Primary tumour sample is manually minced, and all visible clumps removed. Enzymatic digestion follows at 37°C for 45 min with constant rotation using 10 mg/mL of collagenase IV (Worthington), 2.4 units/mL Dispase (Becton Dickinson), 0.05% trypsin (Wisent). Further manual dissociation is done by passing the cell slurry through an 18-gauge needle. Cells are then centrifuged at 1400 rpm for 5 min and washed thrice in PBS. After washing, cells are strained through 70-μm filters to remove remaining clumps. Collected cells were then cyropreserved for later analysis by fluorescence-activated cell sorting (FACS).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For microarray analysis, 500 SP or non-SP cells are sorted into 50 μl of direct lysis buffer which is included in Nugen WT-Ovation One-direct RNA amplification system.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 5-6 μg of cDNA was labeled using NuGEN Encore™ Biotin Module
| | Sample_hyb_protocol | EukGE-WS2v4
| | Sample_scan_protocol | Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data were normalized using robust multi-array average (RMA) algorithm15
| | Sample_platform_id | GPL570
| | Sample_contact_name | Qingxia,,Wei
| | Sample_contact_email | wqingxia@hotmail.com
| | Sample_contact_phone | 416-813-7231
| | Sample_contact_laboratory | Alman Lab
| | Sample_contact_department | Development Biology
| | Sample_contact_institute | Hospital for Sick Children
| | Sample_contact_address | 101 College Street
| | Sample_contact_city | Toronto
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | M5G 1L7
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801489/suppl/GSM801489BA7_MSK0306_SP.CEL.gz
| | Sample_series_id | GSE32375
| | Sample_data_row_count | 54675
| | |
|
GSM801490 | GPL570 |
|
MSK0306 NSP
|
Soft tissue sarcoma
|
cells: Primary Malignant Fibrous Histiocytoma
phenotype: STS(soft tissue sarcoma)-MFH (myofibrosarcoma)
subpopulation: non-SP
|
|
| Sample_geo_accession | GSM801490
| | Sample_status | Public on Jan 17 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | Jan 17 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For SP assays, cells that were recovered from cryopreservation are treated either alone with 2.5 μg/mL of Hoechst 33342 dye (Sigma) for 90 min at 37°C, or in combination with 50 μmol/L verapamil (Sigma), an inhibitor of ABC transporters. Cells are counterstained with 1 μg/mL of propidium iodide (Molecular Probes), and nonviable cells were excluded from both analysis and sorting assays. To detect for SP, cells are analyzed by using a dual wavelength analysis (blue, 424–444 nm; red, 675 nm) after excitation with 350 nm UV light (MoFlow, Cytomation).
| | Sample_growth_protocol_ch1 | Primary tumour sample is manually minced, and all visible clumps removed. Enzymatic digestion follows at 37°C for 45 min with constant rotation using 10 mg/mL of collagenase IV (Worthington), 2.4 units/mL Dispase (Becton Dickinson), 0.05% trypsin (Wisent). Further manual dissociation is done by passing the cell slurry through an 18-gauge needle. Cells are then centrifuged at 1400 rpm for 5 min and washed thrice in PBS. After washing, cells are strained through 70-μm filters to remove remaining clumps. Collected cells were then cyropreserved for later analysis by fluorescence-activated cell sorting (FACS).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For microarray analysis, 500 SP or non-SP cells are sorted into 50 μl of direct lysis buffer which is included in Nugen WT-Ovation One-direct RNA amplification system.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 5-6 μg of cDNA was labeled using NuGEN Encore™ Biotin Module
| | Sample_hyb_protocol | EukGE-WS2v4
| | Sample_scan_protocol | Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data were normalized using robust multi-array average (RMA) algorithm15
| | Sample_platform_id | GPL570
| | Sample_contact_name | Qingxia,,Wei
| | Sample_contact_email | wqingxia@hotmail.com
| | Sample_contact_phone | 416-813-7231
| | Sample_contact_laboratory | Alman Lab
| | Sample_contact_department | Development Biology
| | Sample_contact_institute | Hospital for Sick Children
| | Sample_contact_address | 101 College Street
| | Sample_contact_city | Toronto
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | M5G 1L7
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801490/suppl/GSM801490BA8_MSK0306_NSP.CEL.gz
| | Sample_series_id | GSE32375
| | Sample_data_row_count | 54675
| | |
|
GSM801491 | GPL570 |
|
MSK0293 SP
|
Soft tissue sarcoma
|
cells: Primary Malignant Fibrous Histiocytoma
phenotype: STS(soft tissue sarcoma)-MFH (myofibrosarcoma), GRD.1
subpopulation: SP
|
|
| Sample_geo_accession | GSM801491
| | Sample_status | Public on Jan 17 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | Jan 17 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For SP assays, cells that were recovered from cryopreservation are treated either alone with 2.5 μg/mL of Hoechst 33342 dye (Sigma) for 90 min at 37°C, or in combination with 50 μmol/L verapamil (Sigma), an inhibitor of ABC transporters. Cells are counterstained with 1 μg/mL of propidium iodide (Molecular Probes), and nonviable cells were excluded from both analysis and sorting assays. To detect for SP, cells are analyzed by using a dual wavelength analysis (blue, 424–444 nm; red, 675 nm) after excitation with 350 nm UV light (MoFlow, Cytomation).
| | Sample_growth_protocol_ch1 | Primary tumour sample is manually minced, and all visible clumps removed. Enzymatic digestion follows at 37°C for 45 min with constant rotation using 10 mg/mL of collagenase IV (Worthington), 2.4 units/mL Dispase (Becton Dickinson), 0.05% trypsin (Wisent). Further manual dissociation is done by passing the cell slurry through an 18-gauge needle. Cells are then centrifuged at 1400 rpm for 5 min and washed thrice in PBS. After washing, cells are strained through 70-μm filters to remove remaining clumps. Collected cells were then cyropreserved for later analysis by fluorescence-activated cell sorting (FACS).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For microarray analysis, 500 SP or non-SP cells are sorted into 50 μl of direct lysis buffer which is included in Nugen WT-Ovation One-direct RNA amplification system.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 5-6 μg of cDNA was labeled using NuGEN Encore™ Biotin Module
| | Sample_hyb_protocol | EukGE-WS2v4
| | Sample_scan_protocol | Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data were normalized using robust multi-array average (RMA) algorithm15
| | Sample_platform_id | GPL570
| | Sample_contact_name | Qingxia,,Wei
| | Sample_contact_email | wqingxia@hotmail.com
| | Sample_contact_phone | 416-813-7231
| | Sample_contact_laboratory | Alman Lab
| | Sample_contact_department | Development Biology
| | Sample_contact_institute | Hospital for Sick Children
| | Sample_contact_address | 101 College Street
| | Sample_contact_city | Toronto
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | M5G 1L7
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801491/suppl/GSM801491BA9_MSK0293_SP.CEL.gz
| | Sample_series_id | GSE32375
| | Sample_data_row_count | 54675
| | |
|
GSM801492 | GPL570 |
|
MSK0293 NSP
|
Soft tissue sarcoma
|
cells: Primary Malignant Fibrous Histiocytoma
phenotype: STS(soft tissue sarcoma)-MFH (myofibrosarcoma), GRD.1
subpopulation: non-SP
|
|
| Sample_geo_accession | GSM801492
| | Sample_status | Public on Jan 17 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | Jan 17 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For SP assays, cells that were recovered from cryopreservation are treated either alone with 2.5 μg/mL of Hoechst 33342 dye (Sigma) for 90 min at 37°C, or in combination with 50 μmol/L verapamil (Sigma), an inhibitor of ABC transporters. Cells are counterstained with 1 μg/mL of propidium iodide (Molecular Probes), and nonviable cells were excluded from both analysis and sorting assays. To detect for SP, cells are analyzed by using a dual wavelength analysis (blue, 424–444 nm; red, 675 nm) after excitation with 350 nm UV light (MoFlow, Cytomation).
| | Sample_growth_protocol_ch1 | Primary tumour sample is manually minced, and all visible clumps removed. Enzymatic digestion follows at 37°C for 45 min with constant rotation using 10 mg/mL of collagenase IV (Worthington), 2.4 units/mL Dispase (Becton Dickinson), 0.05% trypsin (Wisent). Further manual dissociation is done by passing the cell slurry through an 18-gauge needle. Cells are then centrifuged at 1400 rpm for 5 min and washed thrice in PBS. After washing, cells are strained through 70-μm filters to remove remaining clumps. Collected cells were then cyropreserved for later analysis by fluorescence-activated cell sorting (FACS).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For microarray analysis, 500 SP or non-SP cells are sorted into 50 μl of direct lysis buffer which is included in Nugen WT-Ovation One-direct RNA amplification system.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 5-6 μg of cDNA was labeled using NuGEN Encore™ Biotin Module
| | Sample_hyb_protocol | EukGE-WS2v4
| | Sample_scan_protocol | Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data were normalized using robust multi-array average (RMA) algorithm15
| | Sample_platform_id | GPL570
| | Sample_contact_name | Qingxia,,Wei
| | Sample_contact_email | wqingxia@hotmail.com
| | Sample_contact_phone | 416-813-7231
| | Sample_contact_laboratory | Alman Lab
| | Sample_contact_department | Development Biology
| | Sample_contact_institute | Hospital for Sick Children
| | Sample_contact_address | 101 College Street
| | Sample_contact_city | Toronto
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | M5G 1L7
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801492/suppl/GSM801492BA10_MSK0293_NSP.CEL.gz
| | Sample_series_id | GSE32375
| | Sample_data_row_count | 54675
| | |
|
GSM801493 | GPL570 |
|
MSK0130 SP
|
Soft tissue sarcoma
|
cells: Primary Malignant Fibrous Histiocytoma
phenotype: MFH (myofibrosarcoma)
subpopulation: SP
|
|
| Sample_geo_accession | GSM801493
| | Sample_status | Public on Jan 17 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | Jan 17 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For SP assays, cells that were recovered from cryopreservation are treated either alone with 2.5 μg/mL of Hoechst 33342 dye (Sigma) for 90 min at 37°C, or in combination with 50 μmol/L verapamil (Sigma), an inhibitor of ABC transporters. Cells are counterstained with 1 μg/mL of propidium iodide (Molecular Probes), and nonviable cells were excluded from both analysis and sorting assays. To detect for SP, cells are analyzed by using a dual wavelength analysis (blue, 424–444 nm; red, 675 nm) after excitation with 350 nm UV light (MoFlow, Cytomation).
| | Sample_growth_protocol_ch1 | Primary tumour sample is manually minced, and all visible clumps removed. Enzymatic digestion follows at 37°C for 45 min with constant rotation using 10 mg/mL of collagenase IV (Worthington), 2.4 units/mL Dispase (Becton Dickinson), 0.05% trypsin (Wisent). Further manual dissociation is done by passing the cell slurry through an 18-gauge needle. Cells are then centrifuged at 1400 rpm for 5 min and washed thrice in PBS. After washing, cells are strained through 70-μm filters to remove remaining clumps. Collected cells were then cyropreserved for later analysis by fluorescence-activated cell sorting (FACS).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For microarray analysis, 500 SP or non-SP cells are sorted into 50 μl of direct lysis buffer which is included in Nugen WT-Ovation One-direct RNA amplification system.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 5-6 μg of cDNA was labeled using NuGEN Encore™ Biotin Module
| | Sample_hyb_protocol | EukGE-WS2v4
| | Sample_scan_protocol | Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data were normalized using robust multi-array average (RMA) algorithm15
| | Sample_platform_id | GPL570
| | Sample_contact_name | Qingxia,,Wei
| | Sample_contact_email | wqingxia@hotmail.com
| | Sample_contact_phone | 416-813-7231
| | Sample_contact_laboratory | Alman Lab
| | Sample_contact_department | Development Biology
| | Sample_contact_institute | Hospital for Sick Children
| | Sample_contact_address | 101 College Street
| | Sample_contact_city | Toronto
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | M5G 1L7
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801493/suppl/GSM801493BA11_MSK0130_SP.CEL.gz
| | Sample_series_id | GSE32375
| | Sample_data_row_count | 54675
| | |
|
GSM801494 | GPL570 |
|
MSK0130 NSP
|
Soft tissue sarcoma
|
cells: Primary Malignant Fibrous Histiocytoma
phenotype: MFH (myofibrosarcoma)
subpopulation: non-SP
|
|
| Sample_geo_accession | GSM801494
| | Sample_status | Public on Jan 17 2012
| | Sample_submission_date | Sep 26 2011
| | Sample_last_update_date | Jan 17 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For SP assays, cells that were recovered from cryopreservation are treated either alone with 2.5 μg/mL of Hoechst 33342 dye (Sigma) for 90 min at 37°C, or in combination with 50 μmol/L verapamil (Sigma), an inhibitor of ABC transporters. Cells are counterstained with 1 μg/mL of propidium iodide (Molecular Probes), and nonviable cells were excluded from both analysis and sorting assays. To detect for SP, cells are analyzed by using a dual wavelength analysis (blue, 424–444 nm; red, 675 nm) after excitation with 350 nm UV light (MoFlow, Cytomation).
| | Sample_growth_protocol_ch1 | Primary tumour sample is manually minced, and all visible clumps removed. Enzymatic digestion follows at 37°C for 45 min with constant rotation using 10 mg/mL of collagenase IV (Worthington), 2.4 units/mL Dispase (Becton Dickinson), 0.05% trypsin (Wisent). Further manual dissociation is done by passing the cell slurry through an 18-gauge needle. Cells are then centrifuged at 1400 rpm for 5 min and washed thrice in PBS. After washing, cells are strained through 70-μm filters to remove remaining clumps. Collected cells were then cyropreserved for later analysis by fluorescence-activated cell sorting (FACS).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For microarray analysis, 500 SP or non-SP cells are sorted into 50 μl of direct lysis buffer which is included in Nugen WT-Ovation One-direct RNA amplification system.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 5-6 μg of cDNA was labeled using NuGEN Encore™ Biotin Module
| | Sample_hyb_protocol | EukGE-WS2v4
| | Sample_scan_protocol | Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data were normalized using robust multi-array average (RMA) algorithm15
| | Sample_platform_id | GPL570
| | Sample_contact_name | Qingxia,,Wei
| | Sample_contact_email | wqingxia@hotmail.com
| | Sample_contact_phone | 416-813-7231
| | Sample_contact_laboratory | Alman Lab
| | Sample_contact_department | Development Biology
| | Sample_contact_institute | Hospital for Sick Children
| | Sample_contact_address | 101 College Street
| | Sample_contact_city | Toronto
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | M5G 1L7
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM801nnn/GSM801494/suppl/GSM801494BA12_MSK0130_NSP.CEL.gz
| | Sample_series_id | GSE32375
| | Sample_data_row_count | 54675
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
