Search results for the GEO ID: GSE6907  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM159303 | GPL201 |
|
HepG2_control rep1
|
human hepatoma cell line, Hep G2
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from untreated Hep G2 cells
|
| Sample_geo_accession | GSM159303
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 29 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159303/suppl/GSM159303.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_series_id | GSE8865
| | Sample_data_row_count | 8793
| | |
|
GSM159305 | GPL201 |
|
HepG2_control rep2
|
human hepatoma cell line, Hep G2
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from untreated Hep G2 cells
|
| Sample_geo_accession | GSM159305
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 29 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159305/suppl/GSM159305.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_series_id | GSE8865
| | Sample_data_row_count | 8793
| | |
|
GSM159306 | GPL201 |
|
HepG2_control rep3
|
human hepatoma cell line, Hep G2
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from untreated Hep G2 cells
|
| Sample_geo_accession | GSM159306
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 29 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 ¡C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 ¡C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 ¡C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159306/suppl/GSM159306.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_series_id | GSE8865
| | Sample_data_row_count | 8793
| | |
|
GSM159312 | GPL201 |
|
HepG2_As rep1
|
Hep G2 treated with Arsenic (III) oxide
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from As treated Hep G2 cells
|
| Sample_geo_accession | GSM159312
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 29 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 20 uM Arsenic (III) oxide for 6h at 37 °C
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159312/suppl/GSM159312.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
| | |
|
GSM159314 | GPL201 |
|
HepG2_As rep2
|
Hep G2 treated with Arsenic (III) oxide
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from As treated Hep G2 cells
|
| Sample_geo_accession | GSM159314
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 29 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 20 uM Arsenic (III) oxide for 6h at 37 °C
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159314/suppl/GSM159314.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
| | |
|
GSM159315 | GPL201 |
|
HepG2_As rep3
|
Hep G2 treated with Arsenic (III) oxide
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from As treated Hep G2 cells
|
| Sample_geo_accession | GSM159315
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 29 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 20 uM Arsenic (III) oxide for 6h at 37 °C
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159315/suppl/GSM159315.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
| | |
|
GSM159316 | GPL201 |
|
HepG2_Cd rep1
|
Hep G2 treated with Cadmium chloride 2.5-hydrate
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from Cd treated Hep G2 cells
|
| Sample_geo_accession | GSM159316
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 29 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 2 uM Cadmium chloride 2.5-hydrate for 6h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159316/suppl/GSM159316.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
| | |
|
GSM159318 | GPL201 |
|
HepG2_Cd rep2
|
Hep G2 treated with Cadmium chloride 2.5-hydrate
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from Cd treated Hep G2 cells
|
| Sample_geo_accession | GSM159318
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 30 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 2 uM Cadmium chloride 2.5-hydrate for 6h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159318/suppl/GSM159318.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
| | |
|
GSM159319 | GPL201 |
|
HepG2_Cd rep3
|
Hep G2 treated with Cadmium chloride 2.5-hydrate
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from Cd treated Hep G2 cells
|
| Sample_geo_accession | GSM159319
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 30 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 2 uM Cadmium chloride 2.5-hydrate for 6h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159319/suppl/GSM159319.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
| | |
|
GSM159322 | GPL201 |
|
HepG2_Ni rep1
|
Hep G2 treated with Nickel (II) chloride hexahydrate
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from Ni treated Hep G2 cells
|
| Sample_geo_accession | GSM159322
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 30 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 6.5 mM Nickel (II) chloride hexahydrate for 6h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten †g of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159322/suppl/GSM159322.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
| | |
|
GSM159324 | GPL201 |
|
HepG2_Ni rep2
|
Hep G2 treated with Nickel (II) chloride hexahydrate
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from Ni treated Hep G2 cells
|
| Sample_geo_accession | GSM159324
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 30 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 6.5 mM Nickel (II) chloride hexahydrate for 6h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten †g of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159324/suppl/GSM159324.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
| | |
|
GSM159325 | GPL201 |
|
HepG2_Ni rep3
|
Hep G2 treated with Nickel (II) chloride hexahydrate
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from Ni treated Hep G2 cells
|
| Sample_geo_accession | GSM159325
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 30 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 6.5 mM Nickel (II) chloride hexahydrate for 6h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159325/suppl/GSM159325.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
| | |
|
GSM159327 | GPL201 |
|
HepG2_Sb rep1
|
Hep G2 treated with Bis [(+)-tartrato] diantimonate (III) dipotassium trihydrate
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from Sb treated Hep G2 cells
|
| Sample_geo_accession | GSM159327
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 30 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 200 uM Bis [(+)-tartrato] diantimonate (III) dipotassium trihydrate for 6h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159327/suppl/GSM159327.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
| | |
|
GSM159328 | GPL201 |
|
HepG2_Sb rep2
|
Hep G2 treated with Bis [(+)-tartrato] diantimonate (III) dipotassium trihydrate
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from Sb treated Hep G2 cells
|
| Sample_geo_accession | GSM159328
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 30 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 200 uM Bis [(+)-tartrato] diantimonate (III) dipotassium trihydrate for 6h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159328/suppl/GSM159328.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
| | |
|
GSM159329 | GPL201 |
|
HepG2_Sb rep3
|
Hep G2 treated with Bis [(+)-tartrato] diantimonate (III) dipotassium trihydrate
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from Sb treated Hep G2 cells
|
| Sample_geo_accession | GSM159329
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 30 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 200 uM Bis [(+)-tartrato] diantimonate (III) dipotassium trihydrate for 6h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159329/suppl/GSM159329.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
| | |
|
GSM159330 | GPL201 |
|
HepG2_Hg rep1
|
Hep G2 treated with Mercury (II) chloride
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from Hg treated Hep G2 cells
|
| Sample_geo_accession | GSM159330
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 30 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 20 uM Mercury (II) chloride for 6h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159330/suppl/GSM159330.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
| | |
|
GSM159331 | GPL201 |
|
HepG2_Hg rep2
|
Hep G2 treated with Mercury (II) chloride
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from Hg treated Hep G2 cells
|
| Sample_geo_accession | GSM159331
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 30 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 20 uM Mercury (II) chloride for 6h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159331/suppl/GSM159331.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
| | |
|
GSM159332 | GPL201 |
|
HepG2_Hg rep3
|
Hep G2 treated with Mercury (II) chloride
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from Hg treated Hep G2 cells
|
| Sample_geo_accession | GSM159332
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 30 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 20 uM Mercury (II) chloride for 6h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159332/suppl/GSM159332.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
| | |
|
GSM159333 | GPL201 |
|
HepG2_Cr rep1
|
Hep G2 treated with Potassium dichromate
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from Cr treated Hep G2 cells
|
| Sample_geo_accession | GSM159333
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 30 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 20 uM Potassium dichromate for 6h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159333/suppl/GSM159333.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
| | |
|
GSM159334 | GPL201 |
|
HepG2_Cr rep2
|
Hep G2 treated with Potassium dichromate
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from Cr treated Hep G2 cells
|
| Sample_geo_accession | GSM159334
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 30 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 20 uM Potassium dichromate for 6h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159334/suppl/GSM159334.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
| | |
|
GSM159335 | GPL201 |
|
HepG2_Cr rep3
|
Hep G2 treated with Potassium dichromate
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from Cr treated Hep G2 cells
|
| Sample_geo_accession | GSM159335
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 30 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 20 uM Potassium dichromate for 6h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | Probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159335/suppl/GSM159335.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
| | |
|
GSM159336 | GPL201 |
|
HepG2_DMNQ rep1
|
Hep G2 treated with 2,3-Dimethoxy-1,4-naphthoquinone
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from DMNQ treated Hep G2 cells
|
| Sample_geo_accession | GSM159336
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 30 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 10 uM 2,3-Dimethoxy-1,4-naphthoquinone for 6h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159336/suppl/GSM159336.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
| | |
|
GSM159337 | GPL201 |
|
HepG2_DMNQ rep2
|
Hep G2 treated with 2,3-Dimethoxy-1,4-naphthoquinone
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from DMNQ treated Hep G2 cells
|
| Sample_geo_accession | GSM159337
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 30 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 10 uM 2,3-Dimethoxy-1,4-naphthoquinone for 6h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159337/suppl/GSM159337.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
| | |
|
GSM159338 | GPL201 |
|
HepG2_DMNQ rep3
|
Hep G2 treated with 2,3-Dimethoxy-1,4-naphthoquinone
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from DMNQ treated Hep G2 cells
|
| Sample_geo_accession | GSM159338
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 30 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 10 uM 2,3-Dimethoxy-1,4-naphthoquinone for 6h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159338/suppl/GSM159338.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
| | |
|
GSM159339 | GPL201 |
|
HepG2_DMN rep1
|
Hep G2 treated with N-Nitrosodimethylamine
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from DMN treated Hep G2 cells
|
| Sample_geo_accession | GSM159339
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 30 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 5.4 mM N-Nitrosodimethylamine for 48h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159339/suppl/GSM159339.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_series_id | GSE8865
| | Sample_data_row_count | 8793
| | |
|
GSM159340 | GPL201 |
|
HepG2_DMN rep2
|
Hep G2 treated with N-Nitrosodimethylamine
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from DMN treated Hep G2 cells
|
| Sample_geo_accession | GSM159340
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 30 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 5.4 mM N-Nitrosodimethylamine for 48h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159340/suppl/GSM159340.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_series_id | GSE8865
| | Sample_data_row_count | 8793
| | |
|
GSM159341 | GPL201 |
|
HepG2_DMN rep3
|
Hep G2 treated with N-Nitrosodimethylamine
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from DMN treated Hep G2 cells
|
| Sample_geo_accession | GSM159341
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 30 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 5.4 mM N-Nitrosodimethylamine for 48h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159341/suppl/GSM159341.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_series_id | GSE8865
| | Sample_data_row_count | 8793
| | |
|
GSM159342 | GPL201 |
|
HepG2_Phenol rep1
|
Hep G2 treated with Phenol
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from Phenol treated Hep G2 cells
|
| Sample_geo_accession | GSM159342
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 30 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 10 mM Phenol for 6h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159342/suppl/GSM159342.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
| | |
|
GSM159343 | GPL201 |
|
HepG2_Phenol rep2
|
Hep G2 treated with Phenol
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from Phenol treated Hep G2 cells
|
| Sample_geo_accession | GSM159343
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 30 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 10 mM Phenol for 6h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159343/suppl/GSM159343.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
| | |
|
GSM159344 | GPL201 |
|
HepG2_Phenol rep3
|
Hep G2 treated with Phenol
|
Cell bank no: RCB1648
Cell name: Hep G2
Sex: male
Age of sampling: 15 years
Tissue derived: liver
Case history: hepatocyte carcinoma
Life span: infinite
Classification: Transformed
|
Gene expression data from Phenol treated Hep G2 cells
|
| Sample_geo_accession | GSM159344
| | Sample_status | Public on Mar 01 2007
| | Sample_submission_date | Jan 30 2007
| | Sample_last_update_date | Feb 02 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | RIKEN BRC CELL BANK
| | Sample_treatment_protocol_ch1 | Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 10 mM Phenol for 6h at 37 °C.
| | Sample_growth_protocol_ch1 | Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The cells were were washed with phosphate buffered saline (PBS) and lysed directly on culture dishes. Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA). Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate. Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C. After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).
| | Sample_platform_id | GPL201
| | Sample_contact_name | Akinobu,,Ito
| | Sample_contact_email | akito@eng.hokudai.ac.jp
| | Sample_contact_phone | +81-11-706-7588
| | Sample_contact_fax | +81-11-706-7588
| | Sample_contact_laboratory | Water Quality Control Engineering
| | Sample_contact_department | Graduate School of Engineering
| | Sample_contact_institute | Hokkaido University
| | Sample_contact_address | North-13, West-8, Kitaku
| | Sample_contact_city | Sapporo
| | Sample_contact_zip/postal_code | 060-8628
| | Sample_contact_country | Japan
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM159nnn/GSM159344/suppl/GSM159344.CEL.gz
| | Sample_series_id | GSE6907
| | Sample_data_row_count | 8793
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