Search results for the GEO ID: GSE48441  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1178760 | GPL201 |
|
HepG2 control rep1
|
human hepatoma cell line, HepG2
|
cell bank no: RCB1648
Sex: male
age of sampling: 15 years
tissue derived: liver
case history: hepatocyte carcinoma
life span: infinite
classification: transformed
treatment: control
|
|
| Sample_geo_accession | GSM1178760
| | Sample_status | Public on Jul 02 2013
| | Sample_submission_date | Jul 01 2013
| | Sample_last_update_date | Jul 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Chemical treatment was done by replacing the culture medium with normal medium (as a control) and that containing arsenic trioxide (As2O3) at five different concentrations (i.e., 0.005 µM, 0.07 µM, 0.5 µM, 6 µM, and 40 µM).
| | Sample_growth_protocol_ch1 | Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation were carried out as described in the manufacturer’s instruction.
| | Sample_hyb_protocol | Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.
| | Sample_scan_protocol | After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).
| | Sample_data_processing | Probe-level data in CEL files were processed and analyzed using the Avadis 4.3 prophetic (Strand Genomics, Redwood City, CA). Data were normalized using MAS5 algorithm, and the features which were NOT flagged “Present” in all three replicates were rejected.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Hiroe,,Hara-Yamamura
| | Sample_contact_email | hy_hiroe@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-5587
| | Sample_contact_laboratory | Laboratory of Water Quality Control
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | Kita 13-jo, Nishi 8-chome
| | Sample_contact_city | Sapporo
| | Sample_contact_state | Hokkaido
| | Sample_contact_zip/postal_code | 0608628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178760/suppl/GSM1178760_HepG2_control_rep1.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178760/suppl/GSM1178760_HepG2_control_rep1.CHP.gz
| | Sample_series_id | GSE48441
| | Sample_data_row_count | 8793
| | |
|
GSM1178761 | GPL201 |
|
HepG2 control rep2
|
human hepatoma cell line, HepG2
|
cell bank no: RCB1648
Sex: male
age of sampling: 15 years
tissue derived: liver
case history: hepatocyte carcinoma
life span: infinite
classification: transformed
treatment: control
|
|
| Sample_geo_accession | GSM1178761
| | Sample_status | Public on Jul 02 2013
| | Sample_submission_date | Jul 01 2013
| | Sample_last_update_date | Jul 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Chemical treatment was done by replacing the culture medium with normal medium (as a control) and that containing arsenic trioxide (As2O3) at five different concentrations (i.e., 0.005 µM, 0.07 µM, 0.5 µM, 6 µM, and 40 µM).
| | Sample_growth_protocol_ch1 | Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation were carried out as described in the manufacturer’s instruction.
| | Sample_hyb_protocol | Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.
| | Sample_scan_protocol | After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).
| | Sample_data_processing | Probe-level data in CEL files were processed and analyzed using the Avadis 4.3 prophetic (Strand Genomics, Redwood City, CA). Data were normalized using MAS5 algorithm, and the features which were NOT flagged “Present” in all three replicates were rejected.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Hiroe,,Hara-Yamamura
| | Sample_contact_email | hy_hiroe@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-5587
| | Sample_contact_laboratory | Laboratory of Water Quality Control
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | Kita 13-jo, Nishi 8-chome
| | Sample_contact_city | Sapporo
| | Sample_contact_state | Hokkaido
| | Sample_contact_zip/postal_code | 0608628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178761/suppl/GSM1178761_HepG2_control_rep2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178761/suppl/GSM1178761_HepG2_control_rep2.CHP.gz
| | Sample_series_id | GSE48441
| | Sample_data_row_count | 8793
| | |
|
GSM1178762 | GPL201 |
|
HepG2 control rep3
|
human hepatoma cell line, HepG2
|
cell bank no: RCB1648
Sex: male
age of sampling: 15 years
tissue derived: liver
case history: hepatocyte carcinoma
life span: infinite
classification: transformed
treatment: control
|
|
| Sample_geo_accession | GSM1178762
| | Sample_status | Public on Jul 02 2013
| | Sample_submission_date | Jul 01 2013
| | Sample_last_update_date | Jul 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Chemical treatment was done by replacing the culture medium with normal medium (as a control) and that containing arsenic trioxide (As2O3) at five different concentrations (i.e., 0.005 µM, 0.07 µM, 0.5 µM, 6 µM, and 40 µM).
| | Sample_growth_protocol_ch1 | Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation were carried out as described in the manufacturer’s instruction.
| | Sample_hyb_protocol | Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.
| | Sample_scan_protocol | After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).
| | Sample_data_processing | Probe-level data in CEL files were processed and analyzed using the Avadis 4.3 prophetic (Strand Genomics, Redwood City, CA). Data were normalized using MAS5 algorithm, and the features which were NOT flagged “Present” in all three replicates were rejected.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Hiroe,,Hara-Yamamura
| | Sample_contact_email | hy_hiroe@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-5587
| | Sample_contact_laboratory | Laboratory of Water Quality Control
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | Kita 13-jo, Nishi 8-chome
| | Sample_contact_city | Sapporo
| | Sample_contact_state | Hokkaido
| | Sample_contact_zip/postal_code | 0608628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178762/suppl/GSM1178762_HepG2_control_rep3.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178762/suppl/GSM1178762_HepG2_control_rep3.CHP.gz
| | Sample_series_id | GSE48441
| | Sample_data_row_count | 8793
| | |
|
GSM1178763 | GPL201 |
|
HepG2 0.005 microM rep1
|
human hepatoma cell line, HepG2
|
cell bank no: RCB1648
Sex: male
age of sampling: 15 years
tissue derived: liver
case history: hepatocyte carcinoma
life span: infinite
classification: transformed
treatment: exposed to 0.005 µM arsenic trioxide
|
|
| Sample_geo_accession | GSM1178763
| | Sample_status | Public on Jul 02 2013
| | Sample_submission_date | Jul 01 2013
| | Sample_last_update_date | Jul 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Chemical treatment was done by replacing the culture medium with normal medium (as a control) and that containing arsenic trioxide (As2O3) at five different concentrations (i.e., 0.005 µM, 0.07 µM, 0.5 µM, 6 µM, and 40 µM).
| | Sample_growth_protocol_ch1 | Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation were carried out as described in the manufacturer’s instruction.
| | Sample_hyb_protocol | Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.
| | Sample_scan_protocol | After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).
| | Sample_data_processing | Probe-level data in CEL files were processed and analyzed using the Avadis 4.3 prophetic (Strand Genomics, Redwood City, CA). Data were normalized using MAS5 algorithm, and the features which were NOT flagged “Present” in all three replicates were rejected.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Hiroe,,Hara-Yamamura
| | Sample_contact_email | hy_hiroe@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-5587
| | Sample_contact_laboratory | Laboratory of Water Quality Control
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | Kita 13-jo, Nishi 8-chome
| | Sample_contact_city | Sapporo
| | Sample_contact_state | Hokkaido
| | Sample_contact_zip/postal_code | 0608628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178763/suppl/GSM1178763_HepG2_0.005_microM_rep1.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178763/suppl/GSM1178763_HepG2_0.005_microM_rep1.CHP.gz
| | Sample_series_id | GSE48441
| | Sample_data_row_count | 8793
| | |
|
GSM1178764 | GPL201 |
|
HepG2 0.005 microM rep2
|
human hepatoma cell line, HepG2
|
cell bank no: RCB1648
Sex: male
age of sampling: 15 years
tissue derived: liver
case history: hepatocyte carcinoma
life span: infinite
classification: transformed
treatment: exposed to 0.005 µM arsenic trioxide
|
|
| Sample_geo_accession | GSM1178764
| | Sample_status | Public on Jul 02 2013
| | Sample_submission_date | Jul 01 2013
| | Sample_last_update_date | Jul 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Chemical treatment was done by replacing the culture medium with normal medium (as a control) and that containing arsenic trioxide (As2O3) at five different concentrations (i.e., 0.005 µM, 0.07 µM, 0.5 µM, 6 µM, and 40 µM).
| | Sample_growth_protocol_ch1 | Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation were carried out as described in the manufacturer’s instruction.
| | Sample_hyb_protocol | Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.
| | Sample_scan_protocol | After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).
| | Sample_data_processing | Probe-level data in CEL files were processed and analyzed using the Avadis 4.3 prophetic (Strand Genomics, Redwood City, CA). Data were normalized using MAS5 algorithm, and the features which were NOT flagged “Present” in all three replicates were rejected.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Hiroe,,Hara-Yamamura
| | Sample_contact_email | hy_hiroe@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-5587
| | Sample_contact_laboratory | Laboratory of Water Quality Control
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | Kita 13-jo, Nishi 8-chome
| | Sample_contact_city | Sapporo
| | Sample_contact_state | Hokkaido
| | Sample_contact_zip/postal_code | 0608628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178764/suppl/GSM1178764_HepG2_0.005_microM_rep2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178764/suppl/GSM1178764_HepG2_0.005_microM_rep2.CHP.gz
| | Sample_series_id | GSE48441
| | Sample_data_row_count | 8793
| | |
|
GSM1178765 | GPL201 |
|
HepG2 0.005 microM rep3
|
human hepatoma cell line, HepG2
|
cell bank no: RCB1648
Sex: male
age of sampling: 15 years
tissue derived: liver
case history: hepatocyte carcinoma
life span: infinite
classification: transformed
treatment: exposed to 0.005 µM arsenic trioxide
|
|
| Sample_geo_accession | GSM1178765
| | Sample_status | Public on Jul 02 2013
| | Sample_submission_date | Jul 01 2013
| | Sample_last_update_date | Jul 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Chemical treatment was done by replacing the culture medium with normal medium (as a control) and that containing arsenic trioxide (As2O3) at five different concentrations (i.e., 0.005 µM, 0.07 µM, 0.5 µM, 6 µM, and 40 µM).
| | Sample_growth_protocol_ch1 | Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation were carried out as described in the manufacturer’s instruction.
| | Sample_hyb_protocol | Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.
| | Sample_scan_protocol | After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).
| | Sample_data_processing | Probe-level data in CEL files were processed and analyzed using the Avadis 4.3 prophetic (Strand Genomics, Redwood City, CA). Data were normalized using MAS5 algorithm, and the features which were NOT flagged “Present” in all three replicates were rejected.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Hiroe,,Hara-Yamamura
| | Sample_contact_email | hy_hiroe@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-5587
| | Sample_contact_laboratory | Laboratory of Water Quality Control
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | Kita 13-jo, Nishi 8-chome
| | Sample_contact_city | Sapporo
| | Sample_contact_state | Hokkaido
| | Sample_contact_zip/postal_code | 0608628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178765/suppl/GSM1178765_HepG2_0.005_microM_rep3.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178765/suppl/GSM1178765_HepG2_0.005_microM_rep3.CHP.gz
| | Sample_series_id | GSE48441
| | Sample_data_row_count | 8793
| | |
|
GSM1178766 | GPL201 |
|
HepG2 0.07 microM rep1
|
human hepatoma cell line, HepG2
|
cell bank no: RCB1648
Sex: male
age of sampling: 15 years
tissue derived: liver
case history: hepatocyte carcinoma
life span: infinite
classification: transformed
treatment: exposed to 0.07 µM arsenic trioxide
|
|
| Sample_geo_accession | GSM1178766
| | Sample_status | Public on Jul 02 2013
| | Sample_submission_date | Jul 01 2013
| | Sample_last_update_date | Jul 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Chemical treatment was done by replacing the culture medium with normal medium (as a control) and that containing arsenic trioxide (As2O3) at five different concentrations (i.e., 0.005 µM, 0.07 µM, 0.5 µM, 6 µM, and 40 µM).
| | Sample_growth_protocol_ch1 | Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation were carried out as described in the manufacturer’s instruction.
| | Sample_hyb_protocol | Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.
| | Sample_scan_protocol | After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).
| | Sample_data_processing | Probe-level data in CEL files were processed and analyzed using the Avadis 4.3 prophetic (Strand Genomics, Redwood City, CA). Data were normalized using MAS5 algorithm, and the features which were NOT flagged “Present” in all three replicates were rejected.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Hiroe,,Hara-Yamamura
| | Sample_contact_email | hy_hiroe@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-5587
| | Sample_contact_laboratory | Laboratory of Water Quality Control
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | Kita 13-jo, Nishi 8-chome
| | Sample_contact_city | Sapporo
| | Sample_contact_state | Hokkaido
| | Sample_contact_zip/postal_code | 0608628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178766/suppl/GSM1178766_HepG2_0.07_microM_rep1.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178766/suppl/GSM1178766_HepG2_0.07_microM_rep1.CHP.gz
| | Sample_series_id | GSE48441
| | Sample_data_row_count | 8793
| | |
|
GSM1178767 | GPL201 |
|
HepG2 0.07 microM rep2
|
human hepatoma cell line, HepG2
|
cell bank no: RCB1648
Sex: male
age of sampling: 15 years
tissue derived: liver
case history: hepatocyte carcinoma
life span: infinite
classification: transformed
treatment: exposed to 0.07 µM arsenic trioxide
|
|
| Sample_geo_accession | GSM1178767
| | Sample_status | Public on Jul 02 2013
| | Sample_submission_date | Jul 01 2013
| | Sample_last_update_date | Jul 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Chemical treatment was done by replacing the culture medium with normal medium (as a control) and that containing arsenic trioxide (As2O3) at five different concentrations (i.e., 0.005 µM, 0.07 µM, 0.5 µM, 6 µM, and 40 µM).
| | Sample_growth_protocol_ch1 | Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation were carried out as described in the manufacturer’s instruction.
| | Sample_hyb_protocol | Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.
| | Sample_scan_protocol | After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).
| | Sample_data_processing | Probe-level data in CEL files were processed and analyzed using the Avadis 4.3 prophetic (Strand Genomics, Redwood City, CA). Data were normalized using MAS5 algorithm, and the features which were NOT flagged “Present” in all three replicates were rejected.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Hiroe,,Hara-Yamamura
| | Sample_contact_email | hy_hiroe@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-5587
| | Sample_contact_laboratory | Laboratory of Water Quality Control
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | Kita 13-jo, Nishi 8-chome
| | Sample_contact_city | Sapporo
| | Sample_contact_state | Hokkaido
| | Sample_contact_zip/postal_code | 0608628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178767/suppl/GSM1178767_HepG2_0.07_microM_rep2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178767/suppl/GSM1178767_HepG2_0.07_microM_rep2.CHP.gz
| | Sample_series_id | GSE48441
| | Sample_data_row_count | 8793
| | |
|
GSM1178768 | GPL201 |
|
HepG2 0.07 microM rep3
|
human hepatoma cell line, HepG2
|
cell bank no: RCB1648
Sex: male
age of sampling: 15 years
tissue derived: liver
case history: hepatocyte carcinoma
life span: infinite
classification: transformed
treatment: exposed to 0.07 µM arsenic trioxide
|
|
| Sample_geo_accession | GSM1178768
| | Sample_status | Public on Jul 02 2013
| | Sample_submission_date | Jul 01 2013
| | Sample_last_update_date | Jul 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Chemical treatment was done by replacing the culture medium with normal medium (as a control) and that containing arsenic trioxide (As2O3) at five different concentrations (i.e., 0.005 µM, 0.07 µM, 0.5 µM, 6 µM, and 40 µM).
| | Sample_growth_protocol_ch1 | Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation were carried out as described in the manufacturer’s instruction.
| | Sample_hyb_protocol | Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.
| | Sample_scan_protocol | After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).
| | Sample_data_processing | Probe-level data in CEL files were processed and analyzed using the Avadis 4.3 prophetic (Strand Genomics, Redwood City, CA). Data were normalized using MAS5 algorithm, and the features which were NOT flagged “Present” in all three replicates were rejected.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Hiroe,,Hara-Yamamura
| | Sample_contact_email | hy_hiroe@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-5587
| | Sample_contact_laboratory | Laboratory of Water Quality Control
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | Kita 13-jo, Nishi 8-chome
| | Sample_contact_city | Sapporo
| | Sample_contact_state | Hokkaido
| | Sample_contact_zip/postal_code | 0608628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178768/suppl/GSM1178768_HepG2_0.07_microM_rep3.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178768/suppl/GSM1178768_HepG2_0.07_microM_rep3.CHP.gz
| | Sample_series_id | GSE48441
| | Sample_data_row_count | 8793
| | |
|
GSM1178769 | GPL201 |
|
HepG2 0.5 microM rep1
|
human hepatoma cell line, HepG2
|
cell bank no: RCB1648
Sex: male
age of sampling: 15 years
tissue derived: liver
case history: hepatocyte carcinoma
life span: infinite
classification: transformed
treatment: exposed to 0.5 µM arsenic trioxide
|
|
| Sample_geo_accession | GSM1178769
| | Sample_status | Public on Jul 02 2013
| | Sample_submission_date | Jul 01 2013
| | Sample_last_update_date | Jul 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Chemical treatment was done by replacing the culture medium with normal medium (as a control) and that containing arsenic trioxide (As2O3) at five different concentrations (i.e., 0.005 µM, 0.07 µM, 0.5 µM, 6 µM, and 40 µM).
| | Sample_growth_protocol_ch1 | Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation were carried out as described in the manufacturer’s instruction.
| | Sample_hyb_protocol | Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.
| | Sample_scan_protocol | After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).
| | Sample_data_processing | Probe-level data in CEL files were processed and analyzed using the Avadis 4.3 prophetic (Strand Genomics, Redwood City, CA). Data were normalized using MAS5 algorithm, and the features which were NOT flagged “Present” in all three replicates were rejected.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Hiroe,,Hara-Yamamura
| | Sample_contact_email | hy_hiroe@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-5587
| | Sample_contact_laboratory | Laboratory of Water Quality Control
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | Kita 13-jo, Nishi 8-chome
| | Sample_contact_city | Sapporo
| | Sample_contact_state | Hokkaido
| | Sample_contact_zip/postal_code | 0608628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178769/suppl/GSM1178769_HepG2_0.5_microM_rep1.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178769/suppl/GSM1178769_HepG2_0.5_microM_rep1.CHP.gz
| | Sample_series_id | GSE48441
| | Sample_data_row_count | 8793
| | |
|
GSM1178770 | GPL201 |
|
HepG2 0.5 microM rep2
|
human hepatoma cell line, HepG2
|
cell bank no: RCB1648
Sex: male
age of sampling: 15 years
tissue derived: liver
case history: hepatocyte carcinoma
life span: infinite
classification: transformed
treatment: exposed to 0.5 µM arsenic trioxide
|
|
| Sample_geo_accession | GSM1178770
| | Sample_status | Public on Jul 02 2013
| | Sample_submission_date | Jul 01 2013
| | Sample_last_update_date | Jul 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Chemical treatment was done by replacing the culture medium with normal medium (as a control) and that containing arsenic trioxide (As2O3) at five different concentrations (i.e., 0.005 µM, 0.07 µM, 0.5 µM, 6 µM, and 40 µM).
| | Sample_growth_protocol_ch1 | Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation were carried out as described in the manufacturer’s instruction.
| | Sample_hyb_protocol | Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.
| | Sample_scan_protocol | After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).
| | Sample_data_processing | Probe-level data in CEL files were processed and analyzed using the Avadis 4.3 prophetic (Strand Genomics, Redwood City, CA). Data were normalized using MAS5 algorithm, and the features which were NOT flagged “Present” in all three replicates were rejected.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Hiroe,,Hara-Yamamura
| | Sample_contact_email | hy_hiroe@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-5587
| | Sample_contact_laboratory | Laboratory of Water Quality Control
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | Kita 13-jo, Nishi 8-chome
| | Sample_contact_city | Sapporo
| | Sample_contact_state | Hokkaido
| | Sample_contact_zip/postal_code | 0608628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178770/suppl/GSM1178770_HepG2_0.5_microM_rep2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178770/suppl/GSM1178770_HepG2_0.5_microM_rep2.CHP.gz
| | Sample_series_id | GSE48441
| | Sample_data_row_count | 8793
| | |
|
GSM1178771 | GPL201 |
|
HepG2 0.5 microM rep3
|
human hepatoma cell line, HepG2
|
cell bank no: RCB1648
Sex: male
age of sampling: 15 years
tissue derived: liver
case history: hepatocyte carcinoma
life span: infinite
classification: transformed
treatment: exposed to 0.5 µM arsenic trioxide
|
|
| Sample_geo_accession | GSM1178771
| | Sample_status | Public on Jul 02 2013
| | Sample_submission_date | Jul 01 2013
| | Sample_last_update_date | Jul 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Chemical treatment was done by replacing the culture medium with normal medium (as a control) and that containing arsenic trioxide (As2O3) at five different concentrations (i.e., 0.005 µM, 0.07 µM, 0.5 µM, 6 µM, and 40 µM).
| | Sample_growth_protocol_ch1 | Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation were carried out as described in the manufacturer’s instruction.
| | Sample_hyb_protocol | Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.
| | Sample_scan_protocol | After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).
| | Sample_data_processing | Probe-level data in CEL files were processed and analyzed using the Avadis 4.3 prophetic (Strand Genomics, Redwood City, CA). Data were normalized using MAS5 algorithm, and the features which were NOT flagged “Present” in all three replicates were rejected.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Hiroe,,Hara-Yamamura
| | Sample_contact_email | hy_hiroe@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-5587
| | Sample_contact_laboratory | Laboratory of Water Quality Control
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | Kita 13-jo, Nishi 8-chome
| | Sample_contact_city | Sapporo
| | Sample_contact_state | Hokkaido
| | Sample_contact_zip/postal_code | 0608628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178771/suppl/GSM1178771_HepG2_0.5_microM_rep3.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178771/suppl/GSM1178771_HepG2_0.5_microM_rep3.CHP.gz
| | Sample_series_id | GSE48441
| | Sample_data_row_count | 8793
| | |
|
GSM1178772 | GPL201 |
|
HepG2 6 microM rep1
|
human hepatoma cell line, HepG2
|
cell bank no: RCB1648
Sex: male
age of sampling: 15 years
tissue derived: liver
case history: hepatocyte carcinoma
life span: infinite
classification: transformed
treatment: exposed to 6 µM arsenic trioxide
|
|
| Sample_geo_accession | GSM1178772
| | Sample_status | Public on Jul 02 2013
| | Sample_submission_date | Jul 01 2013
| | Sample_last_update_date | Jul 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Chemical treatment was done by replacing the culture medium with normal medium (as a control) and that containing arsenic trioxide (As2O3) at five different concentrations (i.e., 0.005 µM, 0.07 µM, 0.5 µM, 6 µM, and 40 µM).
| | Sample_growth_protocol_ch1 | Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation were carried out as described in the manufacturer’s instruction.
| | Sample_hyb_protocol | Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.
| | Sample_scan_protocol | After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).
| | Sample_data_processing | Probe-level data in CEL files were processed and analyzed using the Avadis 4.3 prophetic (Strand Genomics, Redwood City, CA). Data were normalized using MAS5 algorithm, and the features which were NOT flagged “Present” in all three replicates were rejected.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Hiroe,,Hara-Yamamura
| | Sample_contact_email | hy_hiroe@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-5587
| | Sample_contact_laboratory | Laboratory of Water Quality Control
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | Kita 13-jo, Nishi 8-chome
| | Sample_contact_city | Sapporo
| | Sample_contact_state | Hokkaido
| | Sample_contact_zip/postal_code | 0608628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178772/suppl/GSM1178772_HepG2_6_microM_rep1.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178772/suppl/GSM1178772_HepG2_6_microM_rep1.CHP.gz
| | Sample_series_id | GSE48441
| | Sample_data_row_count | 8793
| | |
|
GSM1178773 | GPL201 |
|
HepG2 6 microM rep2
|
human hepatoma cell line, HepG2
|
cell bank no: RCB1648
Sex: male
age of sampling: 15 years
tissue derived: liver
case history: hepatocyte carcinoma
life span: infinite
classification: transformed
treatment: exposed to 6 µM arsenic trioxide
|
|
| Sample_geo_accession | GSM1178773
| | Sample_status | Public on Jul 02 2013
| | Sample_submission_date | Jul 01 2013
| | Sample_last_update_date | Jul 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Chemical treatment was done by replacing the culture medium with normal medium (as a control) and that containing arsenic trioxide (As2O3) at five different concentrations (i.e., 0.005 µM, 0.07 µM, 0.5 µM, 6 µM, and 40 µM).
| | Sample_growth_protocol_ch1 | Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation were carried out as described in the manufacturer’s instruction.
| | Sample_hyb_protocol | Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.
| | Sample_scan_protocol | After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).
| | Sample_data_processing | Probe-level data in CEL files were processed and analyzed using the Avadis 4.3 prophetic (Strand Genomics, Redwood City, CA). Data were normalized using MAS5 algorithm, and the features which were NOT flagged “Present” in all three replicates were rejected.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Hiroe,,Hara-Yamamura
| | Sample_contact_email | hy_hiroe@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-5587
| | Sample_contact_laboratory | Laboratory of Water Quality Control
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | Kita 13-jo, Nishi 8-chome
| | Sample_contact_city | Sapporo
| | Sample_contact_state | Hokkaido
| | Sample_contact_zip/postal_code | 0608628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178773/suppl/GSM1178773_HepG2_6_microM_rep2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178773/suppl/GSM1178773_HepG2_6_microM_rep2.CHP.gz
| | Sample_series_id | GSE48441
| | Sample_data_row_count | 8793
| | |
|
GSM1178774 | GPL201 |
|
HepG2 6 microM rep3
|
human hepatoma cell line, HepG2
|
cell bank no: RCB1648
Sex: male
age of sampling: 15 years
tissue derived: liver
case history: hepatocyte carcinoma
life span: infinite
classification: transformed
treatment: exposed to 6 µM arsenic trioxide
|
|
| Sample_geo_accession | GSM1178774
| | Sample_status | Public on Jul 02 2013
| | Sample_submission_date | Jul 01 2013
| | Sample_last_update_date | Jul 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Chemical treatment was done by replacing the culture medium with normal medium (as a control) and that containing arsenic trioxide (As2O3) at five different concentrations (i.e., 0.005 µM, 0.07 µM, 0.5 µM, 6 µM, and 40 µM).
| | Sample_growth_protocol_ch1 | Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation were carried out as described in the manufacturer’s instruction.
| | Sample_hyb_protocol | Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.
| | Sample_scan_protocol | After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).
| | Sample_data_processing | Probe-level data in CEL files were processed and analyzed using the Avadis 4.3 prophetic (Strand Genomics, Redwood City, CA). Data were normalized using MAS5 algorithm, and the features which were NOT flagged “Present” in all three replicates were rejected.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Hiroe,,Hara-Yamamura
| | Sample_contact_email | hy_hiroe@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-5587
| | Sample_contact_laboratory | Laboratory of Water Quality Control
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | Kita 13-jo, Nishi 8-chome
| | Sample_contact_city | Sapporo
| | Sample_contact_state | Hokkaido
| | Sample_contact_zip/postal_code | 0608628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178774/suppl/GSM1178774_HepG2_6_microM_rep3.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178774/suppl/GSM1178774_HepG2_6_microM_rep3.CHP.gz
| | Sample_series_id | GSE48441
| | Sample_data_row_count | 8793
| | |
|
GSM1178775 | GPL201 |
|
HepG2 40 microM rep1
|
human hepatoma cell line, HepG2
|
cell bank no: RCB1648
Sex: male
age of sampling: 15 years
tissue derived: liver
case history: hepatocyte carcinoma
life span: infinite
classification: transformed
treatment: exposed to 40 µM arsenic trioxide
|
|
| Sample_geo_accession | GSM1178775
| | Sample_status | Public on Jul 02 2013
| | Sample_submission_date | Jul 01 2013
| | Sample_last_update_date | Jul 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Chemical treatment was done by replacing the culture medium with normal medium (as a control) and that containing arsenic trioxide (As2O3) at five different concentrations (i.e., 0.005 µM, 0.07 µM, 0.5 µM, 6 µM, and 40 µM).
| | Sample_growth_protocol_ch1 | Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation were carried out as described in the manufacturer’s instruction.
| | Sample_hyb_protocol | Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.
| | Sample_scan_protocol | After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).
| | Sample_data_processing | Probe-level data in CEL files were processed and analyzed using the Avadis 4.3 prophetic (Strand Genomics, Redwood City, CA). Data were normalized using MAS5 algorithm, and the features which were NOT flagged “Present” in all three replicates were rejected.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Hiroe,,Hara-Yamamura
| | Sample_contact_email | hy_hiroe@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-5587
| | Sample_contact_laboratory | Laboratory of Water Quality Control
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | Kita 13-jo, Nishi 8-chome
| | Sample_contact_city | Sapporo
| | Sample_contact_state | Hokkaido
| | Sample_contact_zip/postal_code | 0608628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178775/suppl/GSM1178775_HepG2_40_microM_rep1.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178775/suppl/GSM1178775_HepG2_40_microM_rep1.CHP.gz
| | Sample_series_id | GSE48441
| | Sample_data_row_count | 8793
| | |
|
GSM1178776 | GPL201 |
|
HepG2 40 microM rep2
|
human hepatoma cell line, HepG2
|
cell bank no: RCB1648
Sex: male
age of sampling: 15 years
tissue derived: liver
case history: hepatocyte carcinoma
life span: infinite
classification: transformed
treatment: exposed to 40 µM arsenic trioxide
|
|
| Sample_geo_accession | GSM1178776
| | Sample_status | Public on Jul 02 2013
| | Sample_submission_date | Jul 01 2013
| | Sample_last_update_date | Jul 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Chemical treatment was done by replacing the culture medium with normal medium (as a control) and that containing arsenic trioxide (As2O3) at five different concentrations (i.e., 0.005 µM, 0.07 µM, 0.5 µM, 6 µM, and 40 µM).
| | Sample_growth_protocol_ch1 | Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation were carried out as described in the manufacturer’s instruction.
| | Sample_hyb_protocol | Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.
| | Sample_scan_protocol | After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).
| | Sample_data_processing | Probe-level data in CEL files were processed and analyzed using the Avadis 4.3 prophetic (Strand Genomics, Redwood City, CA). Data were normalized using MAS5 algorithm, and the features which were NOT flagged “Present” in all three replicates were rejected.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Hiroe,,Hara-Yamamura
| | Sample_contact_email | hy_hiroe@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-5587
| | Sample_contact_laboratory | Laboratory of Water Quality Control
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | Kita 13-jo, Nishi 8-chome
| | Sample_contact_city | Sapporo
| | Sample_contact_state | Hokkaido
| | Sample_contact_zip/postal_code | 0608628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178776/suppl/GSM1178776_HepG2_40_microM_rep2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178776/suppl/GSM1178776_HepG2_40_microM_rep2.CHP.gz
| | Sample_series_id | GSE48441
| | Sample_data_row_count | 8793
| | |
|
GSM1178777 | GPL201 |
|
HepG2 40 microM rep3
|
human hepatoma cell line, HepG2
|
cell bank no: RCB1648
Sex: male
age of sampling: 15 years
tissue derived: liver
case history: hepatocyte carcinoma
life span: infinite
classification: transformed
treatment: exposed to 40 µM arsenic trioxide
|
|
| Sample_geo_accession | GSM1178777
| | Sample_status | Public on Jul 02 2013
| | Sample_submission_date | Jul 01 2013
| | Sample_last_update_date | Jul 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Chemical treatment was done by replacing the culture medium with normal medium (as a control) and that containing arsenic trioxide (As2O3) at five different concentrations (i.e., 0.005 µM, 0.07 µM, 0.5 µM, 6 µM, and 40 µM).
| | Sample_growth_protocol_ch1 | Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation were carried out as described in the manufacturer’s instruction.
| | Sample_hyb_protocol | Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.
| | Sample_scan_protocol | After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).
| | Sample_data_processing | Probe-level data in CEL files were processed and analyzed using the Avadis 4.3 prophetic (Strand Genomics, Redwood City, CA). Data were normalized using MAS5 algorithm, and the features which were NOT flagged “Present” in all three replicates were rejected.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Hiroe,,Hara-Yamamura
| | Sample_contact_email | hy_hiroe@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-5587
| | Sample_contact_laboratory | Laboratory of Water Quality Control
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | Kita 13-jo, Nishi 8-chome
| | Sample_contact_city | Sapporo
| | Sample_contact_state | Hokkaido
| | Sample_contact_zip/postal_code | 0608628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178777/suppl/GSM1178777_HepG2_40_microM_rep3.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178777/suppl/GSM1178777_HepG2_40_microM_rep3.CHP.gz
| | Sample_series_id | GSE48441
| | Sample_data_row_count | 8793
| | |
|
GSM1178778 | GPL201 |
|
HepG2 CAP rep1
|
human hepatoma cell line, HepG2
|
cell bank no: RCB1648
Sex: male
age of sampling: 15 years
tissue derived: liver
case history: hepatocyte carcinoma
life span: infinite
classification: transformed
treatment: exposed to 15 mM ε-caprolactam
|
|
| Sample_geo_accession | GSM1178778
| | Sample_status | Public on Jul 02 2013
| | Sample_submission_date | Jul 01 2013
| | Sample_last_update_date | Jul 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Chemical treatment was done by replacing the culture medium with normal medium (as a control) and that containing arsenic trioxide (As2O3) at five different concentrations (i.e., 0.005 µM, 0.07 µM, 0.5 µM, 6 µM, and 40 µM).
| | Sample_growth_protocol_ch1 | Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation were carried out as described in the manufacturer’s instruction.
| | Sample_hyb_protocol | Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.
| | Sample_scan_protocol | After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).
| | Sample_data_processing | Probe-level data in CEL files were processed and analyzed using the Avadis 4.3 prophetic (Strand Genomics, Redwood City, CA). Data were normalized using MAS5 algorithm, and the features which were NOT flagged “Present” in all three replicates were rejected.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Hiroe,,Hara-Yamamura
| | Sample_contact_email | hy_hiroe@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-5587
| | Sample_contact_laboratory | Laboratory of Water Quality Control
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | Kita 13-jo, Nishi 8-chome
| | Sample_contact_city | Sapporo
| | Sample_contact_state | Hokkaido
| | Sample_contact_zip/postal_code | 0608628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178778/suppl/GSM1178778_HepG2_CAP_rep1.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178778/suppl/GSM1178778_HepG2_CAP_rep1.CHP.gz
| | Sample_series_id | GSE48441
| | Sample_data_row_count | 8793
| | |
|
GSM1178779 | GPL201 |
|
HepG2 CAP rep2
|
human hepatoma cell line, HepG2
|
cell bank no: RCB1648
Sex: male
age of sampling: 15 years
tissue derived: liver
case history: hepatocyte carcinoma
life span: infinite
classification: transformed
treatment: exposed to 15 mM ε-caprolactam
|
|
| Sample_geo_accession | GSM1178779
| | Sample_status | Public on Jul 02 2013
| | Sample_submission_date | Jul 01 2013
| | Sample_last_update_date | Jul 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Chemical treatment was done by replacing the culture medium with normal medium (as a control) and that containing arsenic trioxide (As2O3) at five different concentrations (i.e., 0.005 µM, 0.07 µM, 0.5 µM, 6 µM, and 40 µM).
| | Sample_growth_protocol_ch1 | Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation were carried out as described in the manufacturer’s instruction.
| | Sample_hyb_protocol | Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.
| | Sample_scan_protocol | After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).
| | Sample_data_processing | Probe-level data in CEL files were processed and analyzed using the Avadis 4.3 prophetic (Strand Genomics, Redwood City, CA). Data were normalized using MAS5 algorithm, and the features which were NOT flagged “Present” in all three replicates were rejected.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Hiroe,,Hara-Yamamura
| | Sample_contact_email | hy_hiroe@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-5587
| | Sample_contact_laboratory | Laboratory of Water Quality Control
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | Kita 13-jo, Nishi 8-chome
| | Sample_contact_city | Sapporo
| | Sample_contact_state | Hokkaido
| | Sample_contact_zip/postal_code | 0608628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178779/suppl/GSM1178779_HepG2_CAP_rep2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178779/suppl/GSM1178779_HepG2_CAP_rep2.CHP.gz
| | Sample_series_id | GSE48441
| | Sample_data_row_count | 8793
| | |
|
GSM1178780 | GPL201 |
|
HepG2 CAP rep3
|
human hepatoma cell line, HepG2
|
cell bank no: RCB1648
Sex: male
age of sampling: 15 years
tissue derived: liver
case history: hepatocyte carcinoma
life span: infinite
classification: transformed
treatment: exposed to 15 mM ε-caprolactam
|
|
| Sample_geo_accession | GSM1178780
| | Sample_status | Public on Jul 02 2013
| | Sample_submission_date | Jul 01 2013
| | Sample_last_update_date | Jul 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Chemical treatment was done by replacing the culture medium with normal medium (as a control) and that containing arsenic trioxide (As2O3) at five different concentrations (i.e., 0.005 µM, 0.07 µM, 0.5 µM, 6 µM, and 40 µM).
| | Sample_growth_protocol_ch1 | Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation were carried out as described in the manufacturer’s instruction.
| | Sample_hyb_protocol | Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.
| | Sample_scan_protocol | After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).
| | Sample_data_processing | Probe-level data in CEL files were processed and analyzed using the Avadis 4.3 prophetic (Strand Genomics, Redwood City, CA). Data were normalized using MAS5 algorithm, and the features which were NOT flagged “Present” in all three replicates were rejected.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Hiroe,,Hara-Yamamura
| | Sample_contact_email | hy_hiroe@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-5587
| | Sample_contact_laboratory | Laboratory of Water Quality Control
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | Kita 13-jo, Nishi 8-chome
| | Sample_contact_city | Sapporo
| | Sample_contact_state | Hokkaido
| | Sample_contact_zip/postal_code | 0608628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178780/suppl/GSM1178780_HepG2_CAP_rep3.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178780/suppl/GSM1178780_HepG2_CAP_rep3.CHP.gz
| | Sample_series_id | GSE48441
| | Sample_data_row_count | 8793
| | |
|
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