Search results for the GEO ID: GSE13433  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM338412 | GPL570 |
|
ASPS_Patient_5_Array_1
|
ASPS Tumor
|
Confirmed primary or metastatic ASPS
Patient 5
|
Data from arrays hybridized to tumor RNA was analyzed relative to arrays hybridized to universal RNA to generate an unbiased transcriptome.
|
| Sample_geo_accession | GSM338412
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Oct 30 2008
| | Sample_last_update_date | Nov 03 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA samples were isolated immediately following surgery.
| | Sample_growth_protocol_ch1 | Not Applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rneasy (Qiagen) total RNA extraction
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Target was prepared and hybridized according to the Affymetrix Technical Manual. Total RNA (10 ug) was converted into cDNA using Reverse Transcriptase (Invitrogen) and a modified oligo(dT)24 primer that contains T7 promoter sequences (GenSet).
| | Sample_hyb_protocol | The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides using an In Vitro Transcription kit (Affymetrix). The resultant cRNA product was purified using an RNeasy column (Qiagen) and quantified with a spectrophotometer. The cRNA target (20ug) was incubated at 94ºC for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc). The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix). The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm. GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in an GeneChip® Scanner 3000
| | Sample_data_processing | Expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). All GeneChips were scaled to a median intensity setting of 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luke,Hunter,Stockwin
| | Sample_contact_email | stockwinl@mail.nih.gov
| | Sample_contact_phone | 301-846-5431
| | Sample_contact_department | DTP
| | Sample_contact_institute | NCI Frederick
| | Sample_contact_address | Ft. Detrick
| | Sample_contact_city | Frederick
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21701
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338412/suppl/GSM338412.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338412/suppl/GSM338412.CHP.gz
| | Sample_series_id | GSE13433
| | Sample_data_row_count | 54675
| | |
|
GSM338413 | GPL570 |
|
ASPS_Patient_5_Array_2
|
ASPS Tumor
|
Confirmed primary or metastatic ASPS
Patient 5
|
Data from arrays hybridized to tumor RNA was analyzed relative to arrays hybridized to universal RNA to generate an unbiased transcriptome.
|
| Sample_geo_accession | GSM338413
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Oct 30 2008
| | Sample_last_update_date | Nov 03 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA samples were isolated immediately following surgery.
| | Sample_growth_protocol_ch1 | Not Applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rneasy (Qiagen) total RNA extraction
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Target was prepared and hybridized according to the Affymetrix Technical Manual. Total RNA (10 ug) was converted into cDNA using Reverse Transcriptase (Invitrogen) and a modified oligo(dT)24 primer that contains T7 promoter sequences (GenSet).
| | Sample_hyb_protocol | The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides using an In Vitro Transcription kit (Affymetrix). The resultant cRNA product was purified using an RNeasy column (Qiagen) and quantified with a spectrophotometer. The cRNA target (20ug) was incubated at 94ºC for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc). The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix). The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm. GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in an GeneChip® Scanner 3000
| | Sample_data_processing | Expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). All GeneChips were scaled to a median intensity setting of 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luke,Hunter,Stockwin
| | Sample_contact_email | stockwinl@mail.nih.gov
| | Sample_contact_phone | 301-846-5431
| | Sample_contact_department | DTP
| | Sample_contact_institute | NCI Frederick
| | Sample_contact_address | Ft. Detrick
| | Sample_contact_city | Frederick
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21701
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338413/suppl/GSM338413.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338413/suppl/GSM338413.CHP.gz
| | Sample_series_id | GSE13433
| | Sample_data_row_count | 54675
| | |
|
GSM338963 | GPL570 |
|
ASPS_Patient_6_Array_1
|
ASPS Tumor
|
Confirmed primary or metastatic ASPS
Patient 6
|
Data from arrays hybridized to tumor RNA was analyzed relative to arrays hybridized to universal RNA to generate an unbiased transcriptome.
|
| Sample_geo_accession | GSM338963
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Nov 01 2008
| | Sample_last_update_date | Nov 03 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA samples were isolated immediately following surgery.
| | Sample_growth_protocol_ch1 | Not Applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rneasy (Qiagen) total RNA extraction
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Target was prepared and hybridized according to the Affymetrix Technical Manual. Total RNA (10 ug) was converted into cDNA using Reverse Transcriptase (Invitrogen) and a modified oligo(dT)24 primer that contains T7 promoter sequences (GenSet).
| | Sample_hyb_protocol | The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides using an In Vitro Transcription kit (Affymetrix). The resultant cRNA product was purified using an RNeasy column (Qiagen) and quantified with a spectrophotometer. The cRNA target (20ug) was incubated at 94ºC for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc). The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix). The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm. GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in an GeneChip® Scanner 3000
| | Sample_data_processing | Expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). All GeneChips were scaled to a median intensity setting of 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luke,Hunter,Stockwin
| | Sample_contact_email | stockwinl@mail.nih.gov
| | Sample_contact_phone | 301-846-5431
| | Sample_contact_department | DTP
| | Sample_contact_institute | NCI Frederick
| | Sample_contact_address | Ft. Detrick
| | Sample_contact_city | Frederick
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21701
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338963/suppl/GSM338963.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338963/suppl/GSM338963.CHP.gz
| | Sample_series_id | GSE13433
| | Sample_data_row_count | 54675
| | |
|
GSM338964 | GPL570 |
|
ASPS_Patient_6_Array_2
|
ASPS Tumor
|
Confirmed primary or metastatic ASPS
Patient 6
|
Data from arrays hybridized to tumor RNA was analyzed relative to arrays hybridized to universal RNA to generate an unbiased transcriptome.
|
| Sample_geo_accession | GSM338964
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Nov 01 2008
| | Sample_last_update_date | Nov 03 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA samples were isolated immediately following surgery.
| | Sample_growth_protocol_ch1 | Not Applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rneasy (Qiagen) total RNA extraction
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Target was prepared and hybridized according to the Affymetrix Technical Manual. Total RNA (10 ug) was converted into cDNA using Reverse Transcriptase (Invitrogen) and a modified oligo(dT)24 primer that contains T7 promoter sequences (GenSet).
| | Sample_hyb_protocol | The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides using an In Vitro Transcription kit (Affymetrix). The resultant cRNA product was purified using an RNeasy column (Qiagen) and quantified with a spectrophotometer. The cRNA target (20ug) was incubated at 94ºC for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc). The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix). The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm. GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in an GeneChip® Scanner 3000
| | Sample_data_processing | Expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). All GeneChips were scaled to a median intensity setting of 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luke,Hunter,Stockwin
| | Sample_contact_email | stockwinl@mail.nih.gov
| | Sample_contact_phone | 301-846-5431
| | Sample_contact_department | DTP
| | Sample_contact_institute | NCI Frederick
| | Sample_contact_address | Ft. Detrick
| | Sample_contact_city | Frederick
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21701
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338964/suppl/GSM338964.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338964/suppl/GSM338964.CHP.gz
| | Sample_series_id | GSE13433
| | Sample_data_row_count | 54675
| | |
|
GSM338965 | GPL570 |
|
ASPS_Patient_3_Array_1
|
ASPS Tumor
|
Confirmed primary or metastatic ASPS
Patient 3
|
Data from arrays hybridized to tumor RNA was analyzed relative to arrays hybridized to universal RNA to generate an unbiased transcriptome.
|
| Sample_geo_accession | GSM338965
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Nov 01 2008
| | Sample_last_update_date | Nov 03 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA samples were isolated immediately following surgery.
| | Sample_growth_protocol_ch1 | Not Applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rneasy (Qiagen) total RNA extraction
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Target was prepared and hybridized according to the Affymetrix Technical Manual. Total RNA (10 ug) was converted into cDNA using Reverse Transcriptase (Invitrogen) and a modified oligo(dT)24 primer that contains T7 promoter sequences (GenSet).
| | Sample_hyb_protocol | The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides using an In Vitro Transcription kit (Affymetrix). The resultant cRNA product was purified using an RNeasy column (Qiagen) and quantified with a spectrophotometer. The cRNA target (20ug) was incubated at 94ºC for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc). The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix). The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm. GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in an GeneChip® Scanner 3000
| | Sample_data_processing | Expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). All GeneChips were scaled to a median intensity setting of 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luke,Hunter,Stockwin
| | Sample_contact_email | stockwinl@mail.nih.gov
| | Sample_contact_phone | 301-846-5431
| | Sample_contact_department | DTP
| | Sample_contact_institute | NCI Frederick
| | Sample_contact_address | Ft. Detrick
| | Sample_contact_city | Frederick
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21701
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338965/suppl/GSM338965.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338965/suppl/GSM338965.CHP.gz
| | Sample_series_id | GSE13433
| | Sample_data_row_count | 54675
| | |
|
GSM338966 | GPL570 |
|
ASPS_Patient_3_Array_2
|
ASPS Tumor
|
Confirmed primary or metastatic ASPS
Patient 3
|
Data from arrays hybridized to tumor RNA was analyzed relative to arrays hybridized to universal RNA to generate an unbiased transcriptome.
|
| Sample_geo_accession | GSM338966
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Nov 01 2008
| | Sample_last_update_date | Nov 03 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA samples were isolated immediately following surgery.
| | Sample_growth_protocol_ch1 | Not Applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rneasy (Qiagen) total RNA extraction
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Target was prepared and hybridized according to the Affymetrix Technical Manual. Total RNA (10 ug) was converted into cDNA using Reverse Transcriptase (Invitrogen) and a modified oligo(dT)24 primer that contains T7 promoter sequences (GenSet).
| | Sample_hyb_protocol | The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides using an In Vitro Transcription kit (Affymetrix). The resultant cRNA product was purified using an RNeasy column (Qiagen) and quantified with a spectrophotometer. The cRNA target (20ug) was incubated at 94ºC for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc). The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix). The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm. GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in an GeneChip® Scanner 3000
| | Sample_data_processing | Expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). All GeneChips were scaled to a median intensity setting of 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luke,Hunter,Stockwin
| | Sample_contact_email | stockwinl@mail.nih.gov
| | Sample_contact_phone | 301-846-5431
| | Sample_contact_department | DTP
| | Sample_contact_institute | NCI Frederick
| | Sample_contact_address | Ft. Detrick
| | Sample_contact_city | Frederick
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21701
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338966/suppl/GSM338966.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338966/suppl/GSM338966.CHP.gz
| | Sample_series_id | GSE13433
| | Sample_data_row_count | 54675
| | |
|
GSM338967 | GPL570 |
|
ASPS_Patient_7_Array_1
|
ASPS Tumor
|
Confirmed primary or metastatic ASPS
Patient 7
|
Data from arrays hybridized to tumor RNA was analyzed relative to arrays hybridized to universal RNA to generate an unbiased transcriptome.
|
| Sample_geo_accession | GSM338967
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Nov 01 2008
| | Sample_last_update_date | Nov 03 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA samples were isolated immediately following surgery.
| | Sample_growth_protocol_ch1 | Not Applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rneasy (Qiagen) total RNA extraction
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Target was prepared and hybridized according to the Affymetrix Technical Manual. Total RNA (10 ug) was converted into cDNA using Reverse Transcriptase (Invitrogen) and a modified oligo(dT)24 primer that contains T7 promoter sequences (GenSet).
| | Sample_hyb_protocol | The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides using an In Vitro Transcription kit (Affymetrix). The resultant cRNA product was purified using an RNeasy column (Qiagen) and quantified with a spectrophotometer. The cRNA target (20ug) was incubated at 94ºC for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc). The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix). The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm. GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in an GeneChip® Scanner 3000
| | Sample_data_processing | Expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). All GeneChips were scaled to a median intensity setting of 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luke,Hunter,Stockwin
| | Sample_contact_email | stockwinl@mail.nih.gov
| | Sample_contact_phone | 301-846-5431
| | Sample_contact_department | DTP
| | Sample_contact_institute | NCI Frederick
| | Sample_contact_address | Ft. Detrick
| | Sample_contact_city | Frederick
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21701
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338967/suppl/GSM338967.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338967/suppl/GSM338967.CHP.gz
| | Sample_series_id | GSE13433
| | Sample_data_row_count | 54675
| | |
|
GSM338968 | GPL570 |
|
ASPS_Patient_7_Array_2
|
ASPS Tumor
|
Confirmed primary or metastatic ASPS
Patient 7
|
Data from arrays hybridized to tumor RNA was analyzed relative to arrays hybridized to universal RNA to generate an unbiased transcriptome.
|
| Sample_geo_accession | GSM338968
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Nov 01 2008
| | Sample_last_update_date | Nov 03 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA samples were isolated immediately following surgery.
| | Sample_growth_protocol_ch1 | Not Applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rneasy (Qiagen) total RNA extraction
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Target was prepared and hybridized according to the Affymetrix Technical Manual. Total RNA (10 ug) was converted into cDNA using Reverse Transcriptase (Invitrogen) and a modified oligo(dT)24 primer that contains T7 promoter sequences (GenSet).
| | Sample_hyb_protocol | The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides using an In Vitro Transcription kit (Affymetrix). The resultant cRNA product was purified using an RNeasy column (Qiagen) and quantified with a spectrophotometer. The cRNA target (20ug) was incubated at 94ºC for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc). The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix). The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm. GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in an GeneChip® Scanner 3000
| | Sample_data_processing | Expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). All GeneChips were scaled to a median intensity setting of 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luke,Hunter,Stockwin
| | Sample_contact_email | stockwinl@mail.nih.gov
| | Sample_contact_phone | 301-846-5431
| | Sample_contact_department | DTP
| | Sample_contact_institute | NCI Frederick
| | Sample_contact_address | Ft. Detrick
| | Sample_contact_city | Frederick
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21701
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338968/suppl/GSM338968.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338968/suppl/GSM338968.CHP.gz
| | Sample_series_id | GSE13433
| | Sample_data_row_count | 54675
| | |
|
GSM338969 | GPL570 |
|
ASPS_Patient_1_Array_1
|
ASPS Tumor
|
Confirmed primary or metastatic ASPS
Patient 1
|
Data from arrays hybridized to tumor RNA was analyzed relative to arrays hybridized to universal RNA to generate an unbiased transcriptome.
|
| Sample_geo_accession | GSM338969
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Nov 01 2008
| | Sample_last_update_date | Nov 03 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA samples were isolated immediately following surgery.
| | Sample_growth_protocol_ch1 | Not Applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rneasy (Qiagen) total RNA extraction
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Target was prepared and hybridized according to the Affymetrix Technical Manual. Total RNA (10 ug) was converted into cDNA using Reverse Transcriptase (Invitrogen) and a modified oligo(dT)24 primer that contains T7 promoter sequences (GenSet).
| | Sample_hyb_protocol | The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides using an In Vitro Transcription kit (Affymetrix). The resultant cRNA product was purified using an RNeasy column (Qiagen) and quantified with a spectrophotometer. The cRNA target (20ug) was incubated at 94ºC for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc). The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix). The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm. GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in an GeneChip® Scanner 3000
| | Sample_data_processing | Expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). All GeneChips were scaled to a median intensity setting of 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luke,Hunter,Stockwin
| | Sample_contact_email | stockwinl@mail.nih.gov
| | Sample_contact_phone | 301-846-5431
| | Sample_contact_department | DTP
| | Sample_contact_institute | NCI Frederick
| | Sample_contact_address | Ft. Detrick
| | Sample_contact_city | Frederick
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21701
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338969/suppl/GSM338969.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338969/suppl/GSM338969.CHP.gz
| | Sample_series_id | GSE13433
| | Sample_data_row_count | 54675
| | |
|
GSM338970 | GPL570 |
|
ASPS_Patient_1_Array_2
|
ASPS Tumor
|
Confirmed primary or metastatic ASPS
Patient 1
|
Data from arrays hybridized to tumor RNA was analyzed relative to arrays hybridized to universal RNA to generate an unbiased transcriptome.
|
| Sample_geo_accession | GSM338970
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Nov 01 2008
| | Sample_last_update_date | Nov 03 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA samples were isolated immediately following surgery.
| | Sample_growth_protocol_ch1 | Not Applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rneasy (Qiagen) total RNA extraction
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Target was prepared and hybridized according to the Affymetrix Technical Manual. Total RNA (10 ug) was converted into cDNA using Reverse Transcriptase (Invitrogen) and a modified oligo(dT)24 primer that contains T7 promoter sequences (GenSet).
| | Sample_hyb_protocol | The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides using an In Vitro Transcription kit (Affymetrix). The resultant cRNA product was purified using an RNeasy column (Qiagen) and quantified with a spectrophotometer. The cRNA target (20ug) was incubated at 94ºC for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc). The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix). The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm. GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in an GeneChip® Scanner 3000
| | Sample_data_processing | Expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). All GeneChips were scaled to a median intensity setting of 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luke,Hunter,Stockwin
| | Sample_contact_email | stockwinl@mail.nih.gov
| | Sample_contact_phone | 301-846-5431
| | Sample_contact_department | DTP
| | Sample_contact_institute | NCI Frederick
| | Sample_contact_address | Ft. Detrick
| | Sample_contact_city | Frederick
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21701
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338970/suppl/GSM338970.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338970/suppl/GSM338970.CHP.gz
| | Sample_series_id | GSE13433
| | Sample_data_row_count | 54675
| | |
|
GSM338971 | GPL570 |
|
ASPS_Patient_2_Array_1
|
ASPS Tumor
|
Confirmed primary or metastatic ASPS
Patient 2
|
Data from arrays hybridized to tumor RNA was analyzed relative to arrays hybridized to universal RNA to generate an unbiased transcriptome.
|
| Sample_geo_accession | GSM338971
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Nov 01 2008
| | Sample_last_update_date | Nov 03 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA samples were isolated immediately following surgery.
| | Sample_growth_protocol_ch1 | Not Applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rneasy (Qiagen) total RNA extraction
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Target was prepared and hybridized according to the Affymetrix Technical Manual. Total RNA (10 ug) was converted into cDNA using Reverse Transcriptase (Invitrogen) and a modified oligo(dT)24 primer that contains T7 promoter sequences (GenSet).
| | Sample_hyb_protocol | The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides using an In Vitro Transcription kit (Affymetrix). The resultant cRNA product was purified using an RNeasy column (Qiagen) and quantified with a spectrophotometer. The cRNA target (20ug) was incubated at 94ºC for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc). The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix). The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm. GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in an GeneChip® Scanner 3000
| | Sample_data_processing | Expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). All GeneChips were scaled to a median intensity setting of 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luke,Hunter,Stockwin
| | Sample_contact_email | stockwinl@mail.nih.gov
| | Sample_contact_phone | 301-846-5431
| | Sample_contact_department | DTP
| | Sample_contact_institute | NCI Frederick
| | Sample_contact_address | Ft. Detrick
| | Sample_contact_city | Frederick
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21701
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338971/suppl/GSM338971.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338971/suppl/GSM338971.CHP.gz
| | Sample_series_id | GSE13433
| | Sample_data_row_count | 54675
| | |
|
GSM338972 | GPL570 |
|
ASPS_Patient_2_Array_2
|
ASPS Tumor
|
Confirmed primary or metastatic ASPS
Patient 2
|
Data from arrays hybridized to tumor RNA was analyzed relative to arrays hybridized to universal RNA to generate an unbiased transcriptome.
|
| Sample_geo_accession | GSM338972
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Nov 01 2008
| | Sample_last_update_date | Nov 03 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA samples were isolated immediately following surgery.
| | Sample_growth_protocol_ch1 | Not Applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rneasy (Qiagen) total RNA extraction
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Target was prepared and hybridized according to the Affymetrix Technical Manual. Total RNA (10 ug) was converted into cDNA using Reverse Transcriptase (Invitrogen) and a modified oligo(dT)24 primer that contains T7 promoter sequences (GenSet).
| | Sample_hyb_protocol | The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides using an In Vitro Transcription kit (Affymetrix). The resultant cRNA product was purified using an RNeasy column (Qiagen) and quantified with a spectrophotometer. The cRNA target (20ug) was incubated at 94ºC for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc). The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix). The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm. GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in an GeneChip® Scanner 3000
| | Sample_data_processing | Expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). All GeneChips were scaled to a median intensity setting of 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luke,Hunter,Stockwin
| | Sample_contact_email | stockwinl@mail.nih.gov
| | Sample_contact_phone | 301-846-5431
| | Sample_contact_department | DTP
| | Sample_contact_institute | NCI Frederick
| | Sample_contact_address | Ft. Detrick
| | Sample_contact_city | Frederick
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21701
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338972/suppl/GSM338972.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338972/suppl/GSM338972.CHP.gz
| | Sample_series_id | GSE13433
| | Sample_data_row_count | 54675
| | |
|
GSM338973 | GPL570 |
|
Univ_RNA_Array_1
|
Universal RNA
|
Universal RNA (Promega)
|
Data from arrays hybridized to tumor RNA was analyzed relative to arrays hybridized to universal RNA to generate an unbiased transcriptome.
|
| Sample_geo_accession | GSM338973
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Nov 01 2008
| | Sample_last_update_date | Nov 03 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Not applicable.
| | Sample_growth_protocol_ch1 | Not Applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rneasy (Qiagen) total RNA extraction
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Target was prepared and hybridized according to the Affymetrix Technical Manual. Total RNA (10 ug) was converted into cDNA using Reverse Transcriptase (Invitrogen) and a modified oligo(dT)24 primer that contains T7 promoter sequences (GenSet).
| | Sample_hyb_protocol | The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides using an In Vitro Transcription kit (Affymetrix). The resultant cRNA product was purified using an RNeasy column (Qiagen) and quantified with a spectrophotometer. The cRNA target (20ug) was incubated at 94ºC for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc). The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix). The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm. GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in an GeneChip® Scanner 3000
| | Sample_data_processing | Expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). All GeneChips were scaled to a median intensity setting of 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luke,Hunter,Stockwin
| | Sample_contact_email | stockwinl@mail.nih.gov
| | Sample_contact_phone | 301-846-5431
| | Sample_contact_department | DTP
| | Sample_contact_institute | NCI Frederick
| | Sample_contact_address | Ft. Detrick
| | Sample_contact_city | Frederick
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21701
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338973/suppl/GSM338973.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338973/suppl/GSM338973.CHP.gz
| | Sample_series_id | GSE13433
| | Sample_data_row_count | 54675
| | |
|
GSM338974 | GPL570 |
|
Univ_RNA_Array_2
|
Universal RNA
|
Universal RNA (Promega)
|
Data from arrays hybridized to tumor RNA was analyzed relative to arrays hybridized to universal RNA to generate an unbiased transcriptome.
|
| Sample_geo_accession | GSM338974
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Nov 01 2008
| | Sample_last_update_date | Nov 03 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Not applicable.
| | Sample_growth_protocol_ch1 | Not Applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rneasy (Qiagen) total RNA extraction
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Target was prepared and hybridized according to the Affymetrix Technical Manual. Total RNA (10 ug) was converted into cDNA using Reverse Transcriptase (Invitrogen) and a modified oligo(dT)24 primer that contains T7 promoter sequences (GenSet).
| | Sample_hyb_protocol | The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides using an In Vitro Transcription kit (Affymetrix). The resultant cRNA product was purified using an RNeasy column (Qiagen) and quantified with a spectrophotometer. The cRNA target (20ug) was incubated at 94ºC for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc). The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix). The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm. GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in an GeneChip® Scanner 3000
| | Sample_data_processing | Expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). All GeneChips were scaled to a median intensity setting of 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luke,Hunter,Stockwin
| | Sample_contact_email | stockwinl@mail.nih.gov
| | Sample_contact_phone | 301-846-5431
| | Sample_contact_department | DTP
| | Sample_contact_institute | NCI Frederick
| | Sample_contact_address | Ft. Detrick
| | Sample_contact_city | Frederick
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21701
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338974/suppl/GSM338974.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338974/suppl/GSM338974.CHP.gz
| | Sample_series_id | GSE13433
| | Sample_data_row_count | 54675
| | |
|
GSM338982 | GPL570 |
|
ASPS_Patient_4_Array_1
|
ASPS Tumor
|
Confirmed primary or metastatic ASPS
Patient 4
|
Data from arrays hybridized to tumor RNA was analyzed relative to arrays hybridized to universal RNA to generate an unbiased transcriptome.
|
| Sample_geo_accession | GSM338982
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Nov 01 2008
| | Sample_last_update_date | Nov 03 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA samples were isolated immediately following surgery.
| | Sample_growth_protocol_ch1 | Not Applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rneasy (Qiagen) total RNA extraction
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Target was prepared and hybridized according to the Affymetrix Technical Manual. Total RNA (10 ug) was converted into cDNA using Reverse Transcriptase (Invitrogen) and a modified oligo(dT)24 primer that contains T7 promoter sequences (GenSet).
| | Sample_hyb_protocol | The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides using an In Vitro Transcription kit (Affymetrix). The resultant cRNA product was purified using an RNeasy column (Qiagen) and quantified with a spectrophotometer. The cRNA target (20ug) was incubated at 94ºC for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc). The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix). The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm. GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in an GeneChip® Scanner 3000
| | Sample_data_processing | Expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). All GeneChips were scaled to a median intensity setting of 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luke,Hunter,Stockwin
| | Sample_contact_email | stockwinl@mail.nih.gov
| | Sample_contact_phone | 301-846-5431
| | Sample_contact_department | DTP
| | Sample_contact_institute | NCI Frederick
| | Sample_contact_address | Ft. Detrick
| | Sample_contact_city | Frederick
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21701
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338982/suppl/GSM338982.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338982/suppl/GSM338982.CHP.gz
| | Sample_series_id | GSE13433
| | Sample_data_row_count | 54675
| | |
|
GSM338995 | GPL570 |
|
ASPS_Patient_4_Array_2
|
ASPS Tumor
|
Confirmed primary or metastatic ASPS
Patient 4
|
Data from arrays hybridized to tumor RNA was analyzed relative to arrays hybridized to universal RNA to generate an unbiased transcriptome.
|
| Sample_geo_accession | GSM338995
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Nov 01 2008
| | Sample_last_update_date | Nov 03 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | RNA samples were isolated immediately following surgery.
| | Sample_growth_protocol_ch1 | Not Applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rneasy (Qiagen) total RNA extraction
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Target was prepared and hybridized according to the Affymetrix Technical Manual. Total RNA (10 ug) was converted into cDNA using Reverse Transcriptase (Invitrogen) and a modified oligo(dT)24 primer that contains T7 promoter sequences (GenSet).
| | Sample_hyb_protocol | The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides using an In Vitro Transcription kit (Affymetrix). The resultant cRNA product was purified using an RNeasy column (Qiagen) and quantified with a spectrophotometer. The cRNA target (20ug) was incubated at 94ºC for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc). The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix). The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm. GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.
| | Sample_scan_protocol | Fluorescent images were detected in an GeneChip® Scanner 3000
| | Sample_data_processing | Expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). All GeneChips were scaled to a median intensity setting of 500.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Luke,Hunter,Stockwin
| | Sample_contact_email | stockwinl@mail.nih.gov
| | Sample_contact_phone | 301-846-5431
| | Sample_contact_department | DTP
| | Sample_contact_institute | NCI Frederick
| | Sample_contact_address | Ft. Detrick
| | Sample_contact_city | Frederick
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21701
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338995/suppl/GSM338995.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338995/suppl/GSM338995.CHP.gz
| | Sample_series_id | GSE13433
| | Sample_data_row_count | 54675
| | |
|
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
Enter the group name here: |
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