Search results for the GEO ID: GSE12452  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM312896 | GPL570 |
|
normal nasopharyngeal tissue, specimen N1
|
nasopharynx
|
normal
Biopsy Negative Control
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312896
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312896/suppl/GSM312896.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312897 | GPL570 |
|
normal nasopharyngeal tissue, specimen N2
|
nasopharynx
|
normal
Biopsy Negative Control
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312897
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312897/suppl/GSM312897.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312898 | GPL570 |
|
normal nasopharyngeal tissue, specimen N3
|
nasopharynx
|
normal
Biopsy Negative Control
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312898
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312898/suppl/GSM312898.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312899 | GPL570 |
|
normal nasopharyngeal tissue, specimen N4
|
nasopharynx
|
normal
Biopsy Negative Control
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312899
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312899/suppl/GSM312899.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312900 | GPL570 |
|
normal nasopharyngeal tissue, specimen N5
|
nasopharynx
|
normal
Adjacent pair of T18
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312900
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312900/suppl/GSM312900.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312901 | GPL570 |
|
normal nasopharyngeal tissue, specimen N6
|
nasopharynx
|
normal
Adjacent pair of T20
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312901
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312901/suppl/GSM312901.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312902 | GPL570 |
|
normal nasopharyngeal tissue, specimen N7
|
nasopharynx
|
normal
Adjacent pair of T7
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312902
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312902/suppl/GSM312902.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312903 | GPL570 |
|
normal nasopharyngeal tissue, specimen N8
|
nasopharynx
|
normal
Adjacent pair of T10
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312903
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312903/suppl/GSM312903.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312904 | GPL570 |
|
normal nasopharyngeal tissue, specimen N9
|
nasopharynx
|
normal
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312904
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312904/suppl/GSM312904.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312905 | GPL570 |
|
normal nasopharyngeal tissue, specimen N10
|
nasopharynx
|
normal
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312905
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312905/suppl/GSM312905.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312906 | GPL570 |
|
nasopharyngeal carcinoma, specimen T1
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIB
Tumor Stage: T1N1
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312906
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312906/suppl/GSM312906.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312907 | GPL570 |
|
nasopharyngeal carcinoma, specimen T2
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIB
Tumor Stage: T2N2
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312907
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312907/suppl/GSM312907.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312908 | GPL570 |
|
nasopharyngeal carcinoma, specimen T3
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIA
Tumor Stage: T3N2
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312908
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312908/suppl/GSM312908.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312909 | GPL570 |
|
nasopharyngeal carcinoma, specimen T4
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIA
Tumor Stage: T2N2
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312909
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312909/suppl/GSM312909.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312910 | GPL570 |
|
nasopharyngeal carcinoma, specimen T5
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIB
Tumor Stage: T2N1
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312910
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312910/suppl/GSM312910.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312911 | GPL570 |
|
nasopharyngeal carcinoma, specimen T6
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIA
Tumor Stage: T1N1
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312911
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312911/suppl/GSM312911.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312912 | GPL570 |
|
nasopharyngeal carcinoma, specimen T7
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIA
Tumor Stage: T1N1
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312912
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312912/suppl/GSM312912.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312913 | GPL570 |
|
nasopharyngeal carcinoma, specimen T8
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIA
Tumor Stage: T1N1
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312913
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312913/suppl/GSM312913.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312914 | GPL570 |
|
nasopharyngeal carcinoma, specimen T9
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIB
Tumor Stage: T1N0
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312914
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312914/suppl/GSM312914.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312915 | GPL570 |
|
nasopharyngeal carcinoma, specimen T10
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIB
Tumor Stage: T2N2
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312915
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312915/suppl/GSM312915.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312916 | GPL570 |
|
nasopharyngeal carcinoma, specimen T11
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIB
Tumor Stage: T1N1
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312916
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312916/suppl/GSM312916.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312917 | GPL570 |
|
nasopharyngeal carcinoma, specimen T12
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIB
Tumor Stage: T2N2
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312917
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312917/suppl/GSM312917.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312918 | GPL570 |
|
nasopharyngeal carcinoma, specimen T13
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIA
Tumor Stage: T2N1
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312918
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312918/suppl/GSM312918.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312919 | GPL570 |
|
nasopharyngeal carcinoma, specimen T14
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIA
Tumor Stage: T1N1
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312919
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312919/suppl/GSM312919.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312920 | GPL570 |
|
nasopharyngeal carcinoma, specimen T15
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIA
Tumor Stage: T1N0
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312920
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312920/suppl/GSM312920.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312921 | GPL570 |
|
nasopharyngeal carcinoma, specimen T16
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIA
Tumor Stage: T1N1
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312921
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312921/suppl/GSM312921.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312922 | GPL570 |
|
nasopharyngeal carcinoma, specimen T17
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIA
Tumor Stage: T1N1
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312922
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312922/suppl/GSM312922.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312923 | GPL570 |
|
nasopharyngeal carcinoma, specimen T18
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIB
Tumor Stage: T1N0
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312923
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312923/suppl/GSM312923.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312924 | GPL570 |
|
nasopharyngeal carcinoma, specimen T19
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIB
Tumor Stage: T1N1
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312924
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312924/suppl/GSM312924.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312925 | GPL570 |
|
nasopharyngeal carcinoma, specimen T20
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIA
Tumor Stage: T3N0
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312925
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312925/suppl/GSM312925.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312926 | GPL570 |
|
nasopharyngeal carcinoma, specimen T21
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIB
Tumor Stage: T2N1
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312926
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312926/suppl/GSM312926.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312927 | GPL570 |
|
nasopharyngeal carcinoma, specimen T22
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIB
Tumor Stage: T2N2
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312927
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312927/suppl/GSM312927.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312928 | GPL570 |
|
nasopharyngeal carcinoma, specimen T23
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIA
Tumor Stage: T2N2
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312928
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312928/suppl/GSM312928.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312929 | GPL570 |
|
nasopharyngeal carcinoma, specimen T24
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIB
Tumor Stage: T1N0
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312929
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312929/suppl/GSM312929.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312930 | GPL570 |
|
nasopharyngeal carcinoma, specimen T25
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIA
Tumor Stage: T2N1
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312930
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312930/suppl/GSM312930.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312931 | GPL570 |
|
nasopharyngeal carcinoma, specimen T26
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIB
Tumor Stage: T3N1
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312931
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312931/suppl/GSM312931.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312932 | GPL570 |
|
nasopharyngeal carcinoma, specimen T27
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIA
Tumor Stage: T1N1
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312932
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312932/suppl/GSM312932.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312933 | GPL570 |
|
nasopharyngeal carcinoma, specimen T28
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIA
Tumor Stage: T1N0
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312933
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312933/suppl/GSM312933.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312934 | GPL570 |
|
nasopharyngeal carcinoma, specimen T29
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIB
Tumor Stage: T1N0
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312934
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312934/suppl/GSM312934.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312935 | GPL570 |
|
nasopharyngeal carcinoma, specimen T30
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIA
Tumor Stage: T2N1
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312935
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312935/suppl/GSM312935.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
GSM312936 | GPL570 |
|
nasopharyngeal carcinoma, specimen T31
|
nasopharynx
|
nasopharyngeal carcinoma
WHO histology: IIB
Tumor Stage: T3N2
|
Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.
|
| Sample_geo_accession | GSM312936
| | Sample_status | Public on Aug 16 2008
| | Sample_submission_date | Aug 14 2008
| | Sample_last_update_date | Sep 05 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.
| | Sample_growth_protocol_ch1 | Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).
| | Sample_hyb_protocol | Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.
| | Sample_scan_protocol | Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.
| | Sample_data_processing | Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,,Ahlquist
| | Sample_contact_email | ahlquist@wisc.edu
| | Sample_contact_department | Oncology
| | Sample_contact_institute | University of Wisconsin-Madison
| | Sample_contact_address | 1525 Linden Dr.
| | Sample_contact_city | Madison
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53706
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM312nnn/GSM312936/suppl/GSM312936.CEL.gz
| | Sample_series_id | GSE12452
| | Sample_data_row_count | 54675
| | |
|
| |
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