Search results for the GEO ID: GSE14452  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM361148 | GPL201 |
|
HepG2_control rep4
|
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
|
HepG2_control rep4
|
| Sample_geo_accession | GSM361148
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Jan 15 2009
| | Sample_last_update_date | Jan 22 2009
| | 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/GSM361nnn/GSM361148/suppl/GSM361148.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361148/suppl/GSM361148.CHP.gz
| | Sample_series_id | GSE14452
| | Sample_data_row_count | 8793
| | |
|
GSM361149 | GPL201 |
|
HepG2_control rep5
|
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
|
HepG2_control rep5
|
| Sample_geo_accession | GSM361149
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Jan 15 2009
| | Sample_last_update_date | Jan 22 2009
| | 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/GSM361nnn/GSM361149/suppl/GSM361149.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361149/suppl/GSM361149.CHP.gz
| | Sample_series_id | GSE14452
| | Sample_data_row_count | 8793
| | |
|
GSM361150 | GPL201 |
|
HepG2_control rep6
|
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
|
HepG2_control rep6
|
| Sample_geo_accession | GSM361150
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Jan 15 2009
| | Sample_last_update_date | Jan 22 2009
| | 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/GSM361nnn/GSM361150/suppl/GSM361150.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361150/suppl/GSM361150.CHP.gz
| | Sample_series_id | GSE14452
| | Sample_data_row_count | 8793
| | |
|
GSM361151 | GPL201 |
|
HepG2_nanoAg rep1
|
Hep G2 treated with silver nanoparticles for 24h
|
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
|
HepG2_nanoAg rep1
|
| Sample_geo_accession | GSM361151
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Jan 16 2009
| | Sample_last_update_date | Jan 22 2009
| | 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 1 mg/l of silver nanoparticles (7-10 nm) for 24h 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/GSM361nnn/GSM361151/suppl/GSM361151.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361151/suppl/GSM361151.CHP.gz
| | Sample_series_id | GSE14452
| | Sample_data_row_count | 8793
| | |
|
GSM361152 | GPL201 |
|
HepG2_nanoAg rep2
|
Hep G2 treated with silver nanoparticles for 48h
|
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
|
HepG2_nanoAg rep2
|
| Sample_geo_accession | GSM361152
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Jan 16 2009
| | Sample_last_update_date | Jan 22 2009
| | 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 1 mg/l of silver nanoparticles (7-10 nm) for 24h 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/GSM361nnn/GSM361152/suppl/GSM361152.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361152/suppl/GSM361152.CHP.gz
| | Sample_series_id | GSE14452
| | Sample_data_row_count | 8793
| | |
|
GSM361153 | GPL201 |
|
HepG2_nanoAg rep3
|
Hep G2 treated with silver nanoparticles for 24h
|
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
|
HepG2_nanoAg rep3
|
| Sample_geo_accession | GSM361153
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Jan 16 2009
| | Sample_last_update_date | Jan 22 2009
| | 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 1 mg/l of silver nanoparticles (7-10 nm) for 24h 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/GSM361nnn/GSM361153/suppl/GSM361153.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361153/suppl/GSM361153.CHP.gz
| | Sample_series_id | GSE14452
| | Sample_data_row_count | 8793
| | |
|
GSM361154 | GPL201 |
|
HepG2_PS rep1
|
Hep G2 treated with polystyrene nanoparticles for 24h
|
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
|
HepG2_PS rep1
|
| Sample_geo_accession | GSM361154
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Jan 16 2009
| | Sample_last_update_date | Jan 22 2009
| | 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 1 mg/l of polystyrene nanoparticles (15 nm) for 24h 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/GSM361nnn/GSM361154/suppl/GSM361154.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361154/suppl/GSM361154.CHP.gz
| | Sample_series_id | GSE14452
| | Sample_data_row_count | 8793
| | |
|
GSM361155 | GPL201 |
|
HepG2_PS rep2
|
Hep G2 treated with polystyrene nanoparticles for 24h
|
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
|
HepG2_PS rep2
|
| Sample_geo_accession | GSM361155
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Jan 16 2009
| | Sample_last_update_date | Jan 22 2009
| | 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 1 mg/l of polystyrene nanoparticles (15 nm) for 24h 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/GSM361nnn/GSM361155/suppl/GSM361155.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361155/suppl/GSM361155.CHP.gz
| | Sample_series_id | GSE14452
| | Sample_data_row_count | 8793
| | |
|
GSM361156 | GPL201 |
|
HepG2_PS rep3
|
Hep G2 treated with polystyrene nanoparticles for 24h
|
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
|
HepG2_PS rep3
|
| Sample_geo_accession | GSM361156
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Jan 16 2009
| | Sample_last_update_date | Jan 22 2009
| | 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 1 mg/l of polystyrene nanoparticles (15 nm) for 24h 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/GSM361nnn/GSM361156/suppl/GSM361156.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361156/suppl/GSM361156.CHP.gz
| | Sample_series_id | GSE14452
| | Sample_data_row_count | 8793
| | |
|
GSM361157 | GPL201 |
|
HepG2_Ag2CO3 rep1
|
Hep G2 treated with silver carbonate for 24h
|
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
|
HepG2_Ag2CO3 rep1
|
| Sample_geo_accession | GSM361157
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Jan 16 2009
| | Sample_last_update_date | Jan 22 2009
| | 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 1.3 mg/l of silver carbonate for 24h 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/GSM361nnn/GSM361157/suppl/GSM361157.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361157/suppl/GSM361157.CHP.gz
| | Sample_series_id | GSE14452
| | Sample_data_row_count | 8793
| | |
|
GSM361158 | GPL201 |
|
HepG2_Ag2CO3 rep2
|
Hep G2 treated with silver carbonate for 24h
|
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
|
HepG2_Ag2CO3 rep2
|
| Sample_geo_accession | GSM361158
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Jan 16 2009
| | Sample_last_update_date | Jan 22 2009
| | 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 1.3 mg/l of silver carbonate for 24h 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/GSM361nnn/GSM361158/suppl/GSM361158.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361158/suppl/GSM361158.CHP.gz
| | Sample_series_id | GSE14452
| | Sample_data_row_count | 8793
| | |
|
GSM361159 | GPL201 |
|
HepG2_Ag2CO3 rep3
|
Hep G2 treated with silver carbonate for 24h
|
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
|
HepG2_Ag2CO3 rep3
|
| Sample_geo_accession | GSM361159
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Jan 16 2009
| | Sample_last_update_date | Jan 22 2009
| | 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 1.3 mg/l of silver carbonate for 24h 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/GSM361nnn/GSM361159/suppl/GSM361159.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361159/suppl/GSM361159.CHP.gz
| | Sample_series_id | GSE14452
| | Sample_data_row_count | 8793
| | |
|
GSM361160 | GPL201 |
|
HepG2_nanoAg+cysteine rep1
|
Hep G2 treated with silver nanoparticles and cysteine for 24h
|
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
|
HepG2_nanoAg+cysteine rep1
|
| Sample_geo_accession | GSM361160
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Jan 16 2009
| | Sample_last_update_date | Jan 22 2009
| | 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 1 mg/l of silver nanoparticles and 5mM of N-acetyl-L-cysteinefor 24h 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/GSM361nnn/GSM361160/suppl/GSM361160.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361160/suppl/GSM361160.CHP.gz
| | Sample_series_id | GSE14452
| | Sample_data_row_count | 8793
| | |
|
GSM361161 | GPL201 |
|
HepG2_nanoAg+cysteine rep2
|
Hep G2 treated with silver nanoparticles and cysteine for 24h
|
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
|
HepG2_nanoAg+cysteine rep2
|
| Sample_geo_accession | GSM361161
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Jan 16 2009
| | Sample_last_update_date | Jan 22 2009
| | 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 1 mg/l of silver nanoparticles and 5mM of N-acetyl-L-cysteinefor 24h 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/GSM361nnn/GSM361161/suppl/GSM361161.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361161/suppl/GSM361161.CHP.gz
| | Sample_series_id | GSE14452
| | Sample_data_row_count | 8793
| | |
|
GSM361162 | GPL201 |
|
HepG2_nanoAg+cysteine rep3
|
Hep G2 treated with silver nanoparticles and cysteine for 24h
|
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
|
HepG2_nanoAg+cysteine rep3
|
| Sample_geo_accession | GSM361162
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Jan 16 2009
| | Sample_last_update_date | Jan 22 2009
| | 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 1 mg/l of silver nanoparticles and 5mM of N-acetyl-L-cysteinefor 24h 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/GSM361nnn/GSM361162/suppl/GSM361162.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361162/suppl/GSM361162.CHP.gz
| | Sample_series_id | GSE14452
| | Sample_data_row_count | 8793
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