Search results for the GEO ID: GSE7862 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM190617 | GPL201 |
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Normal buccal keratinocytes (NBK), Sample A
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Buccal mucosa from healthy, non-smoking donor undergoing maxillofacial surgery
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cell type: Normal oral keratinocytes in serum-free culture
experimental factor: Un-exposed control
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Primary cell cultures were derived from tissue digestion with trypsin overnight at 4°C and the mixture was resuspended in a serum-free epithelial medium with high levels of amino acids (EMHA) and plated on dishes pre-coated with fibronectin and collagen.(Grafström R.C. Culture of Epithelial cells, 2nd ed, John Wiley and Sons Inc, NY, 2002). Cultures were transferred on regular tissue culture plastic at about 75 % confluence, and cells in passage 2 were used in the experiments.Total RNA was prepared from 3 x 10^6 cells using the RNeasy Mini Protocol (Qiagen GmbH, Hilden, Germany) from two separate experiments of NBK
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Sample_geo_accession | GSM190617
| Sample_status | Public on Aug 21 2007
| Sample_submission_date | May 21 2007
| Sample_last_update_date | Jul 16 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | Karolinska University Hospital, Stockholm, Sweden
| Sample_growth_protocol_ch1 | Primary cell cultures were derived from tissue digestion with trypsin overnight at 4°C and the mixture was resuspended in a serum-free epithelial medium with high levels of amino acids (EMHA) and plated on dishes pre-coated with fibronectin and collagen.(Grafström R.C. Culture of Epithelial cells, 2nd ed, John Wiley and Sons Inc, NY, 2002). Cultures were transferred on regular tissue culture plastic at about 75 % confluence, and cells in passage 2 were used in the experiments.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | We used RNeasy Mini Protocol (Qiagen GmbH, Hilden, Germany) according to the manufacturer's recommended protocols.
| Sample_label_ch1 | Affymetrix single-stage biotin
| Sample_label_protocol_ch1 | We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.
| Sample_hyb_protocol | We used the Affymetrix Hybridization Oven 640 and GeneChip® Fluidics Station 450 according to the manufacturer's recommended protocols.
| Sample_scan_protocol | We used the Affymetrix GeneChip® Scanner 3000 according to the manufacturer's recommended protocols.
| Sample_data_processing | The data was analyzed using Gene Chip Operating Software (Affymetrix). GCOS was also applied for target intensity scaling of each array to an identical value (100) and quantification of the signal log ratio.
| Sample_platform_id | GPL201
| Sample_contact_name | Roland,,Grafström
| Sample_contact_laboratory | Experimental Cancer Research
| Sample_contact_department | Institute of Environmental Medicine
| Sample_contact_institute | Karolinska Institutet
| Sample_contact_address | Nobelsväg 13
| Sample_contact_city | 17177
| Sample_contact_zip/postal_code | Stockholm
| Sample_contact_country | Sweden
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190617/suppl/GSM190617.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190617/suppl/GSM190617.CHP.gz
| Sample_series_id | GSE7862
| Sample_data_row_count | 8793
| |
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GSM190618 | GPL201 |
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Normal buccal keratinocytes (NBK), sample B
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Buccal mucosa from healthy, non-smoking donor undergoing maxillofacial surgery
|
cell type: Normal oral keratinocytes in serum-free culture
experimental factor: Un-exposed control
|
Primary cell cultures were derived from tissue digestion with trypsin overnight at 4°C and the mixture was resuspended in a serum-free epithelial medium with high levels of amino acids (EMHA) and plated on dishes pre-coated with fibronectin and collagen.(Grafström R.C. Culture of Epithelial cells, 2nd ed, John Wiley and Sons Inc, NY, 2002). Cultures were transferred on regular tissue culture plastic at about 75 % confluence, and cells in passage 2 were used in the experiments.Total RNA was prepared from 3 x 10^6 cells using the RNeasy Mini Protocol (Qiagen GmbH, Hilden, Germany) from two separate experiments of NBK.
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Sample_geo_accession | GSM190618
| Sample_status | Public on Aug 21 2007
| Sample_submission_date | May 21 2007
| Sample_last_update_date | Jul 16 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | Karolinska University Hospital, Stockholm, Sweden
| Sample_growth_protocol_ch1 | Primary cell cultures were derived from tissue digestion with trypsin overnight at 4°C and the mixture was resuspended in a serum-free epithelial medium with high levels of amino acids (EMHA) and plated on dishes pre-coated with fibronectin and collagen.(Grafström R.C. Culture of Epithelial cells, 2nd ed, John Wiley and Sons Inc, NY, 2002). Cultures were transferred on regular tissue culture plastic at about 75 % confluence, and cells in passage 2 were used in the experiments.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | We used the RNeasy Mini Protocol (Qiagen GmbH, Hilden, Germany) according to the manufacturer's recommended protocols.
| Sample_label_ch1 | Affymetrix single-stage biotin
| Sample_label_protocol_ch1 | We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.
| Sample_hyb_protocol | We used the Affymetrix Hybridization Oven 640 and GeneChip® Fluidics Station 450 according to the manufacturer's recommended protocols.
| Sample_scan_protocol | We used the Affymetrix GeneChip® Scanner 3000 according to the manufacturer's recommended protocols.
| Sample_data_processing | The data was analyzed using Gene Chip Operating Software (Affymetrix). GCOS was also applied for target intensity scaling of each array to an identical value (100) and quantification of the signal log ratio.
| Sample_platform_id | GPL201
| Sample_contact_name | Roland,,Grafström
| Sample_contact_laboratory | Experimental Cancer Research
| Sample_contact_department | Institute of Environmental Medicine
| Sample_contact_institute | Karolinska Institutet
| Sample_contact_address | Nobelsväg 13
| Sample_contact_city | 17177
| Sample_contact_zip/postal_code | Stockholm
| Sample_contact_country | Sweden
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190618/suppl/GSM190618.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190618/suppl/GSM190618.CHP.gz
| Sample_series_id | GSE7862
| Sample_data_row_count | 8793
| |
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GSM190619 | GPL201 |
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SV40 T-antigen transfected buccal keratinocyte line (SVpgC2a), Sample A
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Derived by transfection of SV40 T-antigen to human buccal keratinocytes
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cell line: The SVpgC2a cell line is cultured in the same serum-free epithelial medium with high levels of amino acids (EMHA) as normal buccal keratinocytes (Kulkarni et al. Carcinogenesis, 16: 2515-2521, 1995 and Grafström R.C, Culture of Epithelial cells, 2nd ed, John Wiley and Sons Inc, NY, 2002).
experimental factor: Un-exposed control
|
The SVpgC2a cell line is cultured in the same serum-free epithelial medium with high levels of amino acids (EMHA) as normal buccal keratinocytes (Kulkarni et al. Carcinogenesis, 16: 2515-2521, 1995 and Grafström R.C, Culture of Epithelial cells, 2nd ed, John Wiley and Sons Inc, NY, 2002). Total RNA was prepared from 3 x 10^6 cells using the RNeasy Mini Protocol (Qiagen GmbH, Hilden, Germany) from two separate experiments of SVpgC2a in passages 64-72.
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Sample_geo_accession | GSM190619
| Sample_status | Public on Aug 21 2007
| Sample_submission_date | May 21 2007
| Sample_last_update_date | Jul 16 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_growth_protocol_ch1 | The SVpgC2a cell line is cultured in the same serum-free epithelial medium with high levels of amino acids (EMHA) as normal buccal keratinocytes (Kulkarni et al. Carcinogenesis, 16: 2515-2521, 1995 and Grafström R.C, Culture of Epithelial cells, 2nd ed, John Wiley and Sons Inc, NY, 2002). The cells are routinely grown to confluency before passage and when seeded at 4100 cells/cm2 they reach confluency after 5 days.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | We used the RNeasy Mini Protocol (Qiagen GmbH, Hilden, Germany) according to the manufacturer's recommended protocols.
| Sample_label_ch1 | Affymetrix single-stage biotin
| Sample_label_protocol_ch1 | We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.
| Sample_hyb_protocol | We used the Affymetrix Hybridization Oven 640 and GeneChip® Fluidics Station 450 according to the manufacturer's recommended protocols.
| Sample_scan_protocol | We used the Affymetrix GeneChip® Scanner 3000 according to the manufacturer's recommended protocols.
| Sample_data_processing | The data was analyzed using Gene Chip Operating Software (Affymetrix). GCOS was also applied for target intensity scaling of each array to an identical value (100) and quantification of the signal log ratio.
| Sample_platform_id | GPL201
| Sample_contact_name | Roland,,Grafström
| Sample_contact_laboratory | Experimental Cancer Research
| Sample_contact_department | Institute of Environmental Medicine
| Sample_contact_institute | Karolinska Institutet
| Sample_contact_address | Nobelsväg 13
| Sample_contact_city | 17177
| Sample_contact_zip/postal_code | Stockholm
| Sample_contact_country | Sweden
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190619/suppl/GSM190619.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190619/suppl/GSM190619.CHP.gz
| Sample_series_id | GSE7862
| Sample_data_row_count | 8793
| |
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GSM190620 | GPL201 |
|
SV40 T-antigen transfected buccal keratinocyte line (SVpgC2a), Sample B
|
Derived by transfection of SV40 T-antigen to human buccal keratinocytes
|
cell line: The SVpgC2a cell line is cultured in the same serum-free epithelial medium with high levels of amino acids (EMHA) as normal buccal keratinocytes (Kulkarni et al. Carcinogenesis, 16: 2515-2521, 1995 and Grafström R.C, Culture of Epithelial cells, 2nd ed, John Wiley and Sons Inc, NY, 2002).
experimental factor: Un-exposed control
|
The SVpgC2a cell line is cultured in the same serum-free epithelial medium with high levels of amino acids (EMHA) as normal buccal keratinocytes (Kulkarni et al. Carcinogenesis, 16: 2515-2521, 1995 and Grafström R.C, Culture of Epithelial cells, 2nd ed, John Wiley and Sons Inc, NY, 2002). Total RNA was prepared from 3 x 10^6 cells using the RNeasy Mini Protocol (Qiagen GmbH, Hilden, Germany) from two separate experiments of SVpgC2a in passages 64-72.
|
Sample_geo_accession | GSM190620
| Sample_status | Public on Aug 21 2007
| Sample_submission_date | May 21 2007
| Sample_last_update_date | Jul 16 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_growth_protocol_ch1 | The SVpgC2a cell line is cultured in the same serum-free epithelial medium with high levels of amino acids (EMHA) as normal buccal keratinocytes (Kulkarni et al. Carcinogenesis, 16: 2515-2521, 1995 and Grafström R.C, Culture of Epithelial cells, 2nd ed, John Wiley and Sons Inc, NY, 2002). The cells are routinely grown to confluency before passage and when seeded at 4100 cells/cm2 they reach confluency after 5 days.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | We used the RNeasy Mini Protocol (Qiagen GmbH, Hilden, Germany) according to the manufacturer's recommended protocols.
| Sample_label_ch1 | Affymetrix single-stage biotin
| Sample_label_protocol_ch1 | We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.
| Sample_hyb_protocol | We used the Affymetrix Hybridization Oven 640 and GeneChip® Fluidics Station 450 according to the manufacturer's recommended protocols.
| Sample_scan_protocol | We used the Affymetrix GeneChip® Scanner 3000 according to the manufacturer's recommended protocols.
| Sample_data_processing | The data was analyzed using Gene Chip Operating Software (Affymetrix). GCOS was also applied for target intensity scaling of each array to an identical value (100) and quantification of the signal log ratio.
| Sample_platform_id | GPL201
| Sample_contact_name | Roland,,Grafström
| Sample_contact_laboratory | Experimental Cancer Research
| Sample_contact_department | Institute of Environmental Medicine
| Sample_contact_institute | Karolinska Institutet
| Sample_contact_address | Nobelsväg 13
| Sample_contact_city | 17177
| Sample_contact_zip/postal_code | Stockholm
| Sample_contact_country | Sweden
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190620/suppl/GSM190620.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190620/suppl/GSM190620.CHP.gz
| Sample_series_id | GSE7862
| Sample_data_row_count | 8793
| |
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GSM190621 | GPL201 |
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Buccal carcinoma cell line (SqCC/Y1), Sample A
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Buccal carcinoma
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cell line: The SqCC/Y1 cells are cultured in the same serum-free epithelial medium with high levels of amino acids (EMHA) as normal buccal keratinocytes (Sundkvist, K et al. Cancer Commun, 3: 331-340, 1991 and Grafström R.C, Culture of Epithelial cells, 2nd ed, John Wiley and Sons Inc, NY, 2002).
experimental factor: Un-exposed control
|
The SqCC/Y1 cells are cultured in the same serum-free epithelial medium with high levels of amino acids (EMHA) as normal buccal keratinocytes (Sundkvist, K et al. Cancer Commun, 3: 331-340, 1991 and Grafström R.C, Culture of Epithelial cells, 2nd ed, John Wiley and Sons Inc, NY, 2002). Total RNA was prepared from 3 x 10^6 cells using the RNeasy Mini Protocol (Qiagen GmbH, Hilden, Germany) from two separate experiments of SqCC/Y1 in passages 125-129.
|
Sample_geo_accession | GSM190621
| Sample_status | Public on Aug 21 2007
| Sample_submission_date | May 21 2007
| Sample_last_update_date | Jul 16 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_growth_protocol_ch1 | The SqCC/Y1 cells are cultured in the same serum-free epithelial medium with high levels of amino acids (EMHA) as normal buccal keratinocytes (Sundkvist, K et al. Cancer Commun, 3: 331-340, 1991 and Grafström R.C, Culture of Epithelial cells, 2nd ed, John Wiley and Sons Inc, NY, 2002). The cells are routinely grown to between 80-90% confluency before passage. 90% confluency is reached after 5 days when seeded at 10000 cells/cm2.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | We used the RNeasy Mini Protocol (Qiagen GmbH, Hilden, Germany) according to the manufacturer's recommended protocols.
| Sample_label_ch1 | Affymetrix single-stage biotin
| Sample_label_protocol_ch1 | We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.
| Sample_hyb_protocol | We used the Affymetrix Hybridization Oven 640 and GeneChip® Fluidics Station 450 according to the manufacturer's recommended protocols.
| Sample_scan_protocol | We used the Affymetrix GeneChip® Scanner 3000 according to the manufacturer's recommended protocols.
| Sample_data_processing | The data was analyzed using Gene Chip Operating Software (Affymetrix). GCOS was also applied for target intensity scaling of each array to an identical value (100) and quantification of the signal log ratio.
| Sample_platform_id | GPL201
| Sample_contact_name | Roland,,Grafström
| Sample_contact_laboratory | Experimental Cancer Research
| Sample_contact_department | Institute of Environmental Medicine
| Sample_contact_institute | Karolinska Institutet
| Sample_contact_address | Nobelsväg 13
| Sample_contact_city | 17177
| Sample_contact_zip/postal_code | Stockholm
| Sample_contact_country | Sweden
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190621/suppl/GSM190621.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190621/suppl/GSM190621.CHP.gz
| Sample_series_id | GSE7862
| Sample_data_row_count | 8793
| |
|
GSM190622 | GPL201 |
|
Buccal carcinoma cell line (SqCC/Y1), Sample B
|
Buccal carcinoma
|
cell line: The SqCC/Y1 cells are cultured in the same serum-free epithelial medium with high levels of amino acids (EMHA) as normal buccal keratinocytes (Sundkvist, K et al. Cancer Commun, 3: 331-340, 1991 and Grafström R.C, Culture of Epithelial cells, 2nd ed, John Wiley and Sons Inc, NY, 2002).
experimental factor: Un-exposed control
|
The SqCC/Y1 cells are cultured in the same serum-free epithelial medium with high levels of amino acids (EMHA) as normal buccal keratinocytes (Sundkvist, K et al. Cancer Commun, 3: 331-340, 1991 and Grafström R.C, Culture of Epithelial cells, 2nd ed, John Wiley and Sons Inc, NY, 2002). Total RNA was prepared from 3 x 10^6 cells using the RNeasy Mini Protocol (Qiagen GmbH, Hilden, Germany) from two separate experiments of SqCC/Y1 in passages 125-129
|
Sample_geo_accession | GSM190622
| Sample_status | Public on Aug 21 2007
| Sample_submission_date | May 21 2007
| Sample_last_update_date | Jul 16 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_growth_protocol_ch1 | The SqCC/Y1 cells are cultured in the same serum-free epithelial medium with high levels of amino acids (EMHA) as normal buccal keratinocytes (Sundkvist, K et al. Cancer Commun, 3: 331-340, 1991 and Grafström R.C, Culture of Epithelial cells, 2nd ed, John Wiley and Sons Inc, NY, 2002). The cells are routinely grown to between 80-90% confluency before passage. 90% confluency is reached after 5 days when seeded at 10000 cells/cm2.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | We used the RNeasy Mini Protocol (Qiagen GmbH, Hilden, Germany) according to the manufacturer's recommended protocols.
| Sample_label_ch1 | Affymetrix single-stage biotin
| Sample_label_protocol_ch1 | We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.
| Sample_hyb_protocol | We used the Affymetrix Hybridization Oven 640 and GeneChip® Fluidics Station 450 according to the manufacturer's recommended protocols.
| Sample_scan_protocol | We used the Affymetrix GeneChip® Scanner 3000 according to the manufacturer's recommended protocols.
| Sample_data_processing | The data was analyzed using Gene Chip Operating Software (Affymetrix). GCOS was also applied for target intensity scaling of each array to an identical value (100) and quantification of the signal log ratio.
| Sample_platform_id | GPL201
| Sample_contact_name | Roland,,Grafström
| Sample_contact_laboratory | Experimental Cancer Research
| Sample_contact_department | Institute of Environmental Medicine
| Sample_contact_institute | Karolinska Institutet
| Sample_contact_address | Nobelsväg 13
| Sample_contact_city | 17177
| Sample_contact_zip/postal_code | Stockholm
| Sample_contact_country | Sweden
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190622/suppl/GSM190622.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190622/suppl/GSM190622.CHP.gz
| Sample_series_id | GSE7862
| Sample_data_row_count | 8793
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