Search results for the GEO ID: GSE12586  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM315650 | GPL96 |
|
Cultured human PBMC 1
|
Human PBMC from smokers who smoked 10 cig/last 24h, 4.5 pack-years
|
treatment: culture only
age: 33
gender: Male
race: white
|
Gene expression data from culture control 1
|
| Sample_geo_accession | GSM315650
| | 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 | The cultures were then exposed to 2R4F CSC at a final concentration of 40 ug/ml (CSC-treated) for 18h. The CSC-exposed lymphocyte expression was compared to lymphocyte cultures without exposure from the same phlebotomy and subject (paired control cultures).
| | Sample_growth_protocol_ch1 | Blood samples from eight light smokers were collected into BD Vacutainer® CPT tubes, and peripheral blood mononuclear cells were segregated according to the manufacturer’s instructions. The PBMC from each light smoker were cultured in RPMI 1640 medium, supplemented with 1.5% phytohemagglutinin, 1000 U/ml heparin, 2 mM L-glutamine, and 15% fetal bovine serum.
| | 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/GSM315650/suppl/GSM315650.CEL.gz
| | Sample_series_id | GSE12586
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22283
| | |
|
GSM315651 | GPL96 |
|
CSC-exposed human PBMC 1
|
Human PBMC from smokers who smoked 10 cig/last 24h, 4.5 pack-years
|
treatment: CSC exposure
age: 33
gender: Male
race: white
|
Gene expression data from CSC treatment 1
|
| Sample_geo_accession | GSM315651
| | 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 | The cultures were then exposed to 2R4F CSC at a final concentration of 40 ug/ml (CSC-treated) for 18h. The CSC-exposed lymphocyte expression was compared to lymphocyte cultures without exposure from the same phlebotomy and subject (paired control cultures).
| | Sample_growth_protocol_ch1 | Blood samples from eight light smokers were collected into BD Vacutainer® CPT tubes, and peripheral blood mononuclear cells were segregated according to the manufacturer’s instructions. The PBMC from each light smoker were cultured in RPMI 1640 medium, supplemented with 1.5% phytohemagglutinin, 1000 U/ml heparin, 2 mM L-glutamine, and 15% fetal bovine serum.
| | 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/GSM315651/suppl/GSM315651.CEL.gz
| | Sample_series_id | GSE12586
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22283
| | |
|
GSM315652 | GPL96 |
|
Cultured human PBMC 2
|
Human PBMC from smokers who smoked 4 cig/last 24h, 1.25 pack-years
|
treatment: culture only
age: 48
gender: Female
race: black
|
Gene expression data from culture control 2
|
| Sample_geo_accession | GSM315652
| | 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 | The cultures were then exposed to 2R4F CSC at a final concentration of 40 ug/ml (CSC-treated) for 18h. The CSC-exposed lymphocyte expression was compared to lymphocyte cultures without exposure from the same phlebotomy and subject (paired control cultures).
| | Sample_growth_protocol_ch1 | Blood samples from eight light smokers were collected into BD Vacutainer® CPT tubes, and peripheral blood mononuclear cells were segregated according to the manufacturer’s instructions. The PBMC from each light smoker were cultured in RPMI 1640 medium, supplemented with 1.5% phytohemagglutinin, 1000 U/ml heparin, 2 mM L-glutamine, and 15% fetal bovine serum.
| | 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/GSM315652/suppl/GSM315652.CEL.gz
| | Sample_series_id | GSE12586
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22283
| | |
|
GSM315653 | GPL96 |
|
CSC-exposed human PBMC 2
|
Human PBMC from smokers who smoked 4 cig/last 24h, 1.25 pack-years
|
treatment: CSC exposure
age: 48
gender: Female
race: black
|
Gene expression data from CSC treatment 2
|
| Sample_geo_accession | GSM315653
| | 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 | The cultures were then exposed to 2R4F CSC at a final concentration of 40 ug/ml (CSC-treated) for 18h. The CSC-exposed lymphocyte expression was compared to lymphocyte cultures without exposure from the same phlebotomy and subject (paired control cultures).
| | Sample_growth_protocol_ch1 | Blood samples from eight light smokers were collected into BD Vacutainer® CPT tubes, and peripheral blood mononuclear cells were segregated according to the manufacturer’s instructions. The PBMC from each light smoker were cultured in RPMI 1640 medium, supplemented with 1.5% phytohemagglutinin, 1000 U/ml heparin, 2 mM L-glutamine, and 15% fetal bovine serum.
| | 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/GSM315653/suppl/GSM315653.CEL.gz
| | Sample_series_id | GSE12586
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22283
| | |
|
GSM315654 | GPL96 |
|
Cultured human PBMC 3
|
Human PBMC from smokers who smoked 7 cig/last 24h, 2.1 pack-years
|
treatment: culture only
age: 35
gender: Female
race: white
|
Gene expression data from culture control 3
|
| Sample_geo_accession | GSM315654
| | 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 | The cultures were then exposed to 2R4F CSC at a final concentration of 40 ug/ml (CSC-treated) for 18h. The CSC-exposed lymphocyte expression was compared to lymphocyte cultures without exposure from the same phlebotomy and subject (paired control cultures).
| | Sample_growth_protocol_ch1 | Blood samples from eight light smokers were collected into BD Vacutainer® CPT tubes, and peripheral blood mononuclear cells were segregated according to the manufacturer’s instructions. The PBMC from each light smoker were cultured in RPMI 1640 medium, supplemented with 1.5% phytohemagglutinin, 1000 U/ml heparin, 2 mM L-glutamine, and 15% fetal bovine serum.
| | 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/GSM315654/suppl/GSM315654.CEL.gz
| | Sample_series_id | GSE12586
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22283
| | |
|
GSM315655 | GPL96 |
|
CSC-exposed human PBMC 3
|
Human PBMC from smokers who smoked 7 cig/last 24h, 2.1 pack-years
|
treatment: CSC exposure
age: 35
gender: Female
race: white
|
Gene expression data from CSC treatment 3
|
| Sample_geo_accession | GSM315655
| | 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 | The cultures were then exposed to 2R4F CSC at a final concentration of 40 ug/ml (CSC-treated) for 18h. The CSC-exposed lymphocyte expression was compared to lymphocyte cultures without exposure from the same phlebotomy and subject (paired control cultures).
| | Sample_growth_protocol_ch1 | Blood samples from eight light smokers were collected into BD Vacutainer® CPT tubes, and peripheral blood mononuclear cells were segregated according to the manufacturer’s instructions. The PBMC from each light smoker were cultured in RPMI 1640 medium, supplemented with 1.5% phytohemagglutinin, 1000 U/ml heparin, 2 mM L-glutamine, and 15% fetal bovine serum.
| | 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/GSM315655/suppl/GSM315655.CEL.gz
| | Sample_series_id | GSE12586
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22283
| | |
|
GSM315656 | GPL96 |
|
Cultured human PBMC 4
|
Human PBMC from smokers who smoked 8 cig/last 24h, 4 pack-years
|
treatment: culture only
age: 31
gender: Male
race: white
|
Gene expression data from culture control 4
|
| Sample_geo_accession | GSM315656
| | 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 | The cultures were then exposed to 2R4F CSC at a final concentration of 40 ug/ml (CSC-treated) for 18h. The CSC-exposed lymphocyte expression was compared to lymphocyte cultures without exposure from the same phlebotomy and subject (paired control cultures).
| | Sample_growth_protocol_ch1 | Blood samples from eight light smokers were collected into BD Vacutainer® CPT tubes, and peripheral blood mononuclear cells were segregated according to the manufacturer’s instructions. The PBMC from each light smoker were cultured in RPMI 1640 medium, supplemented with 1.5% phytohemagglutinin, 1000 U/ml heparin, 2 mM L-glutamine, and 15% fetal bovine serum.
| | 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/GSM315656/suppl/GSM315656.CEL.gz
| | Sample_series_id | GSE12586
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22283
| | |
|
GSM315657 | GPL96 |
|
CSC-exposed human PBMC 4
|
Human PBMC from smokers who smoked 8 cig/last 24h, 4 pack-years
|
treatment: CSC exposure
age: 31
gender: Male
race: white
|
Gene expression data from CSC treatment 4
|
| Sample_geo_accession | GSM315657
| | 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 | The cultures were then exposed to 2R4F CSC at a final concentration of 40 ug/ml (CSC-treated) for 18h. The CSC-exposed lymphocyte expression was compared to lymphocyte cultures without exposure from the same phlebotomy and subject (paired control cultures).
| | Sample_growth_protocol_ch1 | Blood samples from eight light smokers were collected into BD Vacutainer® CPT tubes, and peripheral blood mononuclear cells were segregated according to the manufacturer’s instructions. The PBMC from each light smoker were cultured in RPMI 1640 medium, supplemented with 1.5% phytohemagglutinin, 1000 U/ml heparin, 2 mM L-glutamine, and 15% fetal bovine serum.
| | 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/GSM315657/suppl/GSM315657.CEL.gz
| | Sample_series_id | GSE12586
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22283
| | |
|
GSM315658 | GPL96 |
|
Cultured human PBMC 5
|
Human PBMC from smokers who smoked 10 cig/last 24h, 15.55 pack-years
|
treatment: culture only
age: 48
gender: Female
race: black
|
Gene expression data from culture control 5
|
| Sample_geo_accession | GSM315658
| | 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 | The cultures were then exposed to 2R4F CSC at a final concentration of 40 ug/ml (CSC-treated) for 18h. The CSC-exposed lymphocyte expression was compared to lymphocyte cultures without exposure from the same phlebotomy and subject (paired control cultures).
| | Sample_growth_protocol_ch1 | Blood samples from eight light smokers were collected into BD Vacutainer® CPT tubes, and peripheral blood mononuclear cells were segregated according to the manufacturer’s instructions. The PBMC from each light smoker were cultured in RPMI 1640 medium, supplemented with 1.5% phytohemagglutinin, 1000 U/ml heparin, 2 mM L-glutamine, and 15% fetal bovine serum.
| | 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/GSM315658/suppl/GSM315658.CEL.gz
| | Sample_series_id | GSE12586
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22283
| | |
|
GSM315659 | GPL96 |
|
CSC-exposed human PBMC 5
|
Human PBMC from smokers who smoked 10 cig/last 24h, 15.55 pack-years
|
treatment: CSC exposure
age: 48
gender: Female
race: black
|
Gene expression data from CSC treatment 5
|
| Sample_geo_accession | GSM315659
| | 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 | The cultures were then exposed to 2R4F CSC at a final concentration of 40 ug/ml (CSC-treated) for 18h. The CSC-exposed lymphocyte expression was compared to lymphocyte cultures without exposure from the same phlebotomy and subject (paired control cultures).
| | Sample_growth_protocol_ch1 | Blood samples from eight light smokers were collected into BD Vacutainer® CPT tubes, and peripheral blood mononuclear cells were segregated according to the manufacturer’s instructions. The PBMC from each light smoker were cultured in RPMI 1640 medium, supplemented with 1.5% phytohemagglutinin, 1000 U/ml heparin, 2 mM L-glutamine, and 15% fetal bovine serum.
| | 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/GSM315659/suppl/GSM315659.CEL.gz
| | Sample_series_id | GSE12586
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22283
| | |
|
GSM315660 | GPL96 |
|
Cultured human PBMC 6
|
Human PBMC from smokers who smoked 8 cig/last 24h, 15.6 pack-years
|
treatment: culture only
age: 49
gender: Female
race: black
|
Gene expression data from culture control 6
|
| Sample_geo_accession | GSM315660
| | 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 | The cultures were then exposed to 2R4F CSC at a final concentration of 40 ug/ml (CSC-treated) for 18h. The CSC-exposed lymphocyte expression was compared to lymphocyte cultures without exposure from the same phlebotomy and subject (paired control cultures).
| | Sample_growth_protocol_ch1 | Blood samples from eight light smokers were collected into BD Vacutainer® CPT tubes, and peripheral blood mononuclear cells were segregated according to the manufacturer’s instructions. The PBMC from each light smoker were cultured in RPMI 1640 medium, supplemented with 1.5% phytohemagglutinin, 1000 U/ml heparin, 2 mM L-glutamine, and 15% fetal bovine serum.
| | 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/GSM315660/suppl/GSM315660.CEL.gz
| | Sample_series_id | GSE12586
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22283
| | |
|
GSM315661 | GPL96 |
|
CSC-exposed human PBMC 6
|
Human PBMC from smokers who smoked 8 cig/last 24h, 15.6 pack-years
|
treatment: CSC exposure
age: 49
gender: Female
race: black
|
Gene expression data from CSC treatment 6
|
| Sample_geo_accession | GSM315661
| | 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 | The cultures were then exposed to 2R4F CSC at a final concentration of 40 ug/ml (CSC-treated) for 18h. The CSC-exposed lymphocyte expression was compared to lymphocyte cultures without exposure from the same phlebotomy and subject (paired control cultures).
| | Sample_growth_protocol_ch1 | Blood samples from eight light smokers were collected into BD Vacutainer® CPT tubes, and peripheral blood mononuclear cells were segregated according to the manufacturer’s instructions. The PBMC from each light smoker were cultured in RPMI 1640 medium, supplemented with 1.5% phytohemagglutinin, 1000 U/ml heparin, 2 mM L-glutamine, and 15% fetal bovine serum.
| | 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/GSM315661/suppl/GSM315661.CEL.gz
| | Sample_series_id | GSE12586
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22283
| | |
|
GSM315662 | GPL96 |
|
Cultured human PBMC 7
|
Human PBMC from smokers who smoked 10 cig/last 24h, 11.5 pack-years
|
treatment: culture only
age: 44
gender: Female
race: white
|
Gene expression data from culture control 7
|
| Sample_geo_accession | GSM315662
| | 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 | The cultures were then exposed to 2R4F CSC at a final concentration of 40 ug/ml (CSC-treated) for 18h. The CSC-exposed lymphocyte expression was compared to lymphocyte cultures without exposure from the same phlebotomy and subject (paired control cultures).
| | Sample_growth_protocol_ch1 | Blood samples from eight light smokers were collected into BD Vacutainer® CPT tubes, and peripheral blood mononuclear cells were segregated according to the manufacturer’s instructions. The PBMC from each light smoker were cultured in RPMI 1640 medium, supplemented with 1.5% phytohemagglutinin, 1000 U/ml heparin, 2 mM L-glutamine, and 15% fetal bovine serum.
| | 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/GSM315662/suppl/GSM315662.CEL.gz
| | Sample_series_id | GSE12586
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22283
| | |
|
GSM315663 | GPL96 |
|
CSC-exposed human PBMC 7
|
Human PBMC from smokers who smoked 10 cig/last 24h, 11.5 pack-years
|
treatment: CSC exposure
age: 44
gender: Female
race: white
|
Gene expression data from CSC treatment 7
|
| Sample_geo_accession | GSM315663
| | 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 | The cultures were then exposed to 2R4F CSC at a final concentration of 40 ug/ml (CSC-treated) for 18h. The CSC-exposed lymphocyte expression was compared to lymphocyte cultures without exposure from the same phlebotomy and subject (paired control cultures).
| | Sample_growth_protocol_ch1 | Blood samples from eight light smokers were collected into BD Vacutainer® CPT tubes, and peripheral blood mononuclear cells were segregated according to the manufacturer’s instructions. The PBMC from each light smoker were cultured in RPMI 1640 medium, supplemented with 1.5% phytohemagglutinin, 1000 U/ml heparin, 2 mM L-glutamine, and 15% fetal bovine serum.
| | 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/GSM315663/suppl/GSM315663.CEL.gz
| | Sample_series_id | GSE12586
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22283
| | |
|
GSM315664 | GPL96 |
|
Cultured human PBMC 8
|
Human PBMC from smokers who smoked 4 cig/last 24h, 5.6 pack-years
|
treatment: culture only
age: 48
gender: Male
race: white
|
Gene expression data from culture control 8
|
| Sample_geo_accession | GSM315664
| | 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 | The cultures were then exposed to 2R4F CSC at a final concentration of 40 ug/ml (CSC-treated) for 18h. The CSC-exposed lymphocyte expression was compared to lymphocyte cultures without exposure from the same phlebotomy and subject (paired control cultures).
| | Sample_growth_protocol_ch1 | Blood samples from eight light smokers were collected into BD Vacutainer® CPT tubes, and peripheral blood mononuclear cells were segregated according to the manufacturer’s instructions. The PBMC from each light smoker were cultured in RPMI 1640 medium, supplemented with 1.5% phytohemagglutinin, 1000 U/ml heparin, 2 mM L-glutamine, and 15% fetal bovine serum.
| | 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/GSM315664/suppl/GSM315664.CEL.gz
| | Sample_series_id | GSE12586
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22283
| | |
|
GSM315665 | GPL96 |
|
CSC-exposed human PBMC 8
|
Human PBMC from smokers who smoked 4 cig/last 24h, 5.6 pack-years
|
treatment: CSC exposure
age: 48
gender: Male
race: white
|
Gene expression data from CSC treatment 8
|
| Sample_geo_accession | GSM315665
| | 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 | The cultures were then exposed to 2R4F CSC at a final concentration of 40 ug/ml (CSC-treated) for 18h. The CSC-exposed lymphocyte expression was compared to lymphocyte cultures without exposure from the same phlebotomy and subject (paired control cultures).
| | Sample_growth_protocol_ch1 | Blood samples from eight light smokers were collected into BD Vacutainer® CPT tubes, and peripheral blood mononuclear cells were segregated according to the manufacturer’s instructions. The PBMC from each light smoker were cultured in RPMI 1640 medium, supplemented with 1.5% phytohemagglutinin, 1000 U/ml heparin, 2 mM L-glutamine, and 15% fetal bovine serum.
| | 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/GSM315665/suppl/GSM315665.CEL.gz
| | Sample_series_id | GSE12586
| | Sample_series_id | GSE12587
| | Sample_data_row_count | 22283
| | |
|
| |
| |
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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