Search results for the GEO ID: GSE13601  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM342530 | GPL8300 |
|
Tongue 001 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342530
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342530/suppl/GSM342530.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342531 | GPL8300 |
|
Tongue 002 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342531
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342531/suppl/GSM342531.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342532 | GPL8300 |
|
Tongue 002 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342532
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342532/suppl/GSM342532.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342533 | GPL8300 |
|
Tongue 003 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342533
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342533/suppl/GSM342533.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342534 | GPL8300 |
|
Tongue 003 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342534
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342534/suppl/GSM342534.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342535 | GPL8300 |
|
Tongue 004 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342535
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342535/suppl/GSM342535.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342536 | GPL8300 |
|
Tongue 004 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342536
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342536/suppl/GSM342536.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342537 | GPL8300 |
|
Tongue 005 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342537
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342537/suppl/GSM342537.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342538 | GPL8300 |
|
Tongue 005 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342538
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342538/suppl/GSM342538.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342539 | GPL8300 |
|
Tongue 006 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342539
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342539/suppl/GSM342539.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342540 | GPL8300 |
|
Tongue 007 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342540
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342540/suppl/GSM342540.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342541 | GPL8300 |
|
Tongue 007 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342541
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342541/suppl/GSM342541.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342542 | GPL8300 |
|
Tongue 009 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342542
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342542/suppl/GSM342542.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342543 | GPL8300 |
|
Tongue 009 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342543
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342543/suppl/GSM342543.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342544 | GPL8300 |
|
Tongue 010 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342544
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342544/suppl/GSM342544.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342545 | GPL8300 |
|
Tongue 010 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342545
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342545/suppl/GSM342545.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342546 | GPL8300 |
|
Tongue 011 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342546
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342546/suppl/GSM342546.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342547 | GPL8300 |
|
Tongue 012 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342547
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342547/suppl/GSM342547.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342548 | GPL8300 |
|
Tongue 013 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342548
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342548/suppl/GSM342548.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342549 | GPL8300 |
|
Tongue 013 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342549
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342549/suppl/GSM342549.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342550 | GPL8300 |
|
Tongue 015 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342550
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342550/suppl/GSM342550.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342551 | GPL8300 |
|
Tongue 015 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342551
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342551/suppl/GSM342551.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342552 | GPL8300 |
|
Tongue 016 LN
|
LN
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342552
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342552/suppl/GSM342552.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342553 | GPL8300 |
|
Tongue 016 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342553
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342553/suppl/GSM342553.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342554 | GPL8300 |
|
Tongue 016 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342554
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342554/suppl/GSM342554.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342555 | GPL8300 |
|
Tongue 017 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342555
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342555/suppl/GSM342555.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342556 | GPL8300 |
|
Tongue 017 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342556
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342556/suppl/GSM342556.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342557 | GPL8300 |
|
Tongue 018 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342557
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342557/suppl/GSM342557.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342558 | GPL8300 |
|
Tongue 019 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342558
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342558/suppl/GSM342558.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342559 | GPL8300 |
|
Tongue 020 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342559
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342559/suppl/GSM342559.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342560 | GPL8300 |
|
Tongue 020 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342560
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342560/suppl/GSM342560.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342561 | GPL8300 |
|
Tongue 021 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342561
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342561/suppl/GSM342561.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342562 | GPL8300 |
|
Tongue 023 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342562
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342562/suppl/GSM342562.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342563 | GPL8300 |
|
Tongue 024 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342563
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342563/suppl/GSM342563.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342564 | GPL8300 |
|
Tongue 025 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342564
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342564/suppl/GSM342564.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342565 | GPL8300 |
|
Tongue 025 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342565
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342565/suppl/GSM342565.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342566 | GPL8300 |
|
Tongue 027 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342566
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342566/suppl/GSM342566.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342567 | GPL8300 |
|
Tongue 028 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342567
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342567/suppl/GSM342567.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342568 | GPL8300 |
|
Tongue 028 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342568
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342568/suppl/GSM342568.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342569 | GPL8300 |
|
Tongue 029 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342569
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342569/suppl/GSM342569.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342570 | GPL8300 |
|
Tongue 029 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342570
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342570/suppl/GSM342570.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342571 | GPL8300 |
|
Tongue 030 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342571
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342571/suppl/GSM342571.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342572 | GPL8300 |
|
Tongue 030 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342572
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342572/suppl/GSM342572.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342573 | GPL8300 |
|
Tongue 031 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342573
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342573/suppl/GSM342573.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342574 | GPL8300 |
|
Tongue 033 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342574
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342574/suppl/GSM342574.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342575 | GPL8300 |
|
Tongue 034 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342575
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342575/suppl/GSM342575.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342576 | GPL8300 |
|
Tongue 035 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342576
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342576/suppl/GSM342576.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342577 | GPL8300 |
|
Tongue 036 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342577
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342577/suppl/GSM342577.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342578 | GPL8300 |
|
Tongue 038 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342578
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342578/suppl/GSM342578.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342579 | GPL8300 |
|
Tongue 038 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342579
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342579/suppl/GSM342579.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342580 | GPL8300 |
|
Tongue 039 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342580
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342580/suppl/GSM342580.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342581 | GPL8300 |
|
Tongue 039 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342581
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342581/suppl/GSM342581.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342582 | GPL8300 |
|
Tongue 040 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342582
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342582/suppl/GSM342582.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342583 | GPL8300 |
|
Tongue 041 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342583
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342583/suppl/GSM342583.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342584 | GPL8300 |
|
Tongue 041 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342584
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342584/suppl/GSM342584.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342585 | GPL8300 |
|
Tongue 042 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342585
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342585/suppl/GSM342585.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342586 | GPL8300 |
|
Tongue 042 Tumor
|
Tumor
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342586
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342586/suppl/GSM342586.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
GSM342587 | GPL8300 |
|
Tongue 043 Normal
|
Normal
|
Tissue: Tongue
|
none
|
| Sample_geo_accession | GSM342587
| | Sample_status | Public on Nov 14 2008
| | Sample_submission_date | Nov 13 2008
| | Sample_last_update_date | Mar 16 2009
| | 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 snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer. The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.
| | Sample_hyb_protocol | Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Gene chips were scanned using the standard Affymetrix supplied scaner
| | Sample_data_processing | Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Nicholas,D,Socci
| | Sample_contact_email | soccin@mskcc.org
| | Sample_contact_laboratory | Bioinformatics Core
| | Sample_contact_department | Computational Biology Center
| | Sample_contact_institute | Memorial Sloan Kettering Cancer Center
| | Sample_contact_address | 1275 York Ave
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM342nnn/GSM342587/suppl/GSM342587.CEL.gz
| | Sample_series_id | GSE13601
| | Sample_data_row_count | 12625
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
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