Search results for the GEO ID: GSE12585  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM315627 | GPL96 |
|
Heavy smoker 1, biological rep1
|
Human PBMC from smokers who smoked 40 cig/last 24h, 86 pack-years
|
age: 57
gender: Male
race: white
|
Gene expression data from heavy smoker
|
| Sample_geo_accession | GSM315627
| | Sample_status | Public on Aug 28 2009
| | Sample_submission_date | Aug 27 2008
| | Sample_last_update_date | Feb 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Subjects were recruited through local print advertising, and screened for eligibility. Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts). Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.
| | Sample_growth_protocol_ch1 | no culture in vitro
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Agilent Scanner 3000.
| | Sample_data_processing | The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Jinguo,,Chen
| | Sample_contact_email | jinguochen@yahoo.com
| | Sample_contact_department | Cancer Genetics and Epidemiology
| | Sample_contact_institute | Georgetown University Lombardi Cancer Center
| | Sample_contact_address | 3800 Reservoir Road NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20057
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315627/suppl/GSM315627.cel.gz
| | Sample_series_id | GSE12585
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22281
| | |
|
GSM315628 | GPL96 |
|
Heavy smoker 2, biological rep2
|
Human PBMC from smokers who smoked 25 cig/last 24h, 45 pack-years
|
age: 58
gender: Male
race: white
|
Gene expression data from heavy smoker
|
| Sample_geo_accession | GSM315628
| | Sample_status | Public on Aug 28 2009
| | Sample_submission_date | Aug 27 2008
| | Sample_last_update_date | Feb 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Subjects were recruited through local print advertising, and screened for eligibility. Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts). Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.
| | Sample_growth_protocol_ch1 | no culture in vitro
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Agilent Scanner 3000.
| | Sample_data_processing | The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Jinguo,,Chen
| | Sample_contact_email | jinguochen@yahoo.com
| | Sample_contact_department | Cancer Genetics and Epidemiology
| | Sample_contact_institute | Georgetown University Lombardi Cancer Center
| | Sample_contact_address | 3800 Reservoir Road NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20057
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315628/suppl/GSM315628.cel.gz
| | Sample_series_id | GSE12585
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22281
| | |
|
GSM315629 | GPL96 |
|
Heavy smoker 3, biological rep3
|
Human PBMC from smokers who smoked 40 cig/last 24h, 88 pack-years
|
age: 63
gender: Male
race: white
|
Gene expression data from heavy smoker
|
| Sample_geo_accession | GSM315629
| | Sample_status | Public on Aug 28 2009
| | Sample_submission_date | Aug 27 2008
| | Sample_last_update_date | Feb 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Subjects were recruited through local print advertising, and screened for eligibility. Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts). Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.
| | Sample_growth_protocol_ch1 | no culture in vitro
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Agilent Scanner 3000.
| | Sample_data_processing | The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Jinguo,,Chen
| | Sample_contact_email | jinguochen@yahoo.com
| | Sample_contact_department | Cancer Genetics and Epidemiology
| | Sample_contact_institute | Georgetown University Lombardi Cancer Center
| | Sample_contact_address | 3800 Reservoir Road NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20057
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315629/suppl/GSM315629.cel.gz
| | Sample_series_id | GSE12585
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22281
| | |
|
GSM315630 | GPL96 |
|
Heavy smoker 4, biological rep4
|
Human PBMC from smokers who smoked 23 cig/last 24h, 26.45 pack-years
|
age: 41
gender: Male
race: black
|
Gene expression data from heavy smoker
|
| Sample_geo_accession | GSM315630
| | Sample_status | Public on Aug 28 2009
| | Sample_submission_date | Aug 27 2008
| | Sample_last_update_date | Feb 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Subjects were recruited through local print advertising, and screened for eligibility. Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts). Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.
| | Sample_growth_protocol_ch1 | no culture in vitro
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Agilent Scanner 3000.
| | Sample_data_processing | The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Jinguo,,Chen
| | Sample_contact_email | jinguochen@yahoo.com
| | Sample_contact_department | Cancer Genetics and Epidemiology
| | Sample_contact_institute | Georgetown University Lombardi Cancer Center
| | Sample_contact_address | 3800 Reservoir Road NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20057
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315630/suppl/GSM315630.cel.gz
| | Sample_series_id | GSE12585
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22281
| | |
|
GSM315631 | GPL96 |
|
Heavy smoker 5, biological rep5
|
Human PBMC from smokers who smoked 40 cig/last 24h, 22 pack-years
|
age: 33
gender: Female
race: black
|
Gene expression data from heavy smoker
|
| Sample_geo_accession | GSM315631
| | Sample_status | Public on Aug 28 2009
| | Sample_submission_date | Aug 27 2008
| | Sample_last_update_date | Feb 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Subjects were recruited through local print advertising, and screened for eligibility. Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts). Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.
| | Sample_growth_protocol_ch1 | no culture in vitro
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Agilent Scanner 3000.
| | Sample_data_processing | The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Jinguo,,Chen
| | Sample_contact_email | jinguochen@yahoo.com
| | Sample_contact_department | Cancer Genetics and Epidemiology
| | Sample_contact_institute | Georgetown University Lombardi Cancer Center
| | Sample_contact_address | 3800 Reservoir Road NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20057
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315631/suppl/GSM315631.cel.gz
| | Sample_series_id | GSE12585
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22281
| | |
|
GSM315632 | GPL96 |
|
Heavy smoker 6, biological rep6
|
Human PBMC from smokers who smoked 36 cig/last 24h, 54 pack-years
|
age: 48
gender: Male
race: black
|
Gene expression data from heavy smoker
|
| Sample_geo_accession | GSM315632
| | Sample_status | Public on Aug 28 2009
| | Sample_submission_date | Aug 27 2008
| | Sample_last_update_date | Feb 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Subjects were recruited through local print advertising, and screened for eligibility. Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts). Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.
| | Sample_growth_protocol_ch1 | no culture in vitro
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Agilent Scanner 3000.
| | Sample_data_processing | The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Jinguo,,Chen
| | Sample_contact_email | jinguochen@yahoo.com
| | Sample_contact_department | Cancer Genetics and Epidemiology
| | Sample_contact_institute | Georgetown University Lombardi Cancer Center
| | Sample_contact_address | 3800 Reservoir Road NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20057
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315632/suppl/GSM315632.cel.gz
| | Sample_series_id | GSE12585
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22281
| | |
|
GSM315633 | GPL96 |
|
Heavy smoker 7, biological rep7
|
Human PBMC from smokers who smoked 50 cig/last 24h, 122.5 pack-years
|
age: 68
gender: Male
race: white
|
Gene expression data from heavy smoker
|
| Sample_geo_accession | GSM315633
| | Sample_status | Public on Aug 28 2009
| | Sample_submission_date | Aug 27 2008
| | Sample_last_update_date | Feb 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Subjects were recruited through local print advertising, and screened for eligibility. Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts). Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.
| | Sample_growth_protocol_ch1 | no culture in vitro
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Agilent Scanner 3000.
| | Sample_data_processing | The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Jinguo,,Chen
| | Sample_contact_email | jinguochen@yahoo.com
| | Sample_contact_department | Cancer Genetics and Epidemiology
| | Sample_contact_institute | Georgetown University Lombardi Cancer Center
| | Sample_contact_address | 3800 Reservoir Road NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20057
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315633/suppl/GSM315633.cel.gz
| | Sample_series_id | GSE12585
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22281
| | |
|
GSM315634 | GPL96 |
|
Heavy smoker 8, biological rep8
|
Human PBMC from smokers who smoked 23 cig/last 24h, 40.25 pack-years
|
age: 54
gender: Female
race: black
|
Gene expression data from heavy smoker
|
| Sample_geo_accession | GSM315634
| | Sample_status | Public on Aug 28 2009
| | Sample_submission_date | Aug 27 2008
| | Sample_last_update_date | Feb 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Subjects were recruited through local print advertising, and screened for eligibility. Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts). Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.
| | Sample_growth_protocol_ch1 | no culture in vitro
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Agilent Scanner 3000.
| | Sample_data_processing | The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Jinguo,,Chen
| | Sample_contact_email | jinguochen@yahoo.com
| | Sample_contact_department | Cancer Genetics and Epidemiology
| | Sample_contact_institute | Georgetown University Lombardi Cancer Center
| | Sample_contact_address | 3800 Reservoir Road NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20057
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315634/suppl/GSM315634.cel.gz
| | Sample_series_id | GSE12585
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22281
| | |
|
GSM315635 | GPL96 |
|
Heavy smoker 9, biological rep9
|
Human PBMC from smokers who smoked 25 cig/last 24h, 35 pack-years
|
age: 41
gender: Female
race: black
|
Gene expression data from heavy smoker
|
| Sample_geo_accession | GSM315635
| | Sample_status | Public on Aug 28 2009
| | Sample_submission_date | Aug 27 2008
| | Sample_last_update_date | Feb 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Subjects were recruited through local print advertising, and screened for eligibility. Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts). Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.
| | Sample_growth_protocol_ch1 | no culture in vitro
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Agilent Scanner 3000.
| | Sample_data_processing | The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Jinguo,,Chen
| | Sample_contact_email | jinguochen@yahoo.com
| | Sample_contact_department | Cancer Genetics and Epidemiology
| | Sample_contact_institute | Georgetown University Lombardi Cancer Center
| | Sample_contact_address | 3800 Reservoir Road NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20057
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315635/suppl/GSM315635.cel.gz
| | Sample_series_id | GSE12585
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22281
| | |
|
GSM315636 | GPL96 |
|
Heavy smoker 10, biological rep10
|
Human PBMC from smokers who smoked 30 cig/last 24h, 61.5 pack-years
|
age: 53
gender: Female
race: black
|
Gene expression data from heavy smoker
|
| Sample_geo_accession | GSM315636
| | Sample_status | Public on Aug 28 2009
| | Sample_submission_date | Aug 27 2008
| | Sample_last_update_date | Feb 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Subjects were recruited through local print advertising, and screened for eligibility. Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts). Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.
| | Sample_growth_protocol_ch1 | no culture in vitro
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Agilent Scanner 3000.
| | Sample_data_processing | The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Jinguo,,Chen
| | Sample_contact_email | jinguochen@yahoo.com
| | Sample_contact_department | Cancer Genetics and Epidemiology
| | Sample_contact_institute | Georgetown University Lombardi Cancer Center
| | Sample_contact_address | 3800 Reservoir Road NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20057
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315636/suppl/GSM315636.cel.gz
| | Sample_series_id | GSE12585
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22281
| | |
|
GSM315637 | GPL96 |
|
Light smoker 1, biological rep1
|
Human PBMC from smokers who smoked 10 cig/last 24h, 10 pack-years
|
age: 40
gender: Female
race: white
|
Gene expression data from light smoker
|
| Sample_geo_accession | GSM315637
| | Sample_status | Public on Aug 28 2009
| | Sample_submission_date | Aug 27 2008
| | Sample_last_update_date | Feb 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Subjects were recruited through local print advertising, and screened for eligibility. Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts). Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.
| | Sample_growth_protocol_ch1 | no culture in vitro
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Agilent Scanner 3000.
| | Sample_data_processing | The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Jinguo,,Chen
| | Sample_contact_email | jinguochen@yahoo.com
| | Sample_contact_department | Cancer Genetics and Epidemiology
| | Sample_contact_institute | Georgetown University Lombardi Cancer Center
| | Sample_contact_address | 3800 Reservoir Road NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20057
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315637/suppl/GSM315637.cel.gz
| | Sample_series_id | GSE12585
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22281
| | |
|
GSM315638 | GPL96 |
|
Light smoker 2, biological rep2
|
Human PBMC from smokers who smoked 7 cig/last 24h, 12.25 pack-years
|
age: 60
gender: Male
race: white
|
Gene expression data from light smoker
|
| Sample_geo_accession | GSM315638
| | Sample_status | Public on Aug 28 2009
| | Sample_submission_date | Aug 27 2008
| | Sample_last_update_date | Feb 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Subjects were recruited through local print advertising, and screened for eligibility. Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts). Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.
| | Sample_growth_protocol_ch1 | no culture in vitro
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Agilent Scanner 3000.
| | Sample_data_processing | The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Jinguo,,Chen
| | Sample_contact_email | jinguochen@yahoo.com
| | Sample_contact_department | Cancer Genetics and Epidemiology
| | Sample_contact_institute | Georgetown University Lombardi Cancer Center
| | Sample_contact_address | 3800 Reservoir Road NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20057
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315638/suppl/GSM315638.cel.gz
| | Sample_series_id | GSE12585
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22281
| | |
|
GSM315639 | GPL96 |
|
Light smoker 3, biological rep3
|
Human PBMC from smokers who smoked 12 cig/last 24h, 27.6 pack-years
|
age: 62
gender: Male
race: black
|
Gene expression data from light smoker
|
| Sample_geo_accession | GSM315639
| | Sample_status | Public on Aug 28 2009
| | Sample_submission_date | Aug 27 2008
| | Sample_last_update_date | Feb 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Subjects were recruited through local print advertising, and screened for eligibility. Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts). Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.
| | Sample_growth_protocol_ch1 | no culture in vitro
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Agilent Scanner 3000.
| | Sample_data_processing | The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Jinguo,,Chen
| | Sample_contact_email | jinguochen@yahoo.com
| | Sample_contact_department | Cancer Genetics and Epidemiology
| | Sample_contact_institute | Georgetown University Lombardi Cancer Center
| | Sample_contact_address | 3800 Reservoir Road NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20057
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315639/suppl/GSM315639.cel.gz
| | Sample_series_id | GSE12585
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22281
| | |
|
GSM315640 | GPL96 |
|
Light smoker 4, biological rep4
|
Human PBMC from smokers who smoked 10 cig/last 24h, 175 pack-years
|
age: 57
gender: Male
race: black
|
Gene expression data from light smoker
|
| Sample_geo_accession | GSM315640
| | Sample_status | Public on Aug 28 2009
| | Sample_submission_date | Aug 27 2008
| | Sample_last_update_date | Feb 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Subjects were recruited through local print advertising, and screened for eligibility. Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts). Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.
| | Sample_growth_protocol_ch1 | no culture in vitro
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Agilent Scanner 3000.
| | Sample_data_processing | The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Jinguo,,Chen
| | Sample_contact_email | jinguochen@yahoo.com
| | Sample_contact_department | Cancer Genetics and Epidemiology
| | Sample_contact_institute | Georgetown University Lombardi Cancer Center
| | Sample_contact_address | 3800 Reservoir Road NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20057
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315640/suppl/GSM315640.cel.gz
| | Sample_series_id | GSE12585
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22281
| | |
|
GSM315641 | GPL96 |
|
Light smoker 5, biological rep5
|
Human PBMC from smokers who smoked 10 cig/last 24h, 4.5 pack-years
|
age: 33
gender: Male
race: white
|
Gene expression data from light smoker
|
| Sample_geo_accession | GSM315641
| | Sample_status | Public on Aug 28 2009
| | Sample_submission_date | Aug 27 2008
| | Sample_last_update_date | Feb 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Subjects were recruited through local print advertising, and screened for eligibility. Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts). Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.
| | Sample_growth_protocol_ch1 | no culture in vitro
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Agilent Scanner 3000.
| | Sample_data_processing | The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Jinguo,,Chen
| | Sample_contact_email | jinguochen@yahoo.com
| | Sample_contact_department | Cancer Genetics and Epidemiology
| | Sample_contact_institute | Georgetown University Lombardi Cancer Center
| | Sample_contact_address | 3800 Reservoir Road NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20057
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315641/suppl/GSM315641.cel.gz
| | Sample_series_id | GSE12585
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22281
| | |
|
GSM315642 | GPL96 |
|
Light smoker 6, biological rep6
|
Human PBMC from smokers who smoked 4 cig/last 24h, 1.25 pack-years
|
age: 48
gender: Female
race: black
|
Gene expression data from light smoker
|
| Sample_geo_accession | GSM315642
| | Sample_status | Public on Aug 28 2009
| | Sample_submission_date | Aug 27 2008
| | Sample_last_update_date | Feb 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Subjects were recruited through local print advertising, and screened for eligibility. Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts). Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.
| | Sample_growth_protocol_ch1 | no culture in vitro
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Agilent Scanner 3000.
| | Sample_data_processing | The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Jinguo,,Chen
| | Sample_contact_email | jinguochen@yahoo.com
| | Sample_contact_department | Cancer Genetics and Epidemiology
| | Sample_contact_institute | Georgetown University Lombardi Cancer Center
| | Sample_contact_address | 3800 Reservoir Road NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20057
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315642/suppl/GSM315642.cel.gz
| | Sample_series_id | GSE12585
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22281
| | |
|
GSM315643 | GPL96 |
|
Light smoker 7, biological rep7
|
Human PBMC from smokers who smoked 10 cig/last 24h, 18.55 pack-years
|
age: 55
gender: Female
race: black
|
Gene expression data from light smoker
|
| Sample_geo_accession | GSM315643
| | Sample_status | Public on Aug 28 2009
| | Sample_submission_date | Aug 27 2008
| | Sample_last_update_date | Feb 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Subjects were recruited through local print advertising, and screened for eligibility. Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts). Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.
| | Sample_growth_protocol_ch1 | no culture in vitro
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Agilent Scanner 3000.
| | Sample_data_processing | The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Jinguo,,Chen
| | Sample_contact_email | jinguochen@yahoo.com
| | Sample_contact_department | Cancer Genetics and Epidemiology
| | Sample_contact_institute | Georgetown University Lombardi Cancer Center
| | Sample_contact_address | 3800 Reservoir Road NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20057
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315643/suppl/GSM315643.cel.gz
| | Sample_series_id | GSE12585
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22281
| | |
|
GSM315644 | GPL96 |
|
Light smoker 8, biological rep8
|
Human PBMC from smokers who smoked 7 cig/last 24h, 2.1 pack-years
|
age: 35
gender: Female
race: white
|
Gene expression data from light smoker
|
| Sample_geo_accession | GSM315644
| | Sample_status | Public on Aug 28 2009
| | Sample_submission_date | Aug 27 2008
| | Sample_last_update_date | Feb 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Subjects were recruited through local print advertising, and screened for eligibility. Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts). Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.
| | Sample_growth_protocol_ch1 | no culture in vitro
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Agilent Scanner 3000.
| | Sample_data_processing | The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Jinguo,,Chen
| | Sample_contact_email | jinguochen@yahoo.com
| | Sample_contact_department | Cancer Genetics and Epidemiology
| | Sample_contact_institute | Georgetown University Lombardi Cancer Center
| | Sample_contact_address | 3800 Reservoir Road NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20057
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315644/suppl/GSM315644.cel.gz
| | Sample_series_id | GSE12585
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22281
| | |
|
GSM315645 | GPL96 |
|
Light smoker 9, biological rep9
|
Human PBMC from smokers who smoked 8 cig/last 24h, 4 pack-years
|
age: 31
gender: Male
race: white
|
Gene expression data from light smoker
|
| Sample_geo_accession | GSM315645
| | Sample_status | Public on Aug 28 2009
| | Sample_submission_date | Aug 27 2008
| | Sample_last_update_date | Feb 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Subjects were recruited through local print advertising, and screened for eligibility. Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts). Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.
| | Sample_growth_protocol_ch1 | no culture in vitro
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Agilent Scanner 3000.
| | Sample_data_processing | The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Jinguo,,Chen
| | Sample_contact_email | jinguochen@yahoo.com
| | Sample_contact_department | Cancer Genetics and Epidemiology
| | Sample_contact_institute | Georgetown University Lombardi Cancer Center
| | Sample_contact_address | 3800 Reservoir Road NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20057
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315645/suppl/GSM315645.cel.gz
| | Sample_series_id | GSE12585
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22281
| | |
|
GSM315646 | GPL96 |
|
Light smoker 10, biological rep10
|
Human PBMC from smokers who smoked 10 cig/last 24h, 15.55 pack-years
|
age: 48
gender: Female
race: black
|
Gene expression data from light smoker
|
| Sample_geo_accession | GSM315646
| | Sample_status | Public on Aug 28 2009
| | Sample_submission_date | Aug 27 2008
| | Sample_last_update_date | Feb 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Subjects were recruited through local print advertising, and screened for eligibility. Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts). Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.
| | Sample_growth_protocol_ch1 | no culture in vitro
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Agilent Scanner 3000.
| | Sample_data_processing | The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Jinguo,,Chen
| | Sample_contact_email | jinguochen@yahoo.com
| | Sample_contact_department | Cancer Genetics and Epidemiology
| | Sample_contact_institute | Georgetown University Lombardi Cancer Center
| | Sample_contact_address | 3800 Reservoir Road NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20057
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315646/suppl/GSM315646.cel.gz
| | Sample_series_id | GSE12585
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22281
| | |
|
GSM315647 | GPL96 |
|
Light smoker 11, biological rep11
|
Human PBMC from smokers who smoked 8 cig/last 24h, 15.6 pack-years
|
age: 49
gender: Female
race: black
|
Gene expression data from light smoker
|
| Sample_geo_accession | GSM315647
| | Sample_status | Public on Aug 28 2009
| | Sample_submission_date | Aug 27 2008
| | Sample_last_update_date | Feb 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Subjects were recruited through local print advertising, and screened for eligibility. Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts). Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.
| | Sample_growth_protocol_ch1 | no culture in vitro
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Agilent Scanner 3000.
| | Sample_data_processing | The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Jinguo,,Chen
| | Sample_contact_email | jinguochen@yahoo.com
| | Sample_contact_department | Cancer Genetics and Epidemiology
| | Sample_contact_institute | Georgetown University Lombardi Cancer Center
| | Sample_contact_address | 3800 Reservoir Road NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20057
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315647/suppl/GSM315647.cel.gz
| | Sample_series_id | GSE12585
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22281
| | |
|
GSM315648 | GPL96 |
|
Light smoker 12, biological rep12
|
Human PBMC from smokers who smoked 10 cig/last 24h, 11.5 pack-years
|
age: 44
gender: Female
race: white
|
Gene expression data from light smoker
|
| Sample_geo_accession | GSM315648
| | Sample_status | Public on Aug 28 2009
| | Sample_submission_date | Aug 27 2008
| | Sample_last_update_date | Feb 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Subjects were recruited through local print advertising, and screened for eligibility. Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts). Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.
| | Sample_growth_protocol_ch1 | no culture in vitro
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Agilent Scanner 3000.
| | Sample_data_processing | The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Jinguo,,Chen
| | Sample_contact_email | jinguochen@yahoo.com
| | Sample_contact_department | Cancer Genetics and Epidemiology
| | Sample_contact_institute | Georgetown University Lombardi Cancer Center
| | Sample_contact_address | 3800 Reservoir Road NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20057
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315648/suppl/GSM315648.cel.gz
| | Sample_series_id | GSE12585
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22281
| | |
|
GSM315649 | GPL96 |
|
Light smoker 13, biological rep13
|
Human PBMC from smokers who smoked 4 cig/last 24h, 5.6 pack-years
|
age: 48
gender: Male
race: white
|
Gene expression data from light smoker
|
| Sample_geo_accession | GSM315649
| | Sample_status | Public on Aug 28 2009
| | Sample_submission_date | Aug 27 2008
| | Sample_last_update_date | Feb 18 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Subjects were recruited through local print advertising, and screened for eligibility. Only healthy smokers without current infections, medication use or illnesses that can affect the immune system were included in this study. All smokers had to have been smoking for at least 5 years and had a stable smoking pattern for the prior 6 months (cigarette brand and cigarettes per day, and no smoking-cessation attempts). Blood samples from each subject were collected into CPT tubes, and peripheral blood mononuclear cells (PBMC), predominantly lymphocytes, were segregated according to the manufacturer’s instructions. The lymphocyte pellets were immediately placed in TRIzol reagent and kept at –80C until RNA isolation (uncultured). All blood samples were delivered and processed within 2 h of phlebotomy.
| | Sample_growth_protocol_ch1 | no culture in vitro
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA and clean-up step using RNeasy Micro Kit were performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Agilent Scanner 3000.
| | Sample_data_processing | The R language affy package , that implements the RMA (Robust Multichip Average) procedure, was used to convert probe signal data (.cel files) to expression values through the following sequence: 1) convolution model background correction; 2) cyclic Loess normalization; and 3) summarization by taking log2 of the probe values and fitting a robust multi-chip linear model using the median polish algorithm.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Jinguo,,Chen
| | Sample_contact_email | jinguochen@yahoo.com
| | Sample_contact_department | Cancer Genetics and Epidemiology
| | Sample_contact_institute | Georgetown University Lombardi Cancer Center
| | Sample_contact_address | 3800 Reservoir Road NW
| | Sample_contact_city | Washington
| | Sample_contact_state | DC
| | Sample_contact_zip/postal_code | 20057
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315649/suppl/GSM315649.cel.gz
| | Sample_series_id | GSE12585
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22281
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
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