Search results for the GEO ID: GSE17548 |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM437457 | GPL570 |
|
Ankara-6 cirrhosis sample
|
Ankara cirrhosis tissue
|
tissue: Liver
genotype: HBV positive
age: Male 50
|
Gene expression data from 50 years old age male cirrhosis tissue
|
Sample_geo_accession | GSM437457
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437457/suppl/GSM437457.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437458 | GPL570 |
|
Ankara-6 tumor sample
|
Ankara HCC tissue
|
tissue: Liver
genotype: HBV positive
age: Male 50
|
Gene expression data from 50 years old age male HCC tissue
|
Sample_geo_accession | GSM437458
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437458/suppl/GSM437458.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437459 | GPL570 |
|
Izmir-10 tumor sample
|
Izmir HCC tissue
|
tissue: Liver
genotype: HBV positive
age: Male 49
|
Gene expression data from 49 years old age male HCC tissue
|
Sample_geo_accession | GSM437459
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437459/suppl/GSM437459.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437461 | GPL570 |
|
Ankara-3 tumor sample
|
Ankara HCC tissue
|
tissue: Liver
genotype: HCV positive
age: Male 62
|
Gene expression data from 62 years old age male HCC tissue
|
Sample_geo_accession | GSM437461
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437461/suppl/GSM437461.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437463 | GPL570 |
|
Izmir-1 cirrhosis sample
|
Izmir cirrhosis tissue
|
tissue: Liver
genotype: HBV positive
age: Male 56
|
Gene expression data from 56 years old age male cirrhosis tissue
|
Sample_geo_accession | GSM437463
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437463/suppl/GSM437463.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437464 | GPL570 |
|
Izmir-1 tumor sample
|
Izmir HCC tissue
|
tissue: Liver
genotype: HBV positive
age: Male 56
|
Gene expression data from 56 years old age male HCC tissue
|
Sample_geo_accession | GSM437464
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437464/suppl/GSM437464.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437465 | GPL570 |
|
Ankara-11 tumor samle
|
Ankara HCC tissue
|
tissue: Liver
age: Male
|
Gene expression data from male patient HCC tissue
|
Sample_geo_accession | GSM437465
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437465/suppl/GSM437465.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437466 | GPL570 |
|
Ankara-2 cirrhosis sample
|
Ankara cirrhosis tissue
|
tissue: Liver
genotype: HBV positive
age: Male 52
|
Gene expression data from 52 years old age male cirrhosis tissue
|
Sample_geo_accession | GSM437466
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437466/suppl/GSM437466.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437467 | GPL570 |
|
Ankara-2 tumor sample
|
Ankara HCC tissue
|
tissue: Liver
genotype: HBV positive
age: Male 52
|
Gene expression data from 52 years old age male HCC tissue
|
Sample_geo_accession | GSM437467
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437467/suppl/GSM437467.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437468 | GPL570 |
|
Izmir-11 tumor sample
|
Izmir HCC tissue
|
tissue: Liver
genotype: HBV positive
age: Male 59
|
Gene expression data from 59 years old age male HCC tissue
|
Sample_geo_accession | GSM437468
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437468/suppl/GSM437468.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437469 | GPL570 |
|
Izmir-2 cirrhosis sample
|
Izmir cirrhosis tissue
|
tissue: Liver
age: Female 44
|
Gene expression data from 44 years old age female cirrhosis tissue
|
Sample_geo_accession | GSM437469
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437469/suppl/GSM437469.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437471 | GPL570 |
|
Izmir-6 cirrhosis sample
|
Izmir cirrhosis tissue
|
tissue: Liver
genotype: HCV positive
age: Male 64
|
Gene expression data from 64 years old age male cirrhosis tissue
|
Sample_geo_accession | GSM437471
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437471/suppl/GSM437471.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437472 | GPL570 |
|
Izmir-12 cirrhosis sample
|
Izmir cirrhosis tissue
|
tissue: Liver
age: Female
|
Gene expression data from female patient cirrhosis tissue
|
Sample_geo_accession | GSM437472
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437472/suppl/GSM437472.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437473 | GPL570 |
|
Ankara-4 cirrhosis sample
|
Ankara cirrhosis tissue
|
tissue: Liver
genotype: HBV positive
age: Male 60
|
Gene expression data from 60 years old age male cirrhosis tissue
|
Sample_geo_accession | GSM437473
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437473/suppl/GSM437473.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437474 | GPL570 |
|
Ankara-4 tumor sample
|
Ankara HCC tissue
|
tissue: Liver
genotype: HBV positive
age: Male 60
|
Gene expression data from 60 years old age male HCC tissue
|
Sample_geo_accession | GSM437474
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437474/suppl/GSM437474.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437476 | GPL570 |
|
Ankara-9 tumor sample
|
Ankara HCC tissue
|
tissue: Liver
genotype: HCV positive
age: Male 62
|
Gene expression data from 62 years old age male HCC tissue
|
Sample_geo_accession | GSM437476
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437476/suppl/GSM437476.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437477 | GPL570 |
|
Izmir-7 cirrhosis sample
|
Izmir cirrhosis tissue
|
tissue: Liver
genotype: HBV+HDV positive
age: Male 41
|
Gene expression data from 41 years old age male cirrhosis tissue
|
Sample_geo_accession | GSM437477
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437477/suppl/GSM437477.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437478 | GPL570 |
|
Ankara-10 tumor sample
|
Ankara HCC tissue
|
tissue: Liver
genotype: HBV positive
age: Male 64
|
Gene expression data from 64 years old age male HCC tissue
|
Sample_geo_accession | GSM437478
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437478/suppl/GSM437478.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437479 | GPL570 |
|
Izmir-11 cirrhosis sample
|
Izmir cirrhosis tissue
|
tissue: Liver
genotype: HBV positive
age: Male 50
|
Gene expression data from 50 years old age male cirrhosis tissue
|
Sample_geo_accession | GSM437479
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437479/suppl/GSM437479.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437480 | GPL570 |
|
Izmir-10 cirrhosis sample
|
Izmir cirrhosis tissue
|
tissue: Liver
genotype: HBV positive
age: Male 48
|
Gene expression data from 48 years old age male cirrhosis tissue
|
Sample_geo_accession | GSM437480
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437480/suppl/GSM437480.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437481 | GPL570 |
|
Izmir-9 cirrhosis sample
|
Izmir cirrhosis tissue
|
tissue: Liver
genotype: HBV positive
age: Male 52
|
Gene expression data from 52 years old age male cirrhosis tissue
|
Sample_geo_accession | GSM437481
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437481/suppl/GSM437481.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437483 | GPL570 |
|
Ankara-5 tumor sample
|
Ankara HCC tissue
|
tissue: Liver
age: Male
|
Gene expression data from male patient HCC tissue
|
Sample_geo_accession | GSM437483
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437483/suppl/GSM437483.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437484 | GPL570 |
|
Izmir-5 cirrhosis sample
|
Izmir cirrhosis tissue
|
tissue: Liver
age: Male
|
Gene expression data from male patient cirrhosis tissue
|
Sample_geo_accession | GSM437484
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437484/suppl/GSM437484.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437486 | GPL570 |
|
Izmir-8 cirrhosis sample
|
Izmir cirrhosis tissue
|
tissue: Liver
genotype: HBV positive
age: Female 48
|
Gene expression data from 48 years old age female cirrhosis tissue
|
Sample_geo_accession | GSM437486
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437486/suppl/GSM437486.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437487 | GPL570 |
|
Ankara-7 tumor sample
|
Ankara HCC tissue
|
tissue: Liver
genotype: HBV positive
age: Male 69
|
Gene expression data from 69 years old age male HCC tissue
|
Sample_geo_accession | GSM437487
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437487/suppl/GSM437487.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437488 | GPL570 |
|
Izmir-4 cirrhosis sample
|
Izmir cirrhosis tissue
|
tissue: Liver
genotype: HCV positive
age: Female 52
|
Gene expression data from 52 years old age female cirrhosis tissue
|
Sample_geo_accession | GSM437488
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437488/suppl/GSM437488.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437489 | GPL570 |
|
Izmir-4 tumor sample
|
Izmir HCC tissue
|
tissue: Liver
genotype: HCV positive
age: Female 52
|
Gene expression data from 52 years old age female HCC tissue
|
Sample_geo_accession | GSM437489
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437489/suppl/GSM437489.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437491 | GPL570 |
|
Izmir-3 tumor sample
|
Izmir HCC tissue
|
tissue: Liver
genotype: HBV positive
age: Male 66
|
Gene expression data from 65 years old age male HCC tissue
|
Sample_geo_accession | GSM437491
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437491/suppl/GSM437491.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437492 | GPL570 |
|
Ankara-1 cirrhosis sample
|
Ankara cirrhosis tissue
|
tissue: Liver
genotype: HBV positive
age: Male 45
|
Gene expression data from 45 years old age male cirrhosis tissue
|
Sample_geo_accession | GSM437492
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437492/suppl/GSM437492.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
GSM437493 | GPL570 |
|
Ankara-1 tumor sample
|
Ankara HCC tissue
|
tissue: Liver
genotype: HBV positive
age: Male 45
|
Gene expression data from 45 years old age male HCC tissue
|
Sample_geo_accession | GSM437493
| Sample_status | Public on May 23 2013
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | May 24 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Frozen tissue samples were cut into thirty 20 um thick slices, and scraped into microtubes for RNA extraction. Two 6 um thick slides were cut for pathological examination.
| Sample_growth_protocol_ch1 | Surgically resected samples were immediately snap frozen in liquid nitrogen, and stored in -80C until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissues were homogenized using 0.8 mm needle before processing. The total RNA were extracted using Nucleospin RNA II kit (MN) according to the manufecturer's protocol.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner. GeneChip Opreating Software (GCOS, Affymetrix) was used to collect and store the data.
| Sample_data_processing | The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The signal intensity was converted to log2 values using Bioconductor package in R 2.4.0.
| Sample_platform_id | GPL570
| Sample_contact_name | Mehmet,,Ozturk
| Sample_contact_email | ozturk@fen.bilkent.edu.tr
| Sample_contact_phone | +90 312 266 45 38
| Sample_contact_fax | +90 312 266 50 97
| Sample_contact_department | BilGen Genetics and Biotechnology Research Center
| Sample_contact_institute | Bilkent University
| Sample_contact_address | Faculty of Science Building
| Sample_contact_city | Ankara
| Sample_contact_zip/postal_code | 06800
| Sample_contact_country | Turkey
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437493/suppl/GSM437493.CEL.gz
| Sample_series_id | GSE17548
| Sample_data_row_count | 54675
| |
|
|
|
Make groups for comparisons |
(2 groups will be compared at a time) |
|
Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|