Search results for the GEO ID: GSE7529  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM182283 | GPL96 |
|
Whole ganglioneuroblastoma intermixed tumor_1134
|
Frozen ganglioneuroblastoma intermixed tumor
|
Phenotype: Ganglioneuroblastoma, intermixed (Schwannian stroma-rich)
|
Gene expression data from whole tumor
|
| Sample_geo_accession | GSM182283
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182283/suppl/GSM182283.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182284 | GPL96 |
|
Whole ganglioneuroma tumor_1172
|
Frozen ganglioneuroma tumor
|
Phenotype: Ganglioneuroma
|
Gene expression data from whole tumor
|
| Sample_geo_accession | GSM182284
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182284/suppl/GSM182284.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182285 | GPL96 |
|
Whole ganglioneuroma tumor_1250
|
Frozen ganglioneuroma tumor
|
Phenotype: Ganglioneuroma
|
Gene expression data from whole tumor
|
| Sample_geo_accession | GSM182285
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182285/suppl/GSM182285.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182286 | GPL96 |
|
Whole ganglioneuroma tumor_1377
|
Frozen ganglioneuroma tumor
|
Phenotype: Ganglioneuroma
|
Gene expression data from whole tumor
|
| Sample_geo_accession | GSM182286
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182286/suppl/GSM182286.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182287 | GPL96 |
|
Whole neuroblastoma tumor_1538
|
Frozen neuroblastoma tumor
|
Phenotype: Neuroblastoma (Schwannian stroma-poor)
|
Gene expression data from whole tumor
|
| Sample_geo_accession | GSM182287
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182287/suppl/GSM182287.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182288 | GPL96 |
|
Whole neuroblastoma tumor_1547
|
Frozen neuroblastoma tumor
|
Phenotype: Neuroblastoma (Schwannian stroma-poor)
|
Gene expression data from whole tumor
|
| Sample_geo_accession | GSM182288
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182288/suppl/GSM182288.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182289 | GPL96 |
|
Whole ganglioneuroblastoma tumor_1589
|
Frozen borderline ganglioneuroma maturing tumor
|
Phenotype: Borderline ganglioneuroma maturing
|
Gene expression data from whole tumor
|
| Sample_geo_accession | GSM182289
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182289/suppl/GSM182289.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182290 | GPL96 |
|
Microdissected area # 1 of 1589 tumor
|
Frozen borderline ganglioneuroma maturing tumor
|
Phenotype: Borderline ganglioneuroma maturing with isle of small round neuroblastic cells
|
Gene expression data from microdissected area # 1 of 1589 tumor
|
| Sample_geo_accession | GSM182290
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182290/suppl/GSM182290.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182291 | GPL96 |
|
Microdissected area # 2 of 1589 tumor
|
Frozen borderline ganglioneuroma maturing tumor
|
Phenotype: Borderline ganglioneuroma maturing with areas of schwannian stromal cells
|
Gene expression data from microdissected area # 2 of 1589 tumor
|
| Sample_geo_accession | GSM182291
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182291/suppl/GSM182291.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182292 | GPL96 |
|
Whole mature ganglioneuroma tumor_1591
|
Frozen ganglioneuroma mature tumor
|
Phenotype: Ganglioneuroma mature
|
Gene expression data from whole tumor
|
| Sample_geo_accession | GSM182292
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182292/suppl/GSM182292.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182293 | GPL96 |
|
Whole borderline ganglioneuroma maturing tumor_1761
|
Frozen borderline ganglioneuroma maturing tumor
|
Phenotype: Borderline ganglioneuroma maturing
|
Gene expression data from whole tumor
|
| Sample_geo_accession | GSM182293
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182293/suppl/GSM182293.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182294 | GPL96 |
|
Microdissected area # 1 of 1761 tumor
|
Frozen borderline ganglioneuroma maturing tumor
|
Phenotype: Borderline ganglioneuroma maturing with areas of schwannian stromal cells
|
Gene expression data from microdissected area # 1 of 1761 tumor
|
| Sample_geo_accession | GSM182294
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182294/suppl/GSM182294.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182295 | GPL96 |
|
Microdissected area # 2 of 1761 tumor
|
Frozen borderline ganglioneuroma maturing tumor
|
Phenotype: Borderline ganglioneuroma maturing with areas of schwannian stromal cells
|
Gene expression data from microdissected area # 2 of 1761 tumor
|
| Sample_geo_accession | GSM182295
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182295/suppl/GSM182295.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182296 | GPL96 |
|
Whole neuroblastoma tumor_1919
|
Frozen neuroblastoma tumor
|
Phenotype: Neuroblastoma (Schwannian stroma-poor)
|
Gene expression data from whole tumor
|
| Sample_geo_accession | GSM182296
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182296/suppl/GSM182296.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182297 | GPL96 |
|
Microdissected area # 1 of 1919 tumor
|
Frozen neuroblastoma tumor
|
Phenotype: Neuroblastoma (Schwannian stroma-poor) with areas of large round neuroblastic cells
|
Gene expression data from microdissected area # 1of 1919 tumor
|
| Sample_geo_accession | GSM182297
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182297/suppl/GSM182297.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182298 | GPL96 |
|
Microdissected area # 2 of 1919 tumor
|
Frozen neuroblastoma tumor
|
Phenotype: Neuroblastoma (Schwannian stroma-poor) with areas of small round neuroblastic cells
|
Gene expression data from microdissected area # 2 of 1919 tumor
|
| Sample_geo_accession | GSM182298
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182298/suppl/GSM182298.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182299 | GPL96 |
|
Whole ganglioneuroblastoma intermixed tumor_1999
|
frozen ganglioneuroblastoma intermixed tumor
|
Phenotype: Ganglioneuroblastoma, intermixed (Schwannian stroma-rich)
|
Gene expression data from whole tumor
|
| Sample_geo_accession | GSM182299
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182299/suppl/GSM182299.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182300 | GPL96 |
|
Whole neuroblastoma tumor_2056
|
Frozen neuroblastoma tumor
|
Phenotype: Neuroblastoma (Schwannian stroma-poor)
|
Gene expression data from whole tumor
|
| Sample_geo_accession | GSM182300
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182300/suppl/GSM182300.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182301 | GPL96 |
|
Whole neuroblastoma tumor_2181
|
Frozen neuroblastoma tumor
|
Phenotype: Neuroblastoma (Schwannian stroma-poor)
|
Gene expression data from whole tumor
|
| Sample_geo_accession | GSM182301
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182301/suppl/GSM182301.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182302 | GPL96 |
|
Whole neuroblastoma tumor_2182
|
Frozen neuroblastoma tumor
|
Phenotype: Neuroblastoma (Schwannian stroma-poor)
|
Gene expression data from whole tumor
|
| Sample_geo_accession | GSM182302
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182302/suppl/GSM182302.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182303 | GPL96 |
|
Microdissected area # 1 of 2182 tumor
|
Frozen neuroblastoma tumor
|
Phenotype: Neuroblastoma (Schwannian stroma-poor) with areas of small round neuroblastic cells
|
Gene expression data from microdissected area # 1 of 2182 tumor
|
| Sample_geo_accession | GSM182303
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182303/suppl/GSM182303.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182304 | GPL96 |
|
Microdissected area # 2 of 2182 tumor
|
Frozen neuroblastoma tumor
|
Phenotype: Neuroblastoma (Schwannian stroma-poor) with areas of large neuroblastic round cells
|
Gene expression data from microdissected area # 2 of 2182 tumor
|
| Sample_geo_accession | GSM182304
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182304/suppl/GSM182304.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182305 | GPL96 |
|
Microdissected area # 3 of 2182 tumor
|
Frozen neuroblastoma tumor
|
Phenotype: Neuroblastoma (Schwannian stroma-poor) with areas of large neuroblastic round cells
|
Gene expression data from microdissected area # 3 of 2182 tumor
|
| Sample_geo_accession | GSM182305
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182305/suppl/GSM182305.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182306 | GPL96 |
|
Whole neuroblastoma tumor_2215
|
Frozen neuroblastoma tumor
|
Phenotype: Neuroblastoma (Schwannian stroma-poor)
|
Gene expression data from whole tumor
|
| Sample_geo_accession | GSM182306
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182306/suppl/GSM182306.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182307 | GPL96 |
|
Whole neuroblastoma tumor_2216
|
Frozen neuroblastoma tumor
|
Phenotype: Neuroblastoma (Schwannian stroma-poor)
|
Gene expression data from whole tumor
|
| Sample_geo_accession | GSM182307
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA). Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA)., total RNA
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182307/suppl/GSM182307.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182308 | GPL96 |
|
Whole neuroblastoma tumor_2237
|
Frozen neuroblastoma tumor
|
Phenotype: Neuroblastoma (Schwannian stroma-poor)
|
Gene expression data from whole tumor
|
| Sample_geo_accession | GSM182308
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182308/suppl/GSM182308.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182309 | GPL96 |
|
Whole neuroblastoma tumor_2259
|
Frozen neuroblastoma tumor
|
Phenotype: Neuroblastoma (Schwannian stroma-poor)
|
Gene expression data from whole tumor
|
| Sample_geo_accession | GSM182309
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182309/suppl/GSM182309.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
|
GSM182310 | GPL96 |
|
Whole ganglioneuroma tumor_2782
|
Frozen ganglioneuroma tumor
|
Phenotype: Ganglioneuroma
|
Gene expression data from whole tumor
|
| Sample_geo_accession | GSM182310
| | Sample_status | Public on Apr 17 2007
| | Sample_submission_date | Apr 16 2007
| | Sample_last_update_date | Apr 16 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
| | Sample_hyb_protocol | In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
| | Sample_scan_protocol | GeneChips were scanned using the laser confocal fluorescence scanner.
| | Sample_data_processing | Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Domenico,,Albino
| | Sample_contact_email | domenico.albino@istge.it
| | Sample_contact_phone | +39-010-5737463
| | Sample_contact_institute | National Institute for Cancer Research (IST)
| | Sample_contact_address | L.go R. Benzi, 10
| | Sample_contact_city | genoa
| | Sample_contact_zip/postal_code | 16132
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM182nnn/GSM182310/suppl/GSM182310.CEL.gz
| | Sample_series_id | GSE7529
| | Sample_data_row_count | 22283
| | |
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