Search results for the GEO ID: GSE22598  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM452629 | GPL570 |
|
patient 006, normal, homogenized
|
surgically resected material
|
metastasis: metastatic recurrence
tissue: normal, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452629
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452629/suppl/GSM452629.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800742
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452630 | GPL570 |
|
patient 011, normal, homogenized
|
surgically resected material
|
metastasis: metastasis
tissue: normal, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452630
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452630/suppl/GSM452630.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800743
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452631 | GPL570 |
|
patient 024, normal, homogenized
|
surgically resected material
|
metastasis: metastasis
tissue: normal, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452631
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452631/suppl/GSM452631.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800744
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452632 | GPL570 |
|
patient 027, normal, homogenized
|
surgically resected material
|
metastasis: none
tissue: normal, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452632
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452632/suppl/GSM452632.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800745
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452633 | GPL570 |
|
patient 028, normal, homogenized
|
surgically resected material
|
metastasis: metastatic recurrence
tissue: normal, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452633
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452633/suppl/GSM452633.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800746
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452634 | GPL570 |
|
patient 030, normal, homogenized
|
surgically resected material
|
metastasis: none
tissue: normal, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452634
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452634/suppl/GSM452634.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800747
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452635 | GPL570 |
|
patient 031, normal, homogenized
|
surgically resected material
|
metastasis: none
tissue: normal, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452635
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452635/suppl/GSM452635.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800748
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452636 | GPL570 |
|
patient 032, normal, homogenized
|
surgically resected material
|
metastasis: none
tissue: normal, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452636
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452636/suppl/GSM452636.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800749
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452637 | GPL570 |
|
patient 033, normal, homogenized
|
surgically resected material
|
metastasis: none
tissue: normal, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452637
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452637/suppl/GSM452637.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800750
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452638 | GPL570 |
|
patient 035, normal, homogenized
|
surgically resected material
|
metastasis: metastasis
tissue: normal, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452638
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452638/suppl/GSM452638.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800751
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452639 | GPL570 |
|
patient 036, normal, homogenized
|
surgically resected material
|
metastasis: none
tissue: normal, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452639
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452639/suppl/GSM452639.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800752
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452640 | GPL570 |
|
patient 038, normal, homogenized
|
surgically resected material
|
metastasis: none
tissue: normal, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452640
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452640/suppl/GSM452640.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800753
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452641 | GPL570 |
|
patient 041, normal, homogenized
|
surgically resected material
|
metastasis: metastatic recurrence
tissue: normal, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452641
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452641/suppl/GSM452641.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800754
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452642 | GPL570 |
|
patient 042, normal, homogenized
|
surgically resected material
|
metastasis: none
tissue: normal, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452642
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452642/suppl/GSM452642.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800755
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452643 | GPL570 |
|
patient 044, normal, homogenized
|
surgically resected material
|
metastasis: none
tissue: normal, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452643
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452643/suppl/GSM452643.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800756
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452644 | GPL570 |
|
patient 045, normal, homogenized
|
surgically resected material
|
metastasis: metastatic recurrence
tissue: normal, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452644
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452644/suppl/GSM452644.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800757
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452645 | GPL570 |
|
patient 047, normal, homogenized
|
surgically resected material
|
metastasis: none
tissue: normal, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452645
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452645/suppl/GSM452645.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800758
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452646 | GPL570 |
|
patient 006, cancer, homogenized
|
surgically resected material
|
metastasis: metastatic recurrence
tissue: cancer, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452646
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452646/suppl/GSM452646.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800759
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452647 | GPL570 |
|
patient 011, cancer, homogenized
|
surgically resected material
|
metastasis: metastasis
tissue: cancer, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452647
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452647/suppl/GSM452647.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800760
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452648 | GPL570 |
|
patient 024, cancer, homogenized
|
surgically resected material
|
metastasis: metastasis
tissue: cancer, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452648
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452648/suppl/GSM452648.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800761
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452649 | GPL570 |
|
patient 027, cancer, homogenized
|
surgically resected material
|
metastasis: none
tissue: cancer, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452649
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452649/suppl/GSM452649.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800762
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452650 | GPL570 |
|
patient 028, cancer, homogenized
|
surgically resected material
|
metastasis: metastatic recurrence
tissue: cancer, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452650
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452650/suppl/GSM452650.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800763
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452651 | GPL570 |
|
patient 030, cancer, homogenized
|
surgically resected material
|
metastasis: none
tissue: cancer, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452651
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452651/suppl/GSM452651.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800764
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452652 | GPL570 |
|
patient 031, cancer, homogenized
|
surgically resected material
|
metastasis: none
tissue: cancer, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452652
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452652/suppl/GSM452652.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800765
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452654 | GPL570 |
|
patient 033, cancer, homogenized
|
surgically resected material
|
metastasis: none
tissue: cancer, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452654
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452654/suppl/GSM452654.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800767
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452655 | GPL570 |
|
patient 035, cancer, homogenized
|
surgically resected material
|
metastasis: metastasis
tissue: cancer, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452655
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452655/suppl/GSM452655.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800768
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452656 | GPL570 |
|
patient 036, cancer, homogenized
|
surgically resected material
|
metastasis: none
tissue: cancer, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452656
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452656/suppl/GSM452656.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800769
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452657 | GPL570 |
|
patient 038, cancer, homogenized
|
surgically resected material
|
metastasis: none
tissue: cancer, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452657
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452657/suppl/GSM452657.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800770
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452658 | GPL570 |
|
patient 041, cancer, homogenized
|
surgically resected material
|
metastasis: metastatic recurrence
tissue: cancer, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452658
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452658/suppl/GSM452658.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800771
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452659 | GPL570 |
|
patient 042, cancer, homogenized
|
surgically resected material
|
metastasis: none
tissue: cancer, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452659
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452659/suppl/GSM452659.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800772
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452660 | GPL570 |
|
patient 044, cancer, homogenized
|
surgically resected material
|
metastasis: none
tissue: cancer, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452660
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452660/suppl/GSM452660.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800773
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452661 | GPL570 |
|
patient 045, cancer, homogenized
|
surgically resected material
|
metastasis: metastatic recurrence
tissue: cancer, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452661
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452661/suppl/GSM452661.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800774
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM452662 | GPL570 |
|
patient 047, cancer, homogenized
|
surgically resected material
|
metastasis: none
tissue: cancer, homogenized
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM452662
| | Sample_status | Public on Feb 04 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452662/suppl/GSM452662.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800775
| | Sample_series_id | GSE18105
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM560745 | GPL570 |
|
HT29 cell line, control
|
HT29 cell line
|
tissue: colorectal cancer cell line
cell line: HT29
treatment group: control
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM560745
| | Sample_status | Public on Dec 04 2011
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Dec 04 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were left untreated (control).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Normalization was performed by robust multi-array average (RMA) method under R 2.6.2 statistical software with affy package from BioConductor. The normalization procedure was separately performed for each data set of clinical samples, HT29 cells, and HCT15 cells. The normalized gene expression levels were presented as log2-transformed values by RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560745/suppl/GSM560745.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800781
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM560746 | GPL570 |
|
HT29 cell line, 5aza treated
|
HT29 cell line
|
tissue: colorectal cancer cell line
cell line: HT29
treatment group: 5aza treated
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM560746
| | Sample_status | Public on Dec 04 2011
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Dec 04 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 0.5 uM 5-aza-2'-deoxycytidine (Sigma Aldrich, St Louis, MO) for 72 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Normalization was performed by robust multi-array average (RMA) method under R 2.6.2 statistical software with affy package from BioConductor. The normalization procedure was separately performed for each data set of clinical samples, HT29 cells, and HCT15 cells. The normalized gene expression levels were presented as log2-transformed values by RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560746/suppl/GSM560746.CEL.gz
| | Sample_relation | Reanalyzed by: GSM800780
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM560747 | GPL570 |
|
HCT15 cell line, control
|
HCT15 cell line
|
tissue: colorectal cancer cell line
cell line: HCT15
treatment group: control
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM560747
| | Sample_status | Public on Dec 04 2011
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Dec 04 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were left untreated (control).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Normalization was performed by robust multi-array average (RMA) method under R 2.6.2 statistical software with affy package from BioConductor. The normalization procedure was separately performed for each data set of clinical samples, HT29 cells, and HCT15 cells. The normalized gene expression levels were presented as log2-transformed values by RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560747/suppl/GSM560747.CEL.gz
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
GSM560748 | GPL570 |
|
HCT15 cell line, 5aza treated
|
HCT15 cell line
|
tissue: colorectal cancer cell line
cell line: HCT15
treatment group: 5aza treated
|
Gene expression profile of surgically resected material
|
| Sample_geo_accession | GSM560748
| | Sample_status | Public on Dec 04 2011
| | Sample_submission_date | Jun 28 2010
| | Sample_last_update_date | Dec 04 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated with 0.5 uM 5-aza-2'-deoxycytidine (Sigma Aldrich, St Louis, MO) for 72 hours.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Normalization was performed by robust multi-array average (RMA) method under R 2.6.2 statistical software with affy package from BioConductor. The normalization procedure was separately performed for each data set of clinical samples, HT29 cells, and HCT15 cells. The normalized gene expression levels were presented as log2-transformed values by RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kaoru,,Mogushi
| | Sample_contact_email | mogushi@bioinfo.tmd.ac.jp
| | Sample_contact_phone | +81-3-5803-4758
| | Sample_contact_department | epartment of Bioinformatics, Medical Research Institute
| | Sample_contact_institute | Tokyo Medical and Dental University
| | Sample_contact_address | 1-5-45 Yushima
| | Sample_contact_city | Bunkyo-ku
| | Sample_contact_state | Tokyo
| | Sample_contact_zip/postal_code | 113-8510
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM560nnn/GSM560748/suppl/GSM560748.CEL.gz
| | Sample_series_id | GSE22598
| | Sample_data_row_count | 54675
| | |
|
| |
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