Search results for the GEO ID: GSE41804  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1024521 | GPL570 |
|
major HCC1
|
resected liver tumor
|
tissue: resected liver tumor
genotype: major [rs8099917 TT]
|
HC-MA1
Gene expression data from resected liver tumor
|
| Sample_geo_accession | GSM1024521
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024521/suppl/GSM1024521_HC-MA1.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024522 | GPL570 |
|
major HCC2
|
resected liver tumor
|
tissue: resected liver tumor
genotype: major [rs8099917 TT]
|
HC-MA2
Gene expression data from resected liver tumor
|
| Sample_geo_accession | GSM1024522
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024522/suppl/GSM1024522_HC-MA2.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024523 | GPL570 |
|
major HCC3
|
resected liver tumor
|
tissue: resected liver tumor
genotype: major [rs8099917 TT]
|
HC-MA3
Gene expression data from resected liver tumor
|
| Sample_geo_accession | GSM1024523
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024523/suppl/GSM1024523_HC-MA3.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024524 | GPL570 |
|
major HCC4
|
resected liver tumor
|
tissue: resected liver tumor
genotype: major [rs8099917 TT]
|
HC-MA4
Gene expression data from resected liver tumor
|
| Sample_geo_accession | GSM1024524
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024524/suppl/GSM1024524_HC-MA4.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024525 | GPL570 |
|
major HCC5
|
resected liver tumor
|
tissue: resected liver tumor
genotype: major [rs8099917 TT]
|
HC-MA5
Gene expression data from resected liver tumor
|
| Sample_geo_accession | GSM1024525
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024525/suppl/GSM1024525_HC-MA5.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024526 | GPL570 |
|
major HCC6
|
resected liver tumor
|
tissue: resected liver tumor
genotype: major [rs8099917 TT]
|
HC-MA6
Gene expression data from resected liver tumor
|
| Sample_geo_accession | GSM1024526
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024526/suppl/GSM1024526_HC-MA6.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024527 | GPL570 |
|
major HCC7
|
resected liver tumor
|
tissue: resected liver tumor
genotype: major [rs8099917 TT]
|
HC-MA7
Gene expression data from resected liver tumor
|
| Sample_geo_accession | GSM1024527
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024527/suppl/GSM1024527_HC-MA7.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024528 | GPL570 |
|
major HCC8
|
resected liver tumor
|
tissue: resected liver tumor
genotype: major [rs8099917 TT]
|
HC-MA8
Gene expression data from resected liver tumor
|
| Sample_geo_accession | GSM1024528
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024528/suppl/GSM1024528_HC-MA8.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024529 | GPL570 |
|
major HCC9
|
resected liver tumor
|
tissue: resected liver tumor
genotype: major [rs8099917 TT]
|
HC-MA9
Gene expression data from resected liver tumor
|
| Sample_geo_accession | GSM1024529
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024529/suppl/GSM1024529_HC-MA9.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024530 | GPL570 |
|
major HCC10
|
resected liver tumor
|
tissue: resected liver tumor
genotype: major [rs8099917 TT]
|
HC-MA10
Gene expression data from resected liver tumor
|
| Sample_geo_accession | GSM1024530
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024530/suppl/GSM1024530_HC-MA10.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024531 | GPL570 |
|
major non-tumor1
|
resected non-tumor liver tissue
|
tissue: resected non-tumor liver tissue
genotype: major [rs8099917 TT]
|
LC-MA1
Gene expression data from resected non-tumor liver tissue
|
| Sample_geo_accession | GSM1024531
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024531/suppl/GSM1024531_LC-MA1.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024532 | GPL570 |
|
major non-tumor2
|
resected non-tumor liver tissue
|
tissue: resected non-tumor liver tissue
genotype: major [rs8099917 TT]
|
LC-MA2
Gene expression data from resected non-tumor liver tissue
|
| Sample_geo_accession | GSM1024532
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024532/suppl/GSM1024532_LC-MA2.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024533 | GPL570 |
|
major non-tumor3
|
resected non-tumor liver tissue
|
tissue: resected non-tumor liver tissue
genotype: major [rs8099917 TT]
|
LC-MA3
Gene expression data from resected non-tumor liver tissue
|
| Sample_geo_accession | GSM1024533
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024533/suppl/GSM1024533_LC-MA3.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024534 | GPL570 |
|
major non-tumor4
|
resected non-tumor liver tissue
|
tissue: resected non-tumor liver tissue
genotype: major [rs8099917 TT]
|
LC-MA4
Gene expression data from resected non-tumor liver tissue
|
| Sample_geo_accession | GSM1024534
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024534/suppl/GSM1024534_LC-MA4.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024535 | GPL570 |
|
major non-tumor5
|
resected non-tumor liver tissue
|
tissue: resected non-tumor liver tissue
genotype: major [rs8099917 TT]
|
LC-MA5
Gene expression data from resected non-tumor liver tissue
|
| Sample_geo_accession | GSM1024535
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024535/suppl/GSM1024535_LC-MA5.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024536 | GPL570 |
|
major non-tumor6
|
resected non-tumor liver tissue
|
tissue: resected non-tumor liver tissue
genotype: major [rs8099917 TT]
|
LC-MA6
Gene expression data from resected non-tumor liver tissue
|
| Sample_geo_accession | GSM1024536
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024536/suppl/GSM1024536_LC-MA6.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024537 | GPL570 |
|
major non-tumor7
|
resected non-tumor liver tissue
|
tissue: resected non-tumor liver tissue
genotype: major [rs8099917 TT]
|
LC-MA7
Gene expression data from resected non-tumor liver tissue
|
| Sample_geo_accession | GSM1024537
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024537/suppl/GSM1024537_LC-MA7.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024538 | GPL570 |
|
major non-tumor8
|
resected non-tumor liver tissue
|
tissue: resected non-tumor liver tissue
genotype: major [rs8099917 TT]
|
LC-MA8
Gene expression data from resected non-tumor liver tissue
|
| Sample_geo_accession | GSM1024538
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024538/suppl/GSM1024538_LC-MA8.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024539 | GPL570 |
|
major non-tumor9
|
resected non-tumor liver tissue
|
tissue: resected non-tumor liver tissue
genotype: major [rs8099917 TT]
|
LC-MA9
Gene expression data from resected non-tumor liver tissue
|
| Sample_geo_accession | GSM1024539
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024539/suppl/GSM1024539_LC-MA9.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024540 | GPL570 |
|
major non-tumor10
|
resected non-tumor liver tissue
|
tissue: resected non-tumor liver tissue
genotype: major [rs8099917 TT]
|
LC-MA10
Gene expression data from resected non-tumor liver tissue
|
| Sample_geo_accession | GSM1024540
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024540/suppl/GSM1024540_LC-MA10.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024541 | GPL570 |
|
minor HCC1
|
resected liver tumor
|
tissue: resected liver tumor
genotype: minor [rs8099917 TG/GG]
|
HC-MI1
Gene expression data from resected liver tumor
|
| Sample_geo_accession | GSM1024541
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024541/suppl/GSM1024541_HC-MI1.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024542 | GPL570 |
|
minor HCC2
|
resected liver tumor
|
tissue: resected liver tumor
genotype: minor [rs8099917 TG/GG]
|
HC-MI2
Gene expression data from resected liver tumor
|
| Sample_geo_accession | GSM1024542
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024542/suppl/GSM1024542_HC-MI2.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024543 | GPL570 |
|
minor HCC3
|
resected liver tumor
|
tissue: resected liver tumor
genotype: minor [rs8099917 TG/GG]
|
HC-MI3
Gene expression data from resected liver tumor
|
| Sample_geo_accession | GSM1024543
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024543/suppl/GSM1024543_HC-MI3.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024544 | GPL570 |
|
minor HCC4
|
resected liver tumor
|
tissue: resected liver tumor
genotype: minor [rs8099917 TG/GG]
|
HC-MI4
Gene expression data from resected liver tumor
|
| Sample_geo_accession | GSM1024544
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024544/suppl/GSM1024544_HC-MI4.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024545 | GPL570 |
|
minor HCC5
|
resected liver tumor
|
tissue: resected liver tumor
genotype: minor [rs8099917 TG/GG]
|
HC-MI5
Gene expression data from resected liver tumor
|
| Sample_geo_accession | GSM1024545
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024545/suppl/GSM1024545_HC-MI5.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024546 | GPL570 |
|
minor HCC6
|
resected liver tumor
|
tissue: resected liver tumor
genotype: minor [rs8099917 TG/GG]
|
HC-MI6
Gene expression data from resected liver tumor
|
| Sample_geo_accession | GSM1024546
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024546/suppl/GSM1024546_HC-MI6.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024547 | GPL570 |
|
minor HCC7
|
resected liver tumor
|
tissue: resected liver tumor
genotype: minor [rs8099917 TG/GG]
|
HC-MI7
Gene expression data from resected liver tumor
|
| Sample_geo_accession | GSM1024547
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024547/suppl/GSM1024547_HC-MI7.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024548 | GPL570 |
|
minor HCC8
|
resected liver tumor
|
tissue: resected liver tumor
genotype: minor [rs8099917 TG/GG]
|
HC-MI8
Gene expression data from resected liver tumor
|
| Sample_geo_accession | GSM1024548
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024548/suppl/GSM1024548_HC-MI8.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024549 | GPL570 |
|
minor HCC9
|
resected liver tumor
|
tissue: resected liver tumor
genotype: minor [rs8099917 TG/GG]
|
HC-MI9
Gene expression data from resected liver tumor
|
| Sample_geo_accession | GSM1024549
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024549/suppl/GSM1024549_HC-MI9.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024550 | GPL570 |
|
minor HCC10
|
resected liver tumor
|
tissue: resected liver tumor
genotype: minor [rs8099917 TG/GG]
|
HC-MI10
Gene expression data from resected liver tumor
|
| Sample_geo_accession | GSM1024550
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024550/suppl/GSM1024550_HC-MI10.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024551 | GPL570 |
|
minor non-tumor1
|
resected non-tumor liver tissue
|
tissue: resected non-tumor liver tissue
genotype: minor [rs8099917 TG/GG]
|
LC-MI1
Gene expression data from resected non-tumor liver tissue
|
| Sample_geo_accession | GSM1024551
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024551/suppl/GSM1024551_LC-MI1.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024552 | GPL570 |
|
minor non-tumor2
|
resected non-tumor liver tissue
|
tissue: resected non-tumor liver tissue
genotype: minor [rs8099917 TG/GG]
|
LC-MI2
Gene expression data from resected non-tumor liver tissue
|
| Sample_geo_accession | GSM1024552
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024552/suppl/GSM1024552_LC-MI2.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024553 | GPL570 |
|
minor non-tumor3
|
resected non-tumor liver tissue
|
tissue: resected non-tumor liver tissue
genotype: minor [rs8099917 TG/GG]
|
LC-MI3
Gene expression data from resected non-tumor liver tissue
|
| Sample_geo_accession | GSM1024553
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024553/suppl/GSM1024553_LC-MI3.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024554 | GPL570 |
|
minor non-tumor4
|
resected non-tumor liver tissue
|
tissue: resected non-tumor liver tissue
genotype: minor [rs8099917 TG/GG]
|
LC-MI4
Gene expression data from resected non-tumor liver tissue
|
| Sample_geo_accession | GSM1024554
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024554/suppl/GSM1024554_LC-MI4.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024555 | GPL570 |
|
minor non-tumor5
|
resected non-tumor liver tissue
|
tissue: resected non-tumor liver tissue
genotype: minor [rs8099917 TG/GG]
|
LC-MI5
Gene expression data from resected non-tumor liver tissue
|
| Sample_geo_accession | GSM1024555
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024555/suppl/GSM1024555_LC-MI5.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024556 | GPL570 |
|
minor non-tumor6
|
resected non-tumor liver tissue
|
tissue: resected non-tumor liver tissue
genotype: minor [rs8099917 TG/GG]
|
LC-MI6
Gene expression data from resected non-tumor liver tissue
|
| Sample_geo_accession | GSM1024556
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024556/suppl/GSM1024556_LC-MI6.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024557 | GPL570 |
|
minor non-tumor7
|
resected non-tumor liver tissue
|
tissue: resected non-tumor liver tissue
genotype: minor [rs8099917 TG/GG]
|
LC-MI7
Gene expression data from resected non-tumor liver tissue
|
| Sample_geo_accession | GSM1024557
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024557/suppl/GSM1024557_LC-MI7.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024558 | GPL570 |
|
minor non-tumor8
|
resected non-tumor liver tissue
|
tissue: resected non-tumor liver tissue
genotype: minor [rs8099917 TG/GG]
|
LC-MI8
Gene expression data from resected non-tumor liver tissue
|
| Sample_geo_accession | GSM1024558
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024558/suppl/GSM1024558_LC-MI8.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024559 | GPL570 |
|
minor non-tumor9
|
resected non-tumor liver tissue
|
tissue: resected non-tumor liver tissue
genotype: minor [rs8099917 TG/GG]
|
LC-MI9
Gene expression data from resected non-tumor liver tissue
|
| Sample_geo_accession | GSM1024559
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024559/suppl/GSM1024559_LC-MI9.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
| | |
|
GSM1024560 | GPL570 |
|
minor non-tumor10
|
resected non-tumor liver tissue
|
tissue: resected non-tumor liver tissue
genotype: minor [rs8099917 TG/GG]
|
LC-MI10
Gene expression data from resected non-tumor liver tissue
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| Sample_geo_accession | GSM1024560
| | Sample_status | Public on May 02 2013
| | Sample_submission_date | Oct 24 2012
| | Sample_last_update_date | May 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.
| | Sample_hyb_protocol | The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).
| | Sample_scan_protocol | The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).
| | Sample_data_processing | Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuji,,Hodo
| | Sample_contact_institute | Kanazawa University Graduate School of Medical Sciences
| | Sample_contact_address | 13-1 Takara-Machi
| | Sample_contact_city | Kanazawa
| | Sample_contact_zip/postal_code | 920-8641
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1024nnn/GSM1024560/suppl/GSM1024560_LC-MI10.CEL.gz
| | Sample_series_id | GSE41804
| | Sample_data_row_count | 54675
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