Search results for the GEO ID: GSE16149  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM404696 | GPL570 |
|
Buccal Cell Smoker 11 replicate A
|
buccal mucosa cells from swab, from both cheeks of smokers or nonsmokers
|
smoking status: smoker
cell type: buccal mucosa cells
|
n/a
|
| Sample_geo_accession | GSM404696
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Buccal samples were taken using a sterile cytobrush plus with a 30 second brushing. Immediately after sampling, each cytobrush was placed in a 2 ml micro-centrifuge containing 1 ml RNAlater.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from buccal samples using the Rneasy Micro Kit with modification as given in Spivack et al. Cancer Res. 2004, 64:6805 and in Kupfer et al submitted.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 50 ng total RNA was both reverse transcribed and amplified using the Ovation RNA amplificztion System V2 (Nugen Technologies). This template material was fragmented and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.).
| | Sample_hyb_protocol | Arrays were hybridized for 18 hours at 45 deg C at 60 rpm in a GeneChip Hybridization Oven model 640 (Affymetric, Inc.). Fluidics protocol FS450_0004 was used with the GeneChip Fluidics Station model 450 to wash the arrays.
| | Sample_scan_protocol | Scanning was done on a GeneChip Laser Scanner model 3000 with system running GCOS version 1.4.
| | Sample_data_processing | GCOS (ver 1.4) report derived with TGT Value set at 100. Bioconductor package AffyQCReport and ProbeLevelModeling was used for quality assessment. Summarized and quantile normalized data was generated using the application at the Automated Microarray Pipeline (http://compbio.dfci.harvard.edu/amp/). Relative differential gene expression analysis comparing smokers to nonsmokers was performed with both SAM, Rank Product Analysis, unsupervised hierarchiacal clustering and T-test were performed using the packages available on the MultiExperiment Viewer, ver 4.3.01 with default settings.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Doris,,Kupfer
| | Sample_contact_email | doris.kupfer@faa.gov
| | Sample_contact_phone | 4059547512
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Aeromedical Research
| | Sample_contact_institute | FAA
| | Sample_contact_address | 6500 MacArthur Blvd
| | Sample_contact_city | Oklahoma City
| | Sample_contact_state | OK
| | Sample_contact_zip/postal_code | 73069
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404696/suppl/GSM404696.CEL.gz
| | Sample_series_id | GSE16149
| | Sample_data_row_count | 54675
| | |
|
GSM404697 | GPL570 |
|
Buccal Cell Smoker 11 replicate B
|
buccal mucosa cells from swab, from both cheeks of smokers or nonsmokers
|
smoking status: smoker
cell type: buccal mucosa cells
|
n/a
|
| Sample_geo_accession | GSM404697
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Buccal samples were taken using a sterile cytobrush plus with a 30 second brushing. Immediately after sampling, each cytobrush was placed in a 2 ml micro-centrifuge containing 1 ml RNAlater.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from buccal samples using the Rneasy Micro Kit with modification as given in Spivack et al. Cancer Res. 2004, 64:6805 and in Kupfer et al submitted.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 50 ng total RNA was both reverse transcribed and amplified using the Ovation RNA amplificztion System V2 (Nugen Technologies). This template material was fragmented and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.).
| | Sample_hyb_protocol | Arrays were hybridized for 18 hours at 45 deg C at 60 rpm in a GeneChip Hybridization Oven model 640 (Affymetric, Inc.). Fluidics protocol FS450_0004 was used with the GeneChip Fluidics Station model 450 to wash the arrays.
| | Sample_scan_protocol | Scanning was done on a GeneChip Laser Scanner model 3000 with system running GCOS version 1.4.
| | Sample_data_processing | GCOS (ver 1.4) report derived with TGT Value set at 100. Bioconductor package AffyQCReport and ProbeLevelModeling was used for quality assessment. Summarized and quantile normalized data was generated using the application at the Automated Microarray Pipeline (http://compbio.dfci.harvard.edu/amp/). Relative differential gene expression analysis comparing smokers to nonsmokers was performed with both SAM, Rank Product Analysis, unsupervised hierarchiacal clustering and T-test were performed using the packages available on the MultiExperiment Viewer, ver 4.3.01 with default settings.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Doris,,Kupfer
| | Sample_contact_email | doris.kupfer@faa.gov
| | Sample_contact_phone | 4059547512
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Aeromedical Research
| | Sample_contact_institute | FAA
| | Sample_contact_address | 6500 MacArthur Blvd
| | Sample_contact_city | Oklahoma City
| | Sample_contact_state | OK
| | Sample_contact_zip/postal_code | 73069
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404697/suppl/GSM404697.CEL.gz
| | Sample_series_id | GSE16149
| | Sample_data_row_count | 54675
| | |
|
GSM404698 | GPL570 |
|
Buccal Cell Non-smoker 12 replicate A
|
buccal mucosa cells from swab, from both cheeks of smokers or nonsmokers
|
smoking status: non-smoker
cell type: buccal mucosa cells
|
n/a
|
| Sample_geo_accession | GSM404698
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Buccal samples were taken using a sterile cytobrush plus with a 30 second brushing. Immediately after sampling, each cytobrush was placed in a 2 ml micro-centrifuge containing 1 ml RNAlater.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from buccal samples using the Rneasy Micro Kit with modification as given in Spivack et al. Cancer Res. 2004, 64:6805 and in Kupfer et al submitted.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 50 ng total RNA was both reverse transcribed and amplified using the Ovation RNA amplificztion System V2 (Nugen Technologies). This template material was fragmented and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.).
| | Sample_hyb_protocol | Arrays were hybridized for 18 hours at 45 deg C at 60 rpm in a GeneChip Hybridization Oven model 640 (Affymetric, Inc.). Fluidics protocol FS450_0004 was used with the GeneChip Fluidics Station model 450 to wash the arrays.
| | Sample_scan_protocol | Scanning was done on a GeneChip Laser Scanner model 3000 with system running GCOS version 1.4.
| | Sample_data_processing | GCOS (ver 1.4) report derived with TGT Value set at 100. Bioconductor package AffyQCReport and ProbeLevelModeling was used for quality assessment. Summarized and quantile normalized data was generated using the application at the Automated Microarray Pipeline (http://compbio.dfci.harvard.edu/amp/). Relative differential gene expression analysis comparing smokers to nonsmokers was performed with both SAM, Rank Product Analysis, unsupervised hierarchiacal clustering and T-test were performed using the packages available on the MultiExperiment Viewer, ver 4.3.01 with default settings.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Doris,,Kupfer
| | Sample_contact_email | doris.kupfer@faa.gov
| | Sample_contact_phone | 4059547512
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Aeromedical Research
| | Sample_contact_institute | FAA
| | Sample_contact_address | 6500 MacArthur Blvd
| | Sample_contact_city | Oklahoma City
| | Sample_contact_state | OK
| | Sample_contact_zip/postal_code | 73069
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404698/suppl/GSM404698.CEL.gz
| | Sample_series_id | GSE16149
| | Sample_data_row_count | 54675
| | |
|
GSM404699 | GPL570 |
|
Buccal Cell Non-smoker 12 replicate B
|
buccal mucosa cells from swab, from both cheeks of smokers or nonsmokers
|
smoking status: non-smoker
cell type: buccal mucosa cells
|
n/a
|
| Sample_geo_accession | GSM404699
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Buccal samples were taken using a sterile cytobrush plus with a 30 second brushing. Immediately after sampling, each cytobrush was placed in a 2 ml micro-centrifuge containing 1 ml RNAlater.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from buccal samples using the Rneasy Micro Kit with modification as given in Spivack et al. Cancer Res. 2004, 64:6805 and in Kupfer et al submitted.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 50 ng total RNA was both reverse transcribed and amplified using the Ovation RNA amplificztion System V2 (Nugen Technologies). This template material was fragmented and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.).
| | Sample_hyb_protocol | Arrays were hybridized for 18 hours at 45 deg C at 60 rpm in a GeneChip Hybridization Oven model 640 (Affymetric, Inc.). Fluidics protocol FS450_0004 was used with the GeneChip Fluidics Station model 450 to wash the arrays.
| | Sample_scan_protocol | Scanning was done on a GeneChip Laser Scanner model 3000 with system running GCOS version 1.4.
| | Sample_data_processing | GCOS (ver 1.4) report derived with TGT Value set at 100. Bioconductor package AffyQCReport and ProbeLevelModeling was used for quality assessment. Summarized and quantile normalized data was generated using the application at the Automated Microarray Pipeline (http://compbio.dfci.harvard.edu/amp/). Relative differential gene expression analysis comparing smokers to nonsmokers was performed with both SAM, Rank Product Analysis, unsupervised hierarchiacal clustering and T-test were performed using the packages available on the MultiExperiment Viewer, ver 4.3.01 with default settings.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Doris,,Kupfer
| | Sample_contact_email | doris.kupfer@faa.gov
| | Sample_contact_phone | 4059547512
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Aeromedical Research
| | Sample_contact_institute | FAA
| | Sample_contact_address | 6500 MacArthur Blvd
| | Sample_contact_city | Oklahoma City
| | Sample_contact_state | OK
| | Sample_contact_zip/postal_code | 73069
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404699/suppl/GSM404699.CEL.gz
| | Sample_series_id | GSE16149
| | Sample_data_row_count | 54675
| | |
|
GSM404700 | GPL570 |
|
Buccal Cell Non-smoker 21 replicate A
|
buccal mucosa cells from swab, from both cheeks of smokers or nonsmokers
|
smoking status: non-smoker
cell type: buccal mucosa cells
|
n/a
|
| Sample_geo_accession | GSM404700
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Buccal samples were taken using a sterile cytobrush plus with a 30 second brushing. Immediately after sampling, each cytobrush was placed in a 2 ml micro-centrifuge containing 1 ml RNAlater.
| | Sample_growth_protocol_ch1 | NA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from buccal samples using the Rneasy Micro Kit with modification as given in Spivack et al. Cancer Res. 2004, 64:6805 and in Kupfer et al submitted.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 20 ng total RNA was both reverse transcribed and amplified using the Ovation RNA amplificztion System V2 (Nugen Technologies). This template material was fragmented and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.).
| | Sample_hyb_protocol | Arrays were hybridized for 18 hours at 45 deg C at 60 rpm in a GeneChip Hybridization Oven model 640 (Affymetric, Inc.). Fluidics protocol FS450_0004 was used with the GeneChip Fluidics Station model 450 to wash the arrays.
| | Sample_scan_protocol | Scanning was done on a GeneChip Laser Scanner model 3000 with system running GCOS version 1.4.
| | Sample_data_processing | GCOS (ver 1.4) report derived with TGT Value set at 100. Bioconductor package AffyQCReport and ProbeLevelModeling was used for quality assessment. Summarized and quantile normalized data was generated using the application at the Automated Microarray Pipeline (http://compbio.dfci.harvard.edu/amp/). Relative differential gene expression analysis comparing smokers to nonsmokers was performed with SAM, Rank Product Analysis, unsupervised hierarchiacal clustering and T-test using the packages available on the MultiExperiment Viewer, ver 4.3.01 with default settings.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Doris,,Kupfer
| | Sample_contact_email | doris.kupfer@faa.gov
| | Sample_contact_phone | 4059547512
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Aeromedical Research
| | Sample_contact_institute | FAA
| | Sample_contact_address | 6500 MacArthur Blvd
| | Sample_contact_city | Oklahoma City
| | Sample_contact_state | OK
| | Sample_contact_zip/postal_code | 73069
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404700/suppl/GSM404700.CEL.gz
| | Sample_series_id | GSE16149
| | Sample_data_row_count | 54675
| | |
|
GSM404701 | GPL570 |
|
Buccal Cell Non-smoker 21 replicate B
|
buccal mucosa cells from swab, from both cheeks of smokers or nonsmokers
|
smoking status: non-smoker
cell type: buccal mucosa cells
|
n/a
|
| Sample_geo_accession | GSM404701
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Buccal samples were taken using a sterile cytobrush plus with a 30 second brushing. Immediately after sampling, each cytobrush was placed in a 2 ml micro-centrifuge containing 1 ml RNAlater.
| | Sample_growth_protocol_ch1 | NA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from buccal samples using the Rneasy Micro Kit with modification as given in Spivack et al. Cancer Res. 2004, 64:6805 and in Kupfer et al submitted.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 20 ng total RNA was both reverse transcribed and amplified using the Ovation RNA amplificztion System V2 (Nugen Technologies). This template material was fragmented and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.).
| | Sample_hyb_protocol | Arrays were hybridized for 18 hours at 45 deg C at 60 rpm in a GeneChip Hybridization Oven model 640 (Affymetric, Inc.). Fluidics protocol FS450_0004 was used with the GeneChip Fluidics Station model 450 to wash the arrays.
| | Sample_scan_protocol | Scanning was done on a GeneChip Laser Scanner model 3000 with system running GCOS version 1.4.
| | Sample_data_processing | GCOS (ver 1.4) report derived with TGT Value set at 100. Bioconductor package AffyQCReport and ProbeLevelModeling was used for quality assessment. Summarized and quantile normalized data was generated using the application at the Automated Microarray Pipeline (http://compbio.dfci.harvard.edu/amp/). Relative differential gene expression analysis comparing smokers to nonsmokers was performed with SAM, Rank Product Analysis, unsupervised hierarchiacal clustering and T-test using the packages available on the MultiExperiment Viewer, ver 4.3.01 with default settings.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Doris,,Kupfer
| | Sample_contact_email | doris.kupfer@faa.gov
| | Sample_contact_phone | 4059547512
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Aeromedical Research
| | Sample_contact_institute | FAA
| | Sample_contact_address | 6500 MacArthur Blvd
| | Sample_contact_city | Oklahoma City
| | Sample_contact_state | OK
| | Sample_contact_zip/postal_code | 73069
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404701/suppl/GSM404701.CEL.gz
| | Sample_series_id | GSE16149
| | Sample_data_row_count | 54675
| | |
|
GSM404702 | GPL570 |
|
Buccal Cell Non-smoker 22 replicate A
|
buccal mucosa cells from swab, from both cheeks of smokers or nonsmokers
|
smoking status: non-smoker
cell type: buccal mucosa cells
|
n/a
|
| Sample_geo_accession | GSM404702
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Buccal samples were taken using a sterile cytobrush plus with a 30 second brushing. Immediately after sampling, each cytobrush was placed in a 2 ml micro-centrifuge containing 1 ml RNAlater.
| | Sample_growth_protocol_ch1 | NA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from buccal samples using the Rneasy Micro Kit with modification as given in Spivack et al. Cancer Res. 2004, 64:6805 and in Kupfer et al submitted.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 20 ng total RNA was both reverse transcribed and amplified using the Ovation RNA amplificztion System V2 (Nugen Technologies). This template material was fragmented and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.).
| | Sample_hyb_protocol | Arrays were hybridized for 18 hours at 45 deg C at 60 rpm in a GeneChip Hybridization Oven model 640 (Affymetric, Inc.). Fluidics protocol FS450_0004 was used with the GeneChip Fluidics Station model 450 to wash the arrays.
| | Sample_scan_protocol | Scanning was done on a GeneChip Laser Scanner model 3000 with system running GCOS version 1.4.
| | Sample_data_processing | GCOS (ver 1.4) report derived with TGT Value set at 100. Bioconductor package AffyQCReport and ProbeLevelModeling was used for quality assessment. Summarized and quantile normalized data was generated using the application at the Automated Microarray Pipeline (http://compbio.dfci.harvard.edu/amp/). Relative differential gene expression analysis comparing smokers to nonsmokers was performed with SAM, Rank Product Analysis, unsupervised hierarchiacal clustering and T-test using the packages available on the MultiExperiment Viewer, ver 4.3.01 with default settings.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Doris,,Kupfer
| | Sample_contact_email | doris.kupfer@faa.gov
| | Sample_contact_phone | 4059547512
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Aeromedical Research
| | Sample_contact_institute | FAA
| | Sample_contact_address | 6500 MacArthur Blvd
| | Sample_contact_city | Oklahoma City
| | Sample_contact_state | OK
| | Sample_contact_zip/postal_code | 73069
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404702/suppl/GSM404702.CEL.gz
| | Sample_series_id | GSE16149
| | Sample_data_row_count | 54675
| | |
|
GSM404703 | GPL570 |
|
Buccal Cell Non-smoker 22 replicate B
|
buccal mucosa cells from swab, from both cheeks of smokers or nonsmokers
|
smoking status: non-smoker
cell type: buccal mucosa cells
|
n/a
|
| Sample_geo_accession | GSM404703
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Buccal samples were taken using a sterile cytobrush plus with a 30 second brushing. Immediately after sampling, each cytobrush was placed in a 2 ml micro-centrifuge containing 1 ml RNAlater.
| | Sample_growth_protocol_ch1 | NA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from buccal samples using the Rneasy Micro Kit with modification as given in Spivack et al. Cancer Res. 2004, 64:6805 and in Kupfer et al submitted.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 20 ng total RNA was both reverse transcribed and amplified using the Ovation RNA amplificztion System V2 (Nugen Technologies). This template material was fragmented and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.).
| | Sample_hyb_protocol | Arrays were hybridized for 18 hours at 45 deg C at 60 rpm in a GeneChip Hybridization Oven model 640 (Affymetric, Inc.). Fluidics protocol FS450_0004 was used with the GeneChip Fluidics Station model 450 to wash the arrays.
| | Sample_scan_protocol | Scanning was done on a GeneChip Laser Scanner model 3000 with system running GCOS version 1.4.
| | Sample_data_processing | GCOS (ver 1.4) report derived with TGT Value set at 100. Bioconductor package AffyQCReport and ProbeLevelModeling was used for quality assessment. Summarized and quantile normalized data was generated using the application at the Automated Microarray Pipeline (http://compbio.dfci.harvard.edu/amp/). Relative differential gene expression analysis comparing smokers to nonsmokers was performed with SAM, Rank Product Analysis, unsupervised hierarchiacal clustering and T-test using the packages available on the MultiExperiment Viewer, ver 4.3.01 with default settings.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Doris,,Kupfer
| | Sample_contact_email | doris.kupfer@faa.gov
| | Sample_contact_phone | 4059547512
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Aeromedical Research
| | Sample_contact_institute | FAA
| | Sample_contact_address | 6500 MacArthur Blvd
| | Sample_contact_city | Oklahoma City
| | Sample_contact_state | OK
| | Sample_contact_zip/postal_code | 73069
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404703/suppl/GSM404703.CEL.gz
| | Sample_series_id | GSE16149
| | Sample_data_row_count | 54675
| | |
|
GSM404704 | GPL570 |
|
Buccal Cell Non-smoker 23 replicate B
|
buccal mucosa cells from swab, from both cheeks of smokers or nonsmokers
|
smoking status: non-smoker
cell type: buccal mucosa cells
|
n/a
|
| Sample_geo_accession | GSM404704
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Buccal samples were taken using a sterile cytobrush plus with a 30 second brushing. Immediately after sampling, each cytobrush was placed in a 2 ml micro-centrifuge containing 1 ml RNAlater.
| | Sample_growth_protocol_ch1 | NA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from buccal samples using the Rneasy Micro Kit with modification as given in Spivack et al. Cancer Res. 2004, 64:6805 and in Kupfer et al submitted.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 20 ng total RNA was both reverse transcribed and amplified using the Ovation RNA amplificztion System V2 (Nugen Technologies). This template material was fragmented and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.).
| | Sample_hyb_protocol | Arrays were hybridized for 18 hours at 45 deg C at 60 rpm in a GeneChip Hybridization Oven model 640 (Affymetric, Inc.). Fluidics protocol FS450_0004 was used with the GeneChip Fluidics Station model 450 to wash the arrays.
| | Sample_scan_protocol | Scanning was done on a GeneChip Laser Scanner model 3000 with system running GCOS version 1.4.
| | Sample_data_processing | GCOS (ver 1.4) report derived with TGT Value set at 100. Bioconductor package AffyQCReport and ProbeLevelModeling was used for quality assessment. Summarized and quantile normalized data was generated using the application at the Automated Microarray Pipeline (http://compbio.dfci.harvard.edu/amp/). Relative differential gene expression analysis comparing smokers to nonsmokers was performed with SAM, Rank Product Analysis, unsupervised hierarchiacal clustering and T-test using the packages available on the MultiExperiment Viewer, ver 4.3.01 with default settings.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Doris,,Kupfer
| | Sample_contact_email | doris.kupfer@faa.gov
| | Sample_contact_phone | 4059547512
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Aeromedical Research
| | Sample_contact_institute | FAA
| | Sample_contact_address | 6500 MacArthur Blvd
| | Sample_contact_city | Oklahoma City
| | Sample_contact_state | OK
| | Sample_contact_zip/postal_code | 73069
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404704/suppl/GSM404704.CEL.gz
| | Sample_series_id | GSE16149
| | Sample_data_row_count | 54675
| | |
|
GSM404705 | GPL570 |
|
Buccal Cell Non-smoker 24 replicate A
|
buccal mucosa cells from swab, from both cheeks of smokers or nonsmokers
|
smoking status: non-smoker
cell type: buccal mucosa cells
|
n/a
|
| Sample_geo_accession | GSM404705
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Buccal samples were taken using a sterile cytobrush plus with a 30 second brushing. Immediately after sampling, each cytobrush was placed in a 2 ml micro-centrifuge containing 1 ml RNAlater.
| | Sample_growth_protocol_ch1 | NA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from buccal samples using the Rneasy Micro Kit with modification as given in Spivack et al. Cancer Res. 2004, 64:6805 and in Kupfer et al submitted.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 20 ng total RNA was both reverse transcribed and amplified using the Ovation RNA amplificztion System V2 (Nugen Technologies). This template material was fragmented and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.).
| | Sample_hyb_protocol | Arrays were hybridized for 18 hours at 45 deg C at 60 rpm in a GeneChip Hybridization Oven model 640 (Affymetric, Inc.). Fluidics protocol FS450_0004 was used with the GeneChip Fluidics Station model 450 to wash the arrays.
| | Sample_scan_protocol | Scanning was done on a GeneChip Laser Scanner model 3000 with system running GCOS version 1.4.
| | Sample_data_processing | GCOS (ver 1.4) report derived with TGT Value set at 100. Bioconductor package AffyQCReport and ProbeLevelModeling was used for quality assessment. Summarized and quantile normalized data was generated using the application at the Automated Microarray Pipeline (http://compbio.dfci.harvard.edu/amp/). Relative differential gene expression analysis comparing smokers to nonsmokers was performed with SAM, Rank Product Analysis, unsupervised hierarchiacal clustering and T-test using the packages available on the MultiExperiment Viewer, ver 4.3.01 with default settings.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Doris,,Kupfer
| | Sample_contact_email | doris.kupfer@faa.gov
| | Sample_contact_phone | 4059547512
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Aeromedical Research
| | Sample_contact_institute | FAA
| | Sample_contact_address | 6500 MacArthur Blvd
| | Sample_contact_city | Oklahoma City
| | Sample_contact_state | OK
| | Sample_contact_zip/postal_code | 73069
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404705/suppl/GSM404705.CEL.gz
| | Sample_series_id | GSE16149
| | Sample_data_row_count | 54675
| | |
|
GSM404706 | GPL570 |
|
Buccal Cell Non-smoker 24 replicate B
|
buccal mucosa cells from swab, from both cheeks of smokers or nonsmokers
|
smoking status: non-smoker
cell type: buccal mucosa cells
|
n/a
|
| Sample_geo_accession | GSM404706
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Buccal samples were taken using a sterile cytobrush plus with a 30 second brushing. Immediately after sampling, each cytobrush was placed in a 2 ml micro-centrifuge containing 1 ml RNAlater.
| | Sample_growth_protocol_ch1 | NA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from buccal samples using the Rneasy Micro Kit with modification as given in Spivack et al. Cancer Res. 2004, 64:6805 and in Kupfer et al submitted.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 20 ng total RNA was both reverse transcribed and amplified using the Ovation RNA amplificztion System V2 (Nugen Technologies). This template material was fragmented and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.).
| | Sample_hyb_protocol | Arrays were hybridized for 18 hours at 45 deg C at 60 rpm in a GeneChip Hybridization Oven model 640 (Affymetric, Inc.). Fluidics protocol FS450_0004 was used with the GeneChip Fluidics Station model 450 to wash the arrays.
| | Sample_scan_protocol | Scanning was done on a GeneChip Laser Scanner model 3000 with system running GCOS version 1.4.
| | Sample_data_processing | GCOS (ver 1.4) report derived with TGT Value set at 100. Bioconductor package AffyQCReport and ProbeLevelModeling was used for quality assessment. Summarized and quantile normalized data was generated using the application at the Automated Microarray Pipeline (http://compbio.dfci.harvard.edu/amp/). Relative differential gene expression analysis comparing smokers to nonsmokers was performed with SAM, Rank Product Analysis, unsupervised hierarchiacal clustering and T-test using the packages available on the MultiExperiment Viewer, ver 4.3.01 with default settings.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Doris,,Kupfer
| | Sample_contact_email | doris.kupfer@faa.gov
| | Sample_contact_phone | 4059547512
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Aeromedical Research
| | Sample_contact_institute | FAA
| | Sample_contact_address | 6500 MacArthur Blvd
| | Sample_contact_city | Oklahoma City
| | Sample_contact_state | OK
| | Sample_contact_zip/postal_code | 73069
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404706/suppl/GSM404706.CEL.gz
| | Sample_series_id | GSE16149
| | Sample_data_row_count | 54675
| | |
|
GSM404707 | GPL570 |
|
Buccal Cell Smoker 25 replicate B
|
buccal mucosa cells from swab, from both cheeks of smokers or nonsmokers
|
smoking status: smoker
cell type: buccal mucosa cells
|
n/a
|
| Sample_geo_accession | GSM404707
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Buccal samples were taken using a sterile cytobrush plus with a 30 second brushing. Immediately after sampling, each cytobrush was placed in a 2 ml micro-centrifuge containing 1 ml RNAlater.
| | Sample_growth_protocol_ch1 | NA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from buccal samples using the Rneasy Micro Kit with modification as given in Spivack et al. Cancer Res. 2004, 64:6805 and in Kupfer et al submitted.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 20 ng total RNA was both reverse transcribed and amplified using the Ovation RNA amplificztion System V2 (Nugen Technologies). This template material was fragmented and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.).
| | Sample_hyb_protocol | Arrays were hybridized for 18 hours at 45 deg C at 60 rpm in a GeneChip Hybridization Oven model 640 (Affymetric, Inc.). Fluidics protocol FS450_0004 was used with the GeneChip Fluidics Station model 450 to wash the arrays.
| | Sample_scan_protocol | Scanning was done on a GeneChip Laser Scanner model 3000 with system running GCOS version 1.4.
| | Sample_data_processing | GCOS (ver 1.4) report derived with TGT Value set at 100. Bioconductor package AffyQCReport and ProbeLevelModeling was used for quality assessment. Summarized and quantile normalized data was generated using the application at the Automated Microarray Pipeline (http://compbio.dfci.harvard.edu/amp/). Relative differential gene expression analysis comparing smokers to nonsmokers was performed with SAM, Rank Product Analysis, unsupervised hierarchiacal clustering and T-test using the packages available on the MultiExperiment Viewer, ver 4.3.01 with default settings.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Doris,,Kupfer
| | Sample_contact_email | doris.kupfer@faa.gov
| | Sample_contact_phone | 4059547512
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Aeromedical Research
| | Sample_contact_institute | FAA
| | Sample_contact_address | 6500 MacArthur Blvd
| | Sample_contact_city | Oklahoma City
| | Sample_contact_state | OK
| | Sample_contact_zip/postal_code | 73069
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404707/suppl/GSM404707.CEL.gz
| | Sample_series_id | GSE16149
| | Sample_data_row_count | 54675
| | |
|
GSM404708 | GPL570 |
|
Buccal Cell Smoker 26 replicate A
|
buccal mucosa cells from swab, from both cheeks of smokers or nonsmokers
|
smoking status: smoker
cell type: buccal mucosa cells
|
n/a
|
| Sample_geo_accession | GSM404708
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Buccal samples were taken using a sterile cytobrush plus with a 30 second brushing. Immediately after sampling, each cytobrush was placed in a 2 ml micro-centrifuge containing 1 ml RNAlater.
| | Sample_growth_protocol_ch1 | NA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from buccal samples using the Rneasy Micro Kit with modification as given in Spivack et al. Cancer Res. 2004, 64:6805 and in Kupfer et al submitted.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 20 ng total RNA was both reverse transcribed and amplified using the Ovation RNA amplificztion System V2 (Nugen Technologies). This template material was fragmented and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.).
| | Sample_hyb_protocol | Arrays were hybridized for 18 hours at 45 deg C at 60 rpm in a GeneChip Hybridization Oven model 640 (Affymetric, Inc.). Fluidics protocol FS450_0004 was used with the GeneChip Fluidics Station model 450 to wash the arrays.
| | Sample_scan_protocol | Scanning was done on a GeneChip Laser Scanner model 3000 with system running GCOS version 1.4.
| | Sample_data_processing | GCOS (ver 1.4) report derived with TGT Value set at 100. Bioconductor package AffyQCReport and ProbeLevelModeling was used for quality assessment. Summarized and quantile normalized data was generated using the application at the Automated Microarray Pipeline (http://compbio.dfci.harvard.edu/amp/). Relative differential gene expression analysis comparing smokers to nonsmokers was performed with SAM, Rank Product Analysis, unsupervised hierarchiacal clustering and T-test using the packages available on the MultiExperiment Viewer, ver 4.3.01 with default settings.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Doris,,Kupfer
| | Sample_contact_email | doris.kupfer@faa.gov
| | Sample_contact_phone | 4059547512
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Aeromedical Research
| | Sample_contact_institute | FAA
| | Sample_contact_address | 6500 MacArthur Blvd
| | Sample_contact_city | Oklahoma City
| | Sample_contact_state | OK
| | Sample_contact_zip/postal_code | 73069
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404708/suppl/GSM404708.CEL.gz
| | Sample_series_id | GSE16149
| | Sample_data_row_count | 54675
| | |
|
GSM404709 | GPL570 |
|
Buccal Cell Smoker 26 replicate B
|
buccal mucosa cells from swab, from both cheeks of smokers or nonsmokers
|
smoking status: smoker
cell type: buccal mucosa cells
|
n/a
|
| Sample_geo_accession | GSM404709
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Buccal samples were taken using a sterile cytobrush plus with a 30 second brushing. Immediately after sampling, each cytobrush was placed in a 2 ml micro-centrifuge containing 1 ml RNAlater.
| | Sample_growth_protocol_ch1 | NA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from buccal samples using the Rneasy Micro Kit with modification as given in Spivack et al. Cancer Res. 2004, 64:6805 and in Kupfer et al submitted.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 20 ng total RNA was both reverse transcribed and amplified using the Ovation RNA amplificztion System V2 (Nugen Technologies). This template material was fragmented and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.).
| | Sample_hyb_protocol | Arrays were hybridized for 18 hours at 45 deg C at 60 rpm in a GeneChip Hybridization Oven model 640 (Affymetric, Inc.). Fluidics protocol FS450_0004 was used with the GeneChip Fluidics Station model 450 to wash the arrays.
| | Sample_scan_protocol | Scanning was done on a GeneChip Laser Scanner model 3000 with system running GCOS version 1.4.
| | Sample_data_processing | GCOS (ver 1.4) report derived with TGT Value set at 100. Bioconductor package AffyQCReport and ProbeLevelModeling was used for quality assessment. Summarized and quantile normalized data was generated using the application at the Automated Microarray Pipeline (http://compbio.dfci.harvard.edu/amp/). Relative differential gene expression analysis comparing smokers to nonsmokers was performed with SAM, Rank Product Analysis, unsupervised hierarchiacal clustering and T-test using the packages available on the MultiExperiment Viewer, ver 4.3.01 with default settings.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Doris,,Kupfer
| | Sample_contact_email | doris.kupfer@faa.gov
| | Sample_contact_phone | 4059547512
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Aeromedical Research
| | Sample_contact_institute | FAA
| | Sample_contact_address | 6500 MacArthur Blvd
| | Sample_contact_city | Oklahoma City
| | Sample_contact_state | OK
| | Sample_contact_zip/postal_code | 73069
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404709/suppl/GSM404709.CEL.gz
| | Sample_series_id | GSE16149
| | Sample_data_row_count | 54675
| | |
|
GSM404710 | GPL570 |
|
Buccal Cell Smoker 27 replicate A
|
buccal mucosa cells from swab, from both cheeks of smokers or nonsmokers
|
smoking status: smoker
cell type: buccal mucosa cells
|
n/a
|
| Sample_geo_accession | GSM404710
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Buccal samples were taken using a sterile cytobrush plus with a 30 second brushing. Immediately after sampling, each cytobrush was placed in a 2 ml micro-centrifuge containing 1 ml RNAlater.
| | Sample_growth_protocol_ch1 | NA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from buccal samples using the Rneasy Micro Kit with modification as given in Spivack et al. Cancer Res. 2004, 64:6805 and in Kupfer et al submitted.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 20 ng total RNA was both reverse transcribed and amplified using the Ovation RNA amplificztion System V2 (Nugen Technologies). This template material was fragmented and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.).
| | Sample_hyb_protocol | Arrays were hybridized for 18 hours at 45 deg C at 60 rpm in a GeneChip Hybridization Oven model 640 (Affymetric, Inc.). Fluidics protocol FS450_0004 was used with the GeneChip Fluidics Station model 450 to wash the arrays.
| | Sample_scan_protocol | Scanning was done on a GeneChip Laser Scanner model 3000 with system running GCOS version 1.4.
| | Sample_data_processing | GCOS (ver 1.4) report derived with TGT Value set at 100. Bioconductor package AffyQCReport and ProbeLevelModeling was used for quality assessment. Summarized and quantile normalized data was generated using the application at the Automated Microarray Pipeline (http://compbio.dfci.harvard.edu/amp/). Relative differential gene expression analysis comparing smokers to nonsmokers was performed with SAM, Rank Product Analysis, unsupervised hierarchiacal clustering and T-test using the packages available on the MultiExperiment Viewer, ver 4.3.01 with default settings.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Doris,,Kupfer
| | Sample_contact_email | doris.kupfer@faa.gov
| | Sample_contact_phone | 4059547512
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Aeromedical Research
| | Sample_contact_institute | FAA
| | Sample_contact_address | 6500 MacArthur Blvd
| | Sample_contact_city | Oklahoma City
| | Sample_contact_state | OK
| | Sample_contact_zip/postal_code | 73069
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404710/suppl/GSM404710.CEL.gz
| | Sample_series_id | GSE16149
| | Sample_data_row_count | 54675
| | |
|
GSM404711 | GPL570 |
|
Buccal Cell Smoker 27 replicate B
|
buccal mucosa cells from swab, from both cheeks of smokers or nonsmokers
|
smoking status: smoker
cell type: buccal mucosa cells
|
n/a
|
| Sample_geo_accession | GSM404711
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Buccal samples were taken using a sterile cytobrush plus with a 30 second brushing. Immediately after sampling, each cytobrush was placed in a 2 ml micro-centrifuge containing 1 ml RNAlater.
| | Sample_growth_protocol_ch1 | NA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from buccal samples using the Rneasy Micro Kit with modification as given in Spivack et al. Cancer Res. 2004, 64:6805 and in Kupfer et al submitted.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 20 ng total RNA was both reverse transcribed and amplified using the Ovation RNA amplificztion System V2 (Nugen Technologies). This template material was fragmented and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.).
| | Sample_hyb_protocol | Arrays were hybridized for 18 hours at 45 deg C at 60 rpm in a GeneChip Hybridization Oven model 640 (Affymetric, Inc.). Fluidics protocol FS450_0004 was used with the GeneChip Fluidics Station model 450 to wash the arrays.
| | Sample_scan_protocol | Scanning was done on a GeneChip Laser Scanner model 3000 with system running GCOS version 1.4.
| | Sample_data_processing | GCOS (ver 1.4) report derived with TGT Value set at 100. Bioconductor package AffyQCReport and ProbeLevelModeling was used for quality assessment. Summarized and quantile normalized data was generated using the application at the Automated Microarray Pipeline (http://compbio.dfci.harvard.edu/amp/). Relative differential gene expression analysis comparing smokers to nonsmokers was performed with SAM, Rank Product Analysis, unsupervised hierarchiacal clustering and T-test using the packages available on the MultiExperiment Viewer, ver 4.3.01 with default settings.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Doris,,Kupfer
| | Sample_contact_email | doris.kupfer@faa.gov
| | Sample_contact_phone | 4059547512
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Aeromedical Research
| | Sample_contact_institute | FAA
| | Sample_contact_address | 6500 MacArthur Blvd
| | Sample_contact_city | Oklahoma City
| | Sample_contact_state | OK
| | Sample_contact_zip/postal_code | 73069
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404711/suppl/GSM404711.CEL.gz
| | Sample_series_id | GSE16149
| | Sample_data_row_count | 54675
| | |
|
GSM404712 | GPL570 |
|
Buccal Cell Smoker 28 replicate A
|
buccal mucosa cells from swab, from both cheeks of smokers or nonsmokers
|
smoking status: smoker
cell type: buccal mucosa cells
|
n/a
|
| Sample_geo_accession | GSM404712
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Buccal samples were taken using a sterile cytobrush plus with a 30 second brushing. Immediately after sampling, each cytobrush was placed in a 2 ml micro-centrifuge containing 1 ml RNAlater.
| | Sample_growth_protocol_ch1 | NA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from buccal samples using the Rneasy Micro Kit with modification as given in Spivack et al. Cancer Res. 2004, 64:6805 and in Kupfer et al submitted.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 20 ng total RNA was both reverse transcribed and amplified using the Ovation RNA amplificztion System V2 (Nugen Technologies). This template material was fragmented and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.).
| | Sample_hyb_protocol | Arrays were hybridized for 18 hours at 45 deg C at 60 rpm in a GeneChip Hybridization Oven model 640 (Affymetric, Inc.). Fluidics protocol FS450_0004 was used with the GeneChip Fluidics Station model 450 to wash the arrays.
| | Sample_scan_protocol | Scanning was done on a GeneChip Laser Scanner model 3000 with system running GCOS version 1.4.
| | Sample_data_processing | GCOS (ver 1.4) report derived with TGT Value set at 100. Bioconductor package AffyQCReport and ProbeLevelModeling was used for quality assessment. Summarized and quantile normalized data was generated using the application at the Automated Microarray Pipeline (http://compbio.dfci.harvard.edu/amp/). Relative differential gene expression analysis comparing smokers to nonsmokers was performed with SAM, Rank Product Analysis, unsupervised hierarchiacal clustering and T-test using the packages available on the MultiExperiment Viewer, ver 4.3.01 with default settings.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Doris,,Kupfer
| | Sample_contact_email | doris.kupfer@faa.gov
| | Sample_contact_phone | 4059547512
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Aeromedical Research
| | Sample_contact_institute | FAA
| | Sample_contact_address | 6500 MacArthur Blvd
| | Sample_contact_city | Oklahoma City
| | Sample_contact_state | OK
| | Sample_contact_zip/postal_code | 73069
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404712/suppl/GSM404712.CEL.gz
| | Sample_series_id | GSE16149
| | Sample_data_row_count | 54675
| | |
|
GSM404713 | GPL570 |
|
Buccal Cell Smoker 28 replicate B
|
buccal mucosa cells from swab, from both cheeks of smokers or nonsmokers
|
smoking status: smoker
cell type: buccal mucosa cells
|
n/a
|
| Sample_geo_accession | GSM404713
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Buccal samples were taken using a sterile cytobrush plus with a 30 second brushing. Immediately after sampling, each cytobrush was placed in a 2 ml micro-centrifuge containing 1 ml RNAlater.
| | Sample_growth_protocol_ch1 | NA
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from buccal samples using the Rneasy Micro Kit with modification as given in Spivack et al. Cancer Res. 2004, 64:6805 and in Kupfer et al submitted.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 20 ng total RNA was both reverse transcribed and amplified using the Ovation RNA amplificztion System V2 (Nugen Technologies). This template material was fragmented and biotin labeled using the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.).
| | Sample_hyb_protocol | Arrays were hybridized for 18 hours at 45 deg C at 60 rpm in a GeneChip Hybridization Oven model 640 (Affymetric, Inc.). Fluidics protocol FS450_0004 was used with the GeneChip Fluidics Station model 450 to wash the arrays.
| | Sample_scan_protocol | Scanning was done on a GeneChip Laser Scanner model 3000 with system running GCOS version 1.4.
| | Sample_data_processing | GCOS (ver 1.4) report derived with TGT Value set at 100. Bioconductor package AffyQCReport and ProbeLevelModeling was used for quality assessment. Summarized and quantile normalized data was generated using the application at the Automated Microarray Pipeline (http://compbio.dfci.harvard.edu/amp/). Relative differential gene expression analysis comparing smokers to nonsmokers was performed with SAM, Rank Product Analysis, unsupervised hierarchiacal clustering and T-test using the packages available on the MultiExperiment Viewer, ver 4.3.01 with default settings.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Doris,,Kupfer
| | Sample_contact_email | doris.kupfer@faa.gov
| | Sample_contact_phone | 4059547512
| | Sample_contact_laboratory | Functional Genomics
| | Sample_contact_department | Aeromedical Research
| | Sample_contact_institute | FAA
| | Sample_contact_address | 6500 MacArthur Blvd
| | Sample_contact_city | Oklahoma City
| | Sample_contact_state | OK
| | Sample_contact_zip/postal_code | 73069
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM404nnn/GSM404713/suppl/GSM404713.CEL.gz
| | Sample_series_id | GSE16149
| | Sample_data_row_count | 54675
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| Select GSMs and click on "Add groups" |
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