Search results for the GEO ID: GSE20559  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM482872 | GPL570 |
|
93-010_Tumor_20
|
Liposarcoma
|
tumor: liposarcoma
subtype: not specified
|
This tumor has been characterized previously to determine which telomere maintenance mechanism is active and interrogated for copy number changes using whole genome profiling (Johnson, J. E., Varkonyi, R. J., Schwalm, J., Cragle, R., Klein-Szanto, A., Patchefsky, A., Cukierman, E., von Mehren, M., and Broccoli, D. (2005) Multiple mechanisms of telomere maintenance exist in liposarcomas. Clin Cancer Res. 11: 5347-5355; Johnson, J. E., Gettings, E. J., Schwalm, J., Pei, J., Testa, J. R., Litwin, S., von Mehren, M., and Broccoli, D. (2007) Whole-genome profiling in liposarcomas reveals genetic alterations common to specific telomere maintenance mechanisms. Cancer Res. 67: 9221-9228.)
|
| Sample_geo_accession | GSM482872
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 10 2009
| | Sample_last_update_date | Apr 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Fox Chase Cancer Center Biorepository
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol:
| | Sample_hyb_protocol | Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM482nnn/GSM482872/suppl/GSM482872_030107_93_010.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM482nnn/GSM482872/suppl/GSM482872_030107_93_010.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM482987 | GPL570 |
|
99_217_Tumor_7
|
Liposarcoma
|
tumor: Liposarcoma
subtype: not specified
|
This tumor has been characterized previously to determine which telomere maintenance mechanism is active and interrogated for copy number changes using whole genome profiling (Johnson, J. E., Varkonyi, R. J., Schwalm, J., Cragle, R., Klein-Szanto, A., Patchefsky, A., Cukierman, E., von Mehren, M., and Broccoli, D. (2005) Multiple mechanisms of telomere maintenance exist in liposarcomas. Clin Cancer Res. 11: 5347-5355; Johnson, J. E., Gettings, E. J., Schwalm, J., Pei, J., Testa, J. R., Litwin, S., von Mehren, M., and Broccoli, D. (2007) Whole-genome profiling in liposarcomas reveals genetic alterations common to specific telomere maintenance mechanisms. Cancer Res. 67: 9221-9228.)
|
| Sample_geo_accession | GSM482987
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 10 2009
| | Sample_last_update_date | Apr 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Fox Chase Cancer Center Biorepository
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol:
| | Sample_hyb_protocol | Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM482nnn/GSM482987/suppl/GSM482987_030107_99_217.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM482nnn/GSM482987/suppl/GSM482987_030107_99_217.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM482988 | GPL570 |
|
98-310_Tumor_17
|
Liposarcoma
|
tumor: Liposarcoma
subtype: not specified
|
This tumor has been characterized previously to determine which telomere maintenance mechanism is active and interrogated for copy number changes using whole genome profiling (Johnson, J. E., Varkonyi, R. J., Schwalm, J., Cragle, R., Klein-Szanto, A., Patchefsky, A., Cukierman, E., von Mehren, M., and Broccoli, D. (2005) Multiple mechanisms of telomere maintenance exist in liposarcomas. Clin Cancer Res. 11: 5347-5355; Johnson, J. E., Gettings, E. J., Schwalm, J., Pei, J., Testa, J. R., Litwin, S., von Mehren, M., and Broccoli, D. (2007) Whole-genome profiling in liposarcomas reveals genetic alterations common to specific telomere maintenance mechanisms. Cancer Res. 67: 9221-9228.)
|
| Sample_geo_accession | GSM482988
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 10 2009
| | Sample_last_update_date | Apr 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Fox Chase Cancer Center Biorepository
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol:
| | Sample_hyb_protocol | Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM482nnn/GSM482988/suppl/GSM482988_021408_98_310.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM482nnn/GSM482988/suppl/GSM482988_021408_98_310.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM482989 | GPL570 |
|
93-185_Tumor_23
|
Liposarcoma
|
tumor: Liposarcoma
subtype: myxoid
|
This tumor has been characterized previously to determine which telomere maintenance mechanism is active and interrogated for copy number changes using whole genome profiling (Johnson, J. E., Varkonyi, R. J., Schwalm, J., Cragle, R., Klein-Szanto, A., Patchefsky, A., Cukierman, E., von Mehren, M., and Broccoli, D. (2005) Multiple mechanisms of telomere maintenance exist in liposarcomas. Clin Cancer Res. 11: 5347-5355; Johnson, J. E., Gettings, E. J., Schwalm, J., Pei, J., Testa, J. R., Litwin, S., von Mehren, M., and Broccoli, D. (2007) Whole-genome profiling in liposarcomas reveals genetic alterations common to specific telomere maintenance mechanisms. Cancer Res. 67: 9221-9228.)
|
| Sample_geo_accession | GSM482989
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 10 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Fox Chase Cancer Center Biorepository
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol:
| | Sample_hyb_protocol | Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM482nnn/GSM482989/suppl/GSM482989_031507_93_185.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM482nnn/GSM482989/suppl/GSM482989_031507_93_185.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM482990 | GPL570 |
|
03-199_Tumor_15
|
Liposarcoma
|
tumor: Liposarcoma
subtype: dedifferentiated
|
This tumor has been characterized previously to determine which telomere maintenance mechanism is active and interrogated for copy number changes using whole genome profiling (Johnson, J. E., Varkonyi, R. J., Schwalm, J., Cragle, R., Klein-Szanto, A., Patchefsky, A., Cukierman, E., von Mehren, M., and Broccoli, D. (2005) Multiple mechanisms of telomere maintenance exist in liposarcomas. Clin Cancer Res. 11: 5347-5355; Johnson, J. E., Gettings, E. J., Schwalm, J., Pei, J., Testa, J. R., Litwin, S., von Mehren, M., and Broccoli, D. (2007) Whole-genome profiling in liposarcomas reveals genetic alterations common to specific telomere maintenance mechanisms. Cancer Res. 67: 9221-9228.)
|
| Sample_geo_accession | GSM482990
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 10 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Fox Chase Cancer Center Biorepository
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol:
| | Sample_hyb_protocol | Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM482nnn/GSM482990/suppl/GSM482990_030107_03_199.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM482nnn/GSM482990/suppl/GSM482990_030107_03_199.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM482991 | GPL570 |
|
6272_Tumor_29
|
Liposarcoma
|
tumor: Liposarcoma
subtype: dedifferentiated
|
This tumor has been characterized previously to determine which telomere maintenance mechanism is active and interrogated for copy number changes using whole genome profiling (Johnson, J. E., Varkonyi, R. J., Schwalm, J., Cragle, R., Klein-Szanto, A., Patchefsky, A., Cukierman, E., von Mehren, M., and Broccoli, D. (2005) Multiple mechanisms of telomere maintenance exist in liposarcomas. Clin Cancer Res. 11: 5347-5355; Johnson, J. E., Gettings, E. J., Schwalm, J., Pei, J., Testa, J. R., Litwin, S., von Mehren, M., and Broccoli, D. (2007) Whole-genome profiling in liposarcomas reveals genetic alterations common to specific telomere maintenance mechanisms. Cancer Res. 67: 9221-9228.)
|
| Sample_geo_accession | GSM482991
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 10 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Fox Chase Cancer Center Biorepository
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol:
| | Sample_hyb_protocol | Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM482nnn/GSM482991/suppl/GSM482991_031507_6272.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM482nnn/GSM482991/suppl/GSM482991_031507_6272.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484715 | GPL570 |
|
96-389_Tumor_6
|
Liposarcoma
|
tumor: Liposarcoma
subtype: well-differentiated
|
This tumor has been characterized previously to determine which telomere maintenance mechanism is active and interrogated for copy number changes using whole genome profiling (Johnson, J. E., Varkonyi, R. J., Schwalm, J., Cragle, R., Klein-Szanto, A., Patchefsky, A., Cukierman, E., von Mehren, M., and Broccoli, D. (2005) Multiple mechanisms of telomere maintenance exist in liposarcomas. Clin Cancer Res. 11: 5347-5355; Johnson, J. E., Gettings, E. J., Schwalm, J., Pei, J., Testa, J. R., Litwin, S., von Mehren, M., and Broccoli, D. (2007) Whole-genome profiling in liposarcomas reveals genetic alterations common to specific telomere maintenance mechanisms. Cancer Res. 67: 9221-9228.)
|
| Sample_geo_accession | GSM484715
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Fox Chase Cancer Center Biorepository
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484715/suppl/GSM484715_031507_96_389.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484715/suppl/GSM484715_1_031507_96_389.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484716 | GPL570 |
|
03-159_Tumor_10
|
Liposarcoma
|
tumor: Liposarcoma
subtype: well-differentiated
|
This tumor has been characterized previously to determine which telomere maintenance mechanism is active and interrogated for copy number changes using whole genome profiling (Johnson, J. E., Varkonyi, R. J., Schwalm, J., Cragle, R., Klein-Szanto, A., Patchefsky, A., Cukierman, E., von Mehren, M., and Broccoli, D. (2005) Multiple mechanisms of telomere maintenance exist in liposarcomas. Clin Cancer Res. 11: 5347-5355; Johnson, J. E., Gettings, E. J., Schwalm, J., Pei, J., Testa, J. R., Litwin, S., von Mehren, M., and Broccoli, D. (2007) Whole-genome profiling in liposarcomas reveals genetic alterations common to specific telomere maintenance mechanisms. Cancer Res. 67: 9221-9228.)
|
| Sample_geo_accession | GSM484716
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Fox Chase Cancer Center Biorepository
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484716/suppl/GSM484716_031507_03_159.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484716/suppl/GSM484716_031507_03_159.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484717 | GPL570 |
|
97-096_Tumor_19
|
Liposarcoma
|
tumor: Liposarcoma
subtype: well-differentiated
|
This tumor has been characterized previously to determine which telomere maintenance mechanism is active and interrogated for copy number changes using whole genome profiling (Johnson, J. E., Varkonyi, R. J., Schwalm, J., Cragle, R., Klein-Szanto, A., Patchefsky, A., Cukierman, E., von Mehren, M., and Broccoli, D. (2005) Multiple mechanisms of telomere maintenance exist in liposarcomas. Clin Cancer Res. 11: 5347-5355; Johnson, J. E., Gettings, E. J., Schwalm, J., Pei, J., Testa, J. R., Litwin, S., von Mehren, M., and Broccoli, D. (2007) Whole-genome profiling in liposarcomas reveals genetic alterations common to specific telomere maintenance mechanisms. Cancer Res. 67: 9221-9228.)
|
| Sample_geo_accession | GSM484717
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Fox Chase Cancer Center Biorepository
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484717/suppl/GSM484717_021408_97_096.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484717/suppl/GSM484717_021408_97_096.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484718 | GPL570 |
|
97-212_Tumor_21
|
Liposarcoma
|
tumor: Liposarcoma
subtype: well-differentiated
|
This tumor has been characterized previously to determine which telomere maintenance mechanism is active and interrogated for copy number changes using whole genome profiling (Johnson, J. E., Varkonyi, R. J., Schwalm, J., Cragle, R., Klein-Szanto, A., Patchefsky, A., Cukierman, E., von Mehren, M., and Broccoli, D. (2005) Multiple mechanisms of telomere maintenance exist in liposarcomas. Clin Cancer Res. 11: 5347-5355; Johnson, J. E., Gettings, E. J., Schwalm, J., Pei, J., Testa, J. R., Litwin, S., von Mehren, M., and Broccoli, D. (2007) Whole-genome profiling in liposarcomas reveals genetic alterations common to specific telomere maintenance mechanisms. Cancer Res. 67: 9221-9228.)
|
| Sample_geo_accession | GSM484718
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Fox Chase Cancer Center Biorepository
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484718/suppl/GSM484718_031507_97_212.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484718/suppl/GSM484718_031507_97_212.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484719 | GPL570 |
|
94-215_Tumor_31R1
|
Liposarcoma
|
tumor: Liposarcoma
subtype: Well-differentiated spindle cell
|
This tumor has been characterized previously to determine which telomere maintenance mechanism is active and interrogated for copy number changes using whole genome profiling (Johnson, J. E., Varkonyi, R. J., Schwalm, J., Cragle, R., Klein-Szanto, A., Patchefsky, A., Cukierman, E., von Mehren, M., and Broccoli, D. (2005) Multiple mechanisms of telomere maintenance exist in liposarcomas. Clin Cancer Res. 11: 5347-5355; Johnson, J. E., Gettings, E. J., Schwalm, J., Pei, J., Testa, J. R., Litwin, S., von Mehren, M., and Broccoli, D. (2007) Whole-genome profiling in liposarcomas reveals genetic alterations common to specific telomere maintenance mechanisms. Cancer Res. 67: 9221-9228.)
|
| Sample_geo_accession | GSM484719
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Fox Chase Cancer Center Biorepository
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484719/suppl/GSM484719_030107_94_215.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484719/suppl/GSM484719_030107_94_215.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484720 | GPL570 |
|
95-124_Tumor_31R2
|
Liposarcoma
|
tumor: Liposarcoma
subtype: pleomorphic
tumor type: Recurrence of Tumor 94-215 (Tumor 31R1)
|
This tumor has been characterized previously to determine which telomere maintenance mechanism is active and interrogated for copy number changes using whole genome profiling (Johnson, J. E., Varkonyi, R. J., Schwalm, J., Cragle, R., Klein-Szanto, A., Patchefsky, A., Cukierman, E., von Mehren, M., and Broccoli, D. (2005) Multiple mechanisms of telomere maintenance exist in liposarcomas. Clin Cancer Res. 11: 5347-5355; Johnson, J. E., Gettings, E. J., Schwalm, J., Pei, J., Testa, J. R., Litwin, S., von Mehren, M., and Broccoli, D. (2007) Whole-genome profiling in liposarcomas reveals genetic alterations common to specific telomere maintenance mechanisms. Cancer Res. 67: 9221-9228.)
|
| Sample_geo_accession | GSM484720
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Fox Chase Cancer Center Biorepository
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484720/suppl/GSM484720_030107_95_124.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484720/suppl/GSM484720_030107_95_124.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484721 | GPL570 |
|
96-249_Tumor_32R1
|
Liposarcoma
|
tumor: Liposarcoma
subtype: well-differentiated spindle cell
|
This tumor has been characterized previously to determine which telomere maintenance mechanism is active and interrogated for copy number changes using whole genome profiling (Johnson, J. E., Varkonyi, R. J., Schwalm, J., Cragle, R., Klein-Szanto, A., Patchefsky, A., Cukierman, E., von Mehren, M., and Broccoli, D. (2005) Multiple mechanisms of telomere maintenance exist in liposarcomas. Clin Cancer Res. 11: 5347-5355; Johnson, J. E., Gettings, E. J., Schwalm, J., Pei, J., Testa, J. R., Litwin, S., von Mehren, M., and Broccoli, D. (2007) Whole-genome profiling in liposarcomas reveals genetic alterations common to specific telomere maintenance mechanisms. Cancer Res. 67: 9221-9228.)
|
| Sample_geo_accession | GSM484721
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Fox Chase Cancer Center Biorepository
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484721/suppl/GSM484721_112807_96_249.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484721/suppl/GSM484721_112807_96_249.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484722 | GPL570 |
|
97-166_Tumor_32R2
|
Liposarcoma
|
tumor: Liposarcoma
subtype: well-differentiated spindle cell
tumor type: Recurrence of 96-249, Tumor 32R1
|
This tumor has been characterized previously to determine which telomere maintenance mechanism is active and interrogated for copy number changes using whole genome profiling (Johnson, J. E., Varkonyi, R. J., Schwalm, J., Cragle, R., Klein-Szanto, A., Patchefsky, A., Cukierman, E., von Mehren, M., and Broccoli, D. (2005) Multiple mechanisms of telomere maintenance exist in liposarcomas. Clin Cancer Res. 11: 5347-5355; Johnson, J. E., Gettings, E. J., Schwalm, J., Pei, J., Testa, J. R., Litwin, S., von Mehren, M., and Broccoli, D. (2007) Whole-genome profiling in liposarcomas reveals genetic alterations common to specific telomere maintenance mechanisms. Cancer Res. 67: 9221-9228.)
|
| Sample_geo_accession | GSM484722
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Fox Chase Cancer Center Biorepository
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484722/suppl/GSM484722_112807_97_166.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484722/suppl/GSM484722_112807_97_166.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484723 | GPL570 |
|
02-390_Tumor_16
|
Liposarcoma
|
tumor: Liposarcoma
subtype: well-differentiated
|
This tumor has been characterized previously to determine which telomere maintenance mechanism is active and interrogated for copy number changes using whole genome profiling (Johnson, J. E., Varkonyi, R. J., Schwalm, J., Cragle, R., Klein-Szanto, A., Patchefsky, A., Cukierman, E., von Mehren, M., and Broccoli, D. (2005) Multiple mechanisms of telomere maintenance exist in liposarcomas. Clin Cancer Res. 11: 5347-5355; Johnson, J. E., Gettings, E. J., Schwalm, J., Pei, J., Testa, J. R., Litwin, S., von Mehren, M., and Broccoli, D. (2007) Whole-genome profiling in liposarcomas reveals genetic alterations common to specific telomere maintenance mechanisms. Cancer Res. 67: 9221-9228.)
|
| Sample_geo_accession | GSM484723
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Fox Chase Cancer Center Biorepository
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484723/suppl/GSM484723_021408_02_390.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484723/suppl/GSM484723_021408_02_390.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484724 | GPL570 |
|
03-098_Tumor_2
|
Liposarcoma
|
tumor: Liposarcoma
subtype: pleomorphic
|
This tumor has been characterized previously to determine which telomere maintenance mechanism is active and interrogated for copy number changes using whole genome profiling (Johnson, J. E., Varkonyi, R. J., Schwalm, J., Cragle, R., Klein-Szanto, A., Patchefsky, A., Cukierman, E., von Mehren, M., and Broccoli, D. (2005) Multiple mechanisms of telomere maintenance exist in liposarcomas. Clin Cancer Res. 11: 5347-5355; Johnson, J. E., Gettings, E. J., Schwalm, J., Pei, J., Testa, J. R., Litwin, S., von Mehren, M., and Broccoli, D. (2007) Whole-genome profiling in liposarcomas reveals genetic alterations common to specific telomere maintenance mechanisms. Cancer Res. 67: 9221-9228.)
|
| Sample_geo_accession | GSM484724
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Fox Chase Cancer Center Biorepository
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484724/suppl/GSM484724_031507_03_098.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484724/suppl/GSM484724_031507_03_098.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484725 | GPL570 |
|
5228_Tumor_27
|
Liposarcoma
|
tumor: Liposarcoma
subtype: pleomorphic
|
This tumor has been characterized previously to determine which telomere maintenance mechanism is active and interrogated for copy number changes using whole genome profiling (Johnson, J. E., Varkonyi, R. J., Schwalm, J., Cragle, R., Klein-Szanto, A., Patchefsky, A., Cukierman, E., von Mehren, M., and Broccoli, D. (2005) Multiple mechanisms of telomere maintenance exist in liposarcomas. Clin Cancer Res. 11: 5347-5355; Johnson, J. E., Gettings, E. J., Schwalm, J., Pei, J., Testa, J. R., Litwin, S., von Mehren, M., and Broccoli, D. (2007) Whole-genome profiling in liposarcomas reveals genetic alterations common to specific telomere maintenance mechanisms. Cancer Res. 67: 9221-9228.)
|
| Sample_geo_accession | GSM484725
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Fox Chase Cancer Center Biorepository
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484725/suppl/GSM484725_030107_5228.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484725/suppl/GSM484725_030107_5228.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484726 | GPL570 |
|
D27669_Tumor_33
|
Liposarcoma
|
tumor: Liposarcoma
subtype: pleomorphic
|
N/A
|
| Sample_geo_accession | GSM484726
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Cooperative Human Tissue Network
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484726/suppl/GSM484726_021408_D27669.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484726/suppl/GSM484726_021408_D27669.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484727 | GPL570 |
|
D27670_Tumor_34
|
Liposarcoma
|
tumor: Liposarcoma
subtype: pleomorphic
|
N/A
|
| Sample_geo_accession | GSM484727
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Cooperative Human Tissue Network
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484727/suppl/GSM484727_112807_D27670.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484727/suppl/GSM484727_112807_D27670.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484728 | GPL570 |
|
D27671_Tumor_35
|
Liposarcoma
|
tumor: Liposarcoma
subtype: pleomorphic
|
N/A
|
| Sample_geo_accession | GSM484728
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Cooperative Human Tissue Network
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484728/suppl/GSM484728_112807_D27671.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484728/suppl/GSM484728_112807_D27671.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484729 | GPL570 |
|
D27673_Tumor_36
|
Liposarcoma
|
tumor: Liposarcoma
subtype: pleomorphic
|
N/A
|
| Sample_geo_accession | GSM484729
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Cooperative Human Tissue Network
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484729/suppl/GSM484729_112807_D27673.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484729/suppl/GSM484729_112807_D27673.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484730 | GPL570 |
|
3000p8573_Tumor_37
|
Liposarcoma
|
tumor: Liposarcoma
subtype: dedifferentiated
|
N/A
|
| Sample_geo_accession | GSM484730
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Cooperative Human Tissue Network
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484730/suppl/GSM484730_021408_3000_30_P8573.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484730/suppl/GSM484730_021408_3000_30_P8573.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484731 | GPL570 |
|
06-05-152A_Tumor_39
|
Liposarcoma
|
tumor: Liposarcoma
subtype: myxoid round cell
|
N/A
|
| Sample_geo_accession | GSM484731
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Cooperative Human Tissue Network
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484731/suppl/GSM484731_112807_06_05_152A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484731/suppl/GSM484731_112807_06_05_152A.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484732 | GPL570 |
|
03-08-1037A_Tumor_40
|
Liposarcoma
|
tumor: Liposarcoma
subtype: well-differentiated
|
N/A
|
| Sample_geo_accession | GSM484732
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Cooperative Human Tissue Network
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484732/suppl/GSM484732_021408_03_08_1037A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484732/suppl/GSM484732_021408_03_08_1037A.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484733 | GPL570 |
|
06-06-A279A_Tumor_41
|
Liposarcoma
|
tumor: Liposarcoma
subtype: well-differentiated
|
N/A
|
| Sample_geo_accession | GSM484733
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Cooperative Human Tissue Network
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484733/suppl/GSM484733_021408_06_06_A279A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484733/suppl/GSM484733_021408_06_06_A279A.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484734 | GPL570 |
|
1071403A2_Tumor_42
|
Liposarcoma
|
tumor: Liposarcoma
subtype: well-differentiated
|
N/A
|
| Sample_geo_accession | GSM484734
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Cooperative Human Tissue Network
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484734/suppl/GSM484734_021408_1071403A2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484734/suppl/GSM484734_021408_1071403A2.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484735 | GPL570 |
|
96-10-P004_Tumor_43
|
Liposarcoma
|
tumor: Liposarcoma
subtype: well-differentiated
|
N/A
|
| Sample_geo_accession | GSM484735
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 13 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Cooperative Human Tissue Network
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484735/suppl/GSM484735_021408_96_10_P004.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484735/suppl/GSM484735_021408_96_10_P004.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484736 | GPL570 |
|
D27666_Tumor_44
|
Liposarcoma
|
tumor: Liposarcoma
subtype: well-differentiated
|
N/A
|
| Sample_geo_accession | GSM484736
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 14 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Cooperative Human Tissue Network
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484736/suppl/GSM484736_021408_D27666.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484736/suppl/GSM484736_021408_D27666.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484737 | GPL570 |
|
D27667_Tumor_45
|
Liposarcoma
|
tumor: Liposarcoma
subtype: well-differentiated
|
N/A
|
| Sample_geo_accession | GSM484737
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 14 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Cooperative Human Tissue Network
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484737/suppl/GSM484737_021408_D27667.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484737/suppl/GSM484737_021408_D27667.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484738 | GPL570 |
|
D27674_Tumor_46
|
Liposarcoma
|
tumor: Liposarcoma
subtype: well-differentiated
|
N/A
|
| Sample_geo_accession | GSM484738
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 14 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Cooperative Human Tissue Network
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484738/suppl/GSM484738_021408_D27674.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484738/suppl/GSM484738_021408_D27674.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM484739 | GPL570 |
|
D27667_Tumor_47
|
Liposarcoma
|
tumor: Liposarcoma
subtype: well-differentiated
|
N/A
|
| Sample_geo_accession | GSM484739
| | Sample_status | Public on Mar 03 2010
| | Sample_submission_date | Dec 14 2009
| | Sample_last_update_date | Mar 03 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Cooperative Human Tissue Network
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484739/suppl/GSM484739_112807_D27677.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM484nnn/GSM484739/suppl/GSM484739_112807_D27677.CHP.gz
| | Sample_series_id | GSE19449
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM516627 | GPL570 |
|
21158_Tumor_49
|
Liposarcoma
|
tumor: Liposarcoma
subtype: dedifferentiated
|
This tumor is ALT-positive.
|
| Sample_geo_accession | GSM516627
| | Sample_status | Public on Mar 02 2010
| | Sample_submission_date | Feb 28 2010
| | Sample_last_update_date | Mar 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Cooperative Human Tissue Network (CHTN)
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516627/suppl/GSM516627__1_21158__HG_U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516627/suppl/GSM516627__1_21158__HG_U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM516628 | GPL570 |
|
MDCC19_Tumor_50
|
Liposarcoma
|
tumor: Liposarcoma
subtype: dedifferentiated
|
This tumor is ALT-positive.
|
| Sample_geo_accession | GSM516628
| | Sample_status | Public on Mar 02 2010
| | Sample_submission_date | Feb 28 2010
| | Sample_last_update_date | Mar 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Anderson Cancer Institute
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516628/suppl/GSM516628__5_MDCC19__HG_U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516628/suppl/GSM516628__5_MDCC19__HG_U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM516629 | GPL570 |
|
MDCC30_Tumor_51
|
Liposarcoma
|
tumor: Liposarcoma
subtype: dedifferentiated
|
This tumor is ALT-positive.
|
| Sample_geo_accession | GSM516629
| | Sample_status | Public on Mar 02 2010
| | Sample_submission_date | Feb 28 2010
| | Sample_last_update_date | Mar 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Anderson Cancer Institute
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516629/suppl/GSM516629__6_MDCC30__HG_U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516629/suppl/GSM516629__6_MDCC30__HG_U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM516630 | GPL570 |
|
MDCC36_Tumor_52
|
Liposarcoma
|
tumor: Liposarcoma
subtype: dedifferentiated
|
This tumor is ALT-positive.
|
| Sample_geo_accession | GSM516630
| | Sample_status | Public on Mar 02 2010
| | Sample_submission_date | Feb 28 2010
| | Sample_last_update_date | Mar 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Anderson Cancer Institute
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516630/suppl/GSM516630__2_MDCC36__HG_U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516630/suppl/GSM516630__2_MDCC36__HG_U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM516631 | GPL570 |
|
MDCC39_Tumor_56
|
Liposarcoma
|
tumor: Liposarcoma
subtype: dedifferentiated
|
This tumor is ALT-positive.
|
| Sample_geo_accession | GSM516631
| | Sample_status | Public on Mar 02 2010
| | Sample_submission_date | Feb 28 2010
| | Sample_last_update_date | Mar 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Anderson Cancer Institute
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516631/suppl/GSM516631__7_MDCC39__HG_U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516631/suppl/GSM516631__7_MDCC39__HG_U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM516632 | GPL570 |
|
44978_Tumor_54
|
Liposarcoma
|
tumor: Liposarcoma
subtype: dedifferentiated
|
This tumor is telomerase-positive.
|
| Sample_geo_accession | GSM516632
| | Sample_status | Public on Mar 02 2010
| | Sample_submission_date | Feb 28 2010
| | Sample_last_update_date | Mar 01 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Cooperative Human Tissue Network (CHTN)
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516632/suppl/GSM516632__3_44978__HG_U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516632/suppl/GSM516632__3_44978__HG_U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
GSM516633 | GPL570 |
|
4080752_Tumor_55
|
Liposarcoma
|
tumor: Liposarcoma
subtype: dedifferentiated
|
N/A
|
| Sample_geo_accession | GSM516633
| | Sample_status | Public on Mar 02 2010
| | Sample_submission_date | Feb 28 2010
| | Sample_last_update_date | Apr 12 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Cooperative Human Tissue Network (CHTN)
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | N/A
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).
| | Sample_hyb_protocol | Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A1 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A1 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A1 Cycle=2
| | Sample_hyb_protocol | Wash B Recovery Mixes=0
| | Sample_hyb_protocol | Wash B Temperature (C)=50
| | Sample_hyb_protocol | Number of Wash B Cycles=6
| | Sample_hyb_protocol | Mixes per Wash B Cycle=15
| | Sample_hyb_protocol | Stain Temperature (C)=35
| | Sample_hyb_protocol | First Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A2 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A2 Temperature (C)=30
| | Sample_hyb_protocol | Number of Wash A2 Cycles=10
| | Sample_hyb_protocol | Mixes per Wash A2 Cycle=4
| | Sample_hyb_protocol | Second Stain Time (seconds)=300
| | Sample_hyb_protocol | Third Stain Time (seconds)=300
| | Sample_hyb_protocol | Wash A3 Recovery Mixes=0
| | Sample_hyb_protocol | Wash A3 Temperature (C)=35
| | Sample_hyb_protocol | Number of Wash A3 Cycles=15
| | Sample_hyb_protocol | Mixes per Wash A3 Cycle=4<
| | Sample_hyb_protocol | Holding Temperature (C)=25
| | Sample_scan_protocol | The probe array was scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Standard Affymetrix protocol
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jay,,Johnson
| | Sample_contact_email | johe@mail.med.upenn.edu
| | Sample_contact_phone | 215-573-6529
| | Sample_contact_laboratory | F. Brad Johnson
| | Sample_contact_department | Pathology and Laboratory Medicine
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 422 Curie Blvd
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516633/suppl/GSM516633__1_4080752__HG_U133_Plus_2_.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516633/suppl/GSM516633__1_4080752__HG_U133_Plus_2_.mas5.CHP.gz
| | Sample_series_id | GSE20559
| | Sample_data_row_count | 54675
| | |
|
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