Search results for the GEO ID: GSE40873  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1003891 | GPL570 |
|
patient LC07, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 97
event: multicentric occurrence
patient id: LC07
|
Gene expression profile of surgically resected material.
LC07N
|
| Sample_geo_accession | GSM1003891
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003891/suppl/GSM1003891_LC_07N-051217.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003892 | GPL570 |
|
patient L08, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 2226
event: no multicentric occurrence
patient id: L08
|
Gene expression profile of surgically resected material.
L08N
|
| Sample_geo_accession | GSM1003892
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003892/suppl/GSM1003892_L08_N-3_H_02.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003893 | GPL570 |
|
patient L10, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 599
event: multicentric occurrence
patient id: L10
|
Gene expression profile of surgically resected material.
L10N
|
| Sample_geo_accession | GSM1003893
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003893/suppl/GSM1003893_chip_array_L10N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003894 | GPL570 |
|
patient L18, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 2144
event: no multicentric occurrence
patient id: L18
|
Gene expression profile of surgically resected material.
L18N
|
| Sample_geo_accession | GSM1003894
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003894/suppl/GSM1003894_chip_array_L18N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003895 | GPL570 |
|
patient L31, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 712
event: multicentric occurrence
patient id: L31
|
Gene expression profile of surgically resected material.
L31N
|
| Sample_geo_accession | GSM1003895
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003895/suppl/GSM1003895_chip_array_L31N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003896 | GPL570 |
|
patient L42, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 85
event: no multicentric occurrence
patient id: L42
|
Gene expression profile of surgically resected material.
L42N
|
| Sample_geo_accession | GSM1003896
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003896/suppl/GSM1003896_chip_array_L42N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003897 | GPL570 |
|
patient L45, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 139
event: no multicentric occurrence
patient id: L45
|
Gene expression profile of surgically resected material.
L45N
|
| Sample_geo_accession | GSM1003897
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003897/suppl/GSM1003897_chip_array_L45N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003898 | GPL570 |
|
patient L47, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 57
event: no multicentric occurrence
patient id: L47
|
Gene expression profile of surgically resected material.
L47N
|
| Sample_geo_accession | GSM1003898
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003898/suppl/GSM1003898_chip_array_L47N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003899 | GPL570 |
|
patient L49, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 482
event: no multicentric occurrence
patient id: L49
|
Gene expression profile of surgically resected material.
L49N
|
| Sample_geo_accession | GSM1003899
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003899/suppl/GSM1003899_chip_array_L49N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003900 | GPL570 |
|
patient L53, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 1607
event: no multicentric occurrence
patient id: L53
|
Gene expression profile of surgically resected material.
L53N
|
| Sample_geo_accession | GSM1003900
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003900/suppl/GSM1003900_chip_array_L53N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003901 | GPL570 |
|
patient L57, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 1901
event: no multicentric occurrence
patient id: L57
|
Gene expression profile of surgically resected material.
L57N
|
| Sample_geo_accession | GSM1003901
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003901/suppl/GSM1003901_chip_array_L57N-1.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003902 | GPL570 |
|
patient L64, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 1843
event: no multicentric occurrence
patient id: L64
|
Gene expression profile of surgically resected material.
L64N
|
| Sample_geo_accession | GSM1003902
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003902/suppl/GSM1003902_chip_array_L64N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003903 | GPL570 |
|
patient L70, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 267
event: multicentric occurrence
patient id: L70
|
Gene expression profile of surgically resected material.
L70N
|
| Sample_geo_accession | GSM1003903
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003903/suppl/GSM1003903_chip_array_L70N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003904 | GPL570 |
|
patient L76, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 823
event: no multicentric occurrence
patient id: L76
|
Gene expression profile of surgically resected material.
L76N
|
| Sample_geo_accession | GSM1003904
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003904/suppl/GSM1003904_chip_array_L76N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003905 | GPL570 |
|
patient L77, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 247
event: multicentric occurrence
patient id: L77
|
Gene expression profile of surgically resected material.
L77N
|
| Sample_geo_accession | GSM1003905
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003905/suppl/GSM1003905_chip_array_L77N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003906 | GPL570 |
|
patient L78, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 764
event: no multicentric occurrence
patient id: L78
|
Gene expression profile of surgically resected material.
L78N
|
| Sample_geo_accession | GSM1003906
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003906/suppl/GSM1003906_chip_array_L78N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003907 | GPL570 |
|
patient L80, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 491
event: multicentric occurrence
patient id: L80
|
Gene expression profile of surgically resected material.
L80N
|
| Sample_geo_accession | GSM1003907
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003907/suppl/GSM1003907_chip_array_L80N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003908 | GPL570 |
|
patient L84, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 734
event: no multicentric occurrence
patient id: L84
|
Gene expression profile of surgically resected material.
L84N
|
| Sample_geo_accession | GSM1003908
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003908/suppl/GSM1003908_chip_array_L84N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003909 | GPL570 |
|
patient L90, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 565
event: no multicentric occurrence
patient id: L90
|
Gene expression profile of surgically resected material.
L90N
|
| Sample_geo_accession | GSM1003909
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003909/suppl/GSM1003909_chip_array_L90N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003910 | GPL570 |
|
patient L96, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 449
event: multicentric occurrence
patient id: L96
|
Gene expression profile of surgically resected material.
L96N
|
| Sample_geo_accession | GSM1003910
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003910/suppl/GSM1003910_chip_array_L96N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003911 | GPL570 |
|
patient L104, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 1631
event: no multicentric occurrence
patient id: L104
|
Gene expression profile of surgically resected material.
L104N
|
| Sample_geo_accession | GSM1003911
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003911/suppl/GSM1003911_chip_array_L104N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003912 | GPL570 |
|
patient L105, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 1623
event: no multicentric occurrence
patient id: L105
|
Gene expression profile of surgically resected material.
L105N
|
| Sample_geo_accession | GSM1003912
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003912/suppl/GSM1003912_chip_array_L105N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003913 | GPL570 |
|
patient L107, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 279
event: no multicentric occurrence
patient id: L107
|
Gene expression profile of surgically resected material.
L107N
|
| Sample_geo_accession | GSM1003913
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003913/suppl/GSM1003913_chip_array_L107N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003914 | GPL570 |
|
patient L109, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 64
event: no multicentric occurrence
patient id: L109
|
Gene expression profile of surgically resected material.
L109N
|
| Sample_geo_accession | GSM1003914
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003914/suppl/GSM1003914_chip_array_L109N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003915 | GPL570 |
|
patient L111, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 43
event: no multicentric occurrence
patient id: L111
|
Gene expression profile of surgically resected material.
L111N
|
| Sample_geo_accession | GSM1003915
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003915/suppl/GSM1003915_chip_array_L111N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003916 | GPL570 |
|
patient L120, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 87
event: no multicentric occurrence
patient id: L120
|
Gene expression profile of surgically resected material.
L120N
|
| Sample_geo_accession | GSM1003916
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003916/suppl/GSM1003916_chip_array_L120N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003917 | GPL570 |
|
patient L121, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 200
event: no multicentric occurrence
patient id: L121
|
Gene expression profile of surgically resected material.
L121N
|
| Sample_geo_accession | GSM1003917
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003917/suppl/GSM1003917_chip_array_L121N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003918 | GPL570 |
|
patient L123, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 129
event: multicentric occurrence
patient id: L123
|
Gene expression profile of surgically resected material.
L123N
|
| Sample_geo_accession | GSM1003918
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003918/suppl/GSM1003918_chip_array_L123N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003919 | GPL570 |
|
patient L122, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 283
event: no multicentric occurrence
patient id: L122
|
Gene expression profile of surgically resected material.
L122N
|
| Sample_geo_accession | GSM1003919
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003919/suppl/GSM1003919_chip_array_L122N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003920 | GPL570 |
|
patient L126, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 206
event: multicentric occurrence
patient id: L126
|
Gene expression profile of surgically resected material.
L126N
|
| Sample_geo_accession | GSM1003920
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003920/suppl/GSM1003920_chip_array_L126N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003921 | GPL570 |
|
patient L128, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 452
event: multicentric occurrence
patient id: L128
|
Gene expression profile of surgically resected material.
L128N
|
| Sample_geo_accession | GSM1003921
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003921/suppl/GSM1003921_chip_array_L128N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003922 | GPL570 |
|
patient L127, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 1338
event: no multicentric occurrence
patient id: L127
|
Gene expression profile of surgically resected material.
L127N
|
| Sample_geo_accession | GSM1003922
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003922/suppl/GSM1003922_chip_array_L127N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003923 | GPL570 |
|
patient L134, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 426
event: multicentric occurrence
patient id: L134
|
Gene expression profile of surgically resected material.
L134N
|
| Sample_geo_accession | GSM1003923
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003923/suppl/GSM1003923_chiparray_L134N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003924 | GPL570 |
|
patient L130, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 221
event: multicentric occurrence
patient id: L130
|
Gene expression profile of surgically resected material.
L130N
|
| Sample_geo_accession | GSM1003924
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003924/suppl/GSM1003924_chip_array_L130N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003925 | GPL570 |
|
patient L110, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 340
event: multicentric occurrence
patient id: L110
|
Gene expression profile of surgically resected material.
L110N
|
| Sample_geo_accession | GSM1003925
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003925/suppl/GSM1003925_chip_array_L110N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003926 | GPL570 |
|
patient L137, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 601
event: no multicentric occurrence
patient id: L137
|
Gene expression profile of surgically resected material.
L137N
|
| Sample_geo_accession | GSM1003926
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003926/suppl/GSM1003926_chiparray_L137N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003927 | GPL570 |
|
patient L140, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 1427
event: no multicentric occurrence
patient id: L140
|
Gene expression profile of surgically resected material.
L140N
|
| Sample_geo_accession | GSM1003927
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003927/suppl/GSM1003927_chiparray_L140N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003928 | GPL570 |
|
patient L141, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 76
event: multicentric occurrence
patient id: L141
|
Gene expression profile of surgically resected material.
L141N
|
| Sample_geo_accession | GSM1003928
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003928/suppl/GSM1003928_chiparray_L141N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003929 | GPL570 |
|
patient L143, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 1044
event: no multicentric occurrence
patient id: L143
|
Gene expression profile of surgically resected material.
L143N
|
| Sample_geo_accession | GSM1003929
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003929/suppl/GSM1003929_chip_array_L143N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003930 | GPL570 |
|
patient L147, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 264
event: multicentric occurrence
patient id: L147
|
Gene expression profile of surgically resected material.
L147N
|
| Sample_geo_accession | GSM1003930
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003930/suppl/GSM1003930_chip_array_L147N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003931 | GPL570 |
|
patient L150, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 368
event: no multicentric occurrence
patient id: L150
|
Gene expression profile of surgically resected material.
L150N
|
| Sample_geo_accession | GSM1003931
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003931/suppl/GSM1003931_chip_array_L150N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003932 | GPL570 |
|
patient L108, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 648
event: multicentric occurrence
patient id: L108
|
Gene expression profile of surgically resected material.
L108N
|
| Sample_geo_accession | GSM1003932
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003932/suppl/GSM1003932_chip_array_L108N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003933 | GPL570 |
|
patient L71, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 224
event: multicentric occurrence
patient id: L71
|
Gene expression profile of surgically resected material.
L71N
|
| Sample_geo_accession | GSM1003933
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003933/suppl/GSM1003933_chip_array_L71N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003934 | GPL570 |
|
patient L144, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 1388
event: no multicentric occurrence
patient id: L144
|
Gene expression profile of surgically resected material.
L144N
|
| Sample_geo_accession | GSM1003934
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003934/suppl/GSM1003934_chip_array_L144N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003935 | GPL570 |
|
patient L154, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 280
event: no multicentric occurrence
patient id: L154
|
Gene expression profile of surgically resected material.
L154N
|
| Sample_geo_accession | GSM1003935
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003935/suppl/GSM1003935_chip_array_L154N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003936 | GPL570 |
|
patient L155, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 258
event: no multicentric occurrence
patient id: L155
|
Gene expression profile of surgically resected material.
L155N
|
| Sample_geo_accession | GSM1003936
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003936/suppl/GSM1003936_chip_array_L155N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003937 | GPL570 |
|
patient L157, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 264
event: no multicentric occurrence
patient id: L157
|
Gene expression profile of surgically resected material.
L157N
|
| Sample_geo_accession | GSM1003937
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003937/suppl/GSM1003937_chiparray_L157N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003938 | GPL570 |
|
patient L163, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 396
event: no multicentric occurrence
patient id: L163
|
Gene expression profile of surgically resected material.
L163N
|
| Sample_geo_accession | GSM1003938
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003938/suppl/GSM1003938_chip_array_L163N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
GSM1003939 | GPL570 |
|
patient L165, noncancerous liver tissue
|
surgically resected material, noncancerous liver
|
disease state: hepatocellular carcinoma (HCC)
tissue: noncancerous liver
multicentric occurrence-free survival (days): 378
event: no multicentric occurrence
patient id: L165
|
Gene expression profile of surgically resected material.
L165N
|
| Sample_geo_accession | GSM1003939
| | Sample_status | Public on Apr 01 2013
| | Sample_submission_date | Sep 13 2012
| | Sample_last_update_date | Apr 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1003nnn/GSM1003939/suppl/GSM1003939_chip_array_L165N.CEL.gz
| | Sample_series_id | GSE40873
| | Sample_data_row_count | 54675
| | |
|
| |
| |
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(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
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