Search results for the GEO ID: GSE19018  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM470491 | GPL570 |
|
Young cells (PD 30) under 20% oxygen, biological rep1
|
Imr90 cells, young (PD 30), 20% oxygen growth conditions
|
cell line: Imr90
oxygen growth conditions: 20%
growth stage: Young
|
Gene expression data of young cells grown under 20% oxygen growth conditions
|
| Sample_geo_accession | GSM470491
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 13 2009
| | Sample_last_update_date | Dec 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Treatment was the 3% oxygen growth conditions.
| | Sample_growth_protocol_ch1 = Imr90 (human lung fibroblast) cells were obtained from ATCC at population doubling (PD) 27. Cells were cultured as monolayers in Dubelco's modified medium (DMEM; ATCC) supplemented with 10% (v/v) fetal bovine serum (FBS; Atlanta Biologicals) and 5% carbon dioxide humidified air at 37 ºC. Monolayers were grown to 80% confluency in T-150 flasks with the growth medium (25 ml) changed every 2-3 days. Separate incubators were used for both the 3% and 20% oxygen growth conditions. Nitrogen gas was used to maintain steady levels of 3% oxygen in the 3% oxygen incubator. Cells were passaged by removing the DMEM, washing with phosphate-buffered saline (PBS, 10 ml; Gibco), and treating the cultures with 2 ml of 1x trypsin-EDTA (Gibco) for 5 minutes in the incubator. The released cells were then resuspended in supplemented DMEM (8 ml), with 200 µl aliquots removed for cell counting and a 2 ml aliquot was removed for the seeding of a new flask for cell growth containing supplemented DMEM (30 ml). Population doublings were calculated by the following formula: log (N/Ni) x 3.33 (N = number of cells, Ni | initial seeded number of cells). Age-matched young and old cells were harvested under both 3% and 20% oxygen conditions for total RNA extraction and subsequent microarray analysis. The old cells grown under the 20% oxygen condition were senescent.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using TRIzol Reagent (Invitrogen) following the manufacurer's protocol on young (PD 30 at 3% and 20% oxygen), old (PD 53 at 3% oxygen), and senescent (PD 48 at 20% oxygen) Imr90 cells. No more than 5 x 10^6 cells were used for the extractions and were collected at 80% confluency.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Between 1 and 10 µg of total RNA from each sample was used to generate a high fidelity cDNA, which was modified at the 3' end to contain an initiation site for T7 RNA polymerase. Staining was performed in the Affymetrix fluidics module as per the manufacturer's protocol using Streptavidin-phycoerythrin stain (SAPE; Molecular Probes), a fluorescent conjugate used to detect the hybridized target sequences.
| | Sample_hyb_protocol | Hybridization and washing of all arrays were performed in the Affymetrix fluidics module as per the manufacturer's protocol on the Affymetrix Human U133A oligonucleotide Array.
| | Sample_scan_protocol | GeneChips were scanned using the GeneArray Scanner 3000, set to scan each array twice at a factory set PMT level and resolution.
| | Sample_data_processing | The data were analyzed with GeneSpring GX (Agilent Technologies). The RMA aligorithm was used for background subtraction, normalization, and summarization of data. An ANOVA (asymptotic) was used to determine the significance of transcriptional alterations. The data was permuted from all spots randomly 100 times to determine the FDR. The FDR was corrected for multiple testing using the Benjamini-Hochberg approach. The Q-Value cutoff for the experiment was 0.05 with probe sets with Q-values greater than 0.05 considered insignificant expressors across the experiment. Spots showing changes of 2 fold or more across one or more conditions were considered significant.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bernd,Robert,Stab II
| | Sample_contact_email | bstab@vt.edu
| | Sample_contact_laboratory | Dr. Helm's Laboratory
| | Sample_contact_department | Biochemistry
| | Sample_contact_institute | Virginia Tech
| | Sample_contact_address | Life Sciences 1 Washington Str
| | Sample_contact_city | Blacksburg
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 24061
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470491/suppl/GSM470491_20%_Young_1.CEL.gz
| | Sample_series_id | GSE19018
| | Sample_data_row_count | 54675
| | |
|
GSM470492 | GPL570 |
|
Young cells (PD 30) under 20% oxygen, biological rep2
|
Imr90 cells, young (PD 30), 20% oxygen growth conditions
|
cell line: Imr90
oxygen growth conditions: 20%
growth stage: Young
|
Gene expression data of young cells grown under 20% oxygen growth conditions
|
| Sample_geo_accession | GSM470492
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 13 2009
| | Sample_last_update_date | Dec 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Treatment was the 3% oxygen growth conditions.
| | Sample_growth_protocol_ch1 = Imr90 (human lung fibroblast) cells were obtained from ATCC at population doubling (PD) 27. Cells were cultured as monolayers in Dubelco's modified medium (DMEM; ATCC) supplemented with 10% (v/v) fetal bovine serum (FBS; Atlanta Biologicals) and 5% carbon dioxide humidified air at 37 ºC. Monolayers were grown to 80% confluency in T-150 flasks with the growth medium (25 ml) changed every 2-3 days. Separate incubators were used for both the 3% and 20% oxygen growth conditions. Nitrogen gas was used to maintain steady levels of 3% oxygen in the 3% oxygen incubator. Cells were passaged by removing the DMEM, washing with phosphate-buffered saline (PBS, 10 ml; Gibco), and treating the cultures with 2 ml of 1x trypsin-EDTA (Gibco) for 5 minutes in the incubator. The released cells were then resuspended in supplemented DMEM (8 ml), with 200 µl aliquots removed for cell counting and a 2 ml aliquot was removed for the seeding of a new flask for cell growth containing supplemented DMEM (30 ml). Population doublings were calculated by the following formula: log (N/Ni) x 3.33 (N = number of cells, Ni | initial seeded number of cells). Age-matched young and old cells were harvested under both 3% and 20% oxygen conditions for total RNA extraction and subsequent microarray analysis. The old cells grown under the 20% oxygen condition were senescent.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using TRIzol Reagent (Invitrogen) following the manufacurer's protocol on young (PD 30 at 3% and 20% oxygen), old (PD 53 at 3% oxygen), and senescent (PD 48 at 20% oxygen) Imr90 cells. No more than 5 x 10^6 cells were used for the extractions and were collected at 80% confluency.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Between 1 and 10 µg of total RNA from each sample was used to generate a high fidelity cDNA, which was modified at the 3' end to contain an initiation site for T7 RNA polymerase. Staining was performed in the Affymetrix fluidics module as per the manufacturer's protocol using Streptavidin-phycoerythrin stain (SAPE; Molecular Probes), a fluorescent conjugate used to detect the hybridized target sequences.
| | Sample_hyb_protocol | Hybridization and washing of all arrays were performed in the Affymetrix fluidics module as per the manufacturer's protocol on the Affymetrix Human U133A oligonucleotide Array.
| | Sample_scan_protocol | GeneChips were scanned using the GeneArray Scanner 3000, set to scan each array twice at a factory set PMT level and resolution.
| | Sample_data_processing | The data were analyzed with GeneSpring GX (Agilent Technologies). The RMA aligorithm was used for background subtraction, normalization, and summarization of data. An ANOVA (asymptotic) was used to determine the significance of transcriptional alterations. The data was permuted from all spots randomly 100 times to determine the FDR. The FDR was corrected for multiple testing using the Benjamini-Hochberg approach. The Q-Value cutoff for the experiment was 0.05 with probe sets with Q-values greater than 0.05 considered insignificant expressors across the experiment. Spots showing changes of 2 fold or more across one or more conditions were considered significant.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bernd,Robert,Stab II
| | Sample_contact_email | bstab@vt.edu
| | Sample_contact_laboratory | Dr. Helm's Laboratory
| | Sample_contact_department | Biochemistry
| | Sample_contact_institute | Virginia Tech
| | Sample_contact_address | Life Sciences 1 Washington Str
| | Sample_contact_city | Blacksburg
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 24061
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470492/suppl/GSM470492_20%_Young_2.CEL.gz
| | Sample_series_id | GSE19018
| | Sample_data_row_count | 54675
| | |
|
GSM470493 | GPL570 |
|
Young cells (PD 30) under 20% oxygen, biological rep3
|
Imr90 cells, young (PD 30), 20% oxygen growth conditions
|
cell line: Imr90
oxygen growth conditions: 20%
growth stage: Young
|
Gene expression data of young cells grown under 20% oxygen growth conditions
|
| Sample_geo_accession | GSM470493
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 13 2009
| | Sample_last_update_date | Dec 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Treatment was the 3% oxygen growth conditions.
| | Sample_growth_protocol_ch1 = Imr90 (human lung fibroblast) cells were obtained from ATCC at population doubling (PD) 27. Cells were cultured as monolayers in Dubelco's modified medium (DMEM; ATCC) supplemented with 10% (v/v) fetal bovine serum (FBS; Atlanta Biologicals) and 5% carbon dioxide humidified air at 37 ºC. Monolayers were grown to 80% confluency in T-150 flasks with the growth medium (25 ml) changed every 2-3 days. Separate incubators were used for both the 3% and 20% oxygen growth conditions. Nitrogen gas was used to maintain steady levels of 3% oxygen in the 3% oxygen incubator. Cells were passaged by removing the DMEM, washing with phosphate-buffered saline (PBS, 10 ml; Gibco), and treating the cultures with 2 ml of 1x trypsin-EDTA (Gibco) for 5 minutes in the incubator. The released cells were then resuspended in supplemented DMEM (8 ml), with 200 µl aliquots removed for cell counting and a 2 ml aliquot was removed for the seeding of a new flask for cell growth containing supplemented DMEM (30 ml). Population doublings were calculated by the following formula: log (N/Ni) x 3.33 (N = number of cells, Ni | initial seeded number of cells). Age-matched young and old cells were harvested under both 3% and 20% oxygen conditions for total RNA extraction and subsequent microarray analysis. The old cells grown under the 20% oxygen condition were senescent.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using TRIzol Reagent (Invitrogen) following the manufacurer's protocol on young (PD 30 at 3% and 20% oxygen), old (PD 53 at 3% oxygen), and senescent (PD 48 at 20% oxygen) Imr90 cells. No more than 5 x 10^6 cells were used for the extractions and were collected at 80% confluency.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Between 1 and 10 µg of total RNA from each sample was used to generate a high fidelity cDNA, which was modified at the 3' end to contain an initiation site for T7 RNA polymerase. Staining was performed in the Affymetrix fluidics module as per the manufacturer's protocol using Streptavidin-phycoerythrin stain (SAPE; Molecular Probes), a fluorescent conjugate used to detect the hybridized target sequences.
| | Sample_hyb_protocol | Hybridization and washing of all arrays were performed in the Affymetrix fluidics module as per the manufacturer's protocol on the Affymetrix Human U133A oligonucleotide Array.
| | Sample_scan_protocol | GeneChips were scanned using the GeneArray Scanner 3000, set to scan each array twice at a factory set PMT level and resolution.
| | Sample_data_processing | The data were analyzed with GeneSpring GX (Agilent Technologies). The RMA aligorithm was used for background subtraction, normalization, and summarization of data. An ANOVA (asymptotic) was used to determine the significance of transcriptional alterations. The data was permuted from all spots randomly 100 times to determine the FDR. The FDR was corrected for multiple testing using the Benjamini-Hochberg approach. The Q-Value cutoff for the experiment was 0.05 with probe sets with Q-values greater than 0.05 considered insignificant expressors across the experiment. Spots showing changes of 2 fold or more across one or more conditions were considered significant.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bernd,Robert,Stab II
| | Sample_contact_email | bstab@vt.edu
| | Sample_contact_laboratory | Dr. Helm's Laboratory
| | Sample_contact_department | Biochemistry
| | Sample_contact_institute | Virginia Tech
| | Sample_contact_address | Life Sciences 1 Washington Str
| | Sample_contact_city | Blacksburg
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 24061
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470493/suppl/GSM470493_20%_Young_3.CEL.gz
| | Sample_series_id | GSE19018
| | Sample_data_row_count | 54675
| | |
|
GSM470494 | GPL570 |
|
Senescent cells (PD 48) under 20% oxygen, biological rep1
|
Imr90 cells, senescent (PD 48), 20% oxygen growth conditions
|
cell line: Imr90
oxygen growth conditions: 20%
growth stage: Old
|
Gene expression data of senescent cells grown under 20% oxygen growth conditions
|
| Sample_geo_accession | GSM470494
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 13 2009
| | Sample_last_update_date | Dec 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Treatment was the 3% oxygen growth conditions.
| | Sample_growth_protocol_ch1 = Imr90 (human lung fibroblast) cells were obtained from ATCC at population doubling (PD) 27. Cells were cultured as monolayers in Dubelco's modified medium (DMEM; ATCC) supplemented with 10% (v/v) fetal bovine serum (FBS; Atlanta Biologicals) and 5% carbon dioxide humidified air at 37 ºC. Monolayers were grown to 80% confluency in T-150 flasks with the growth medium (25 ml) changed every 2-3 days. Separate incubators were used for both the 3% and 20% oxygen growth conditions. Nitrogen gas was used to maintain steady levels of 3% oxygen in the 3% oxygen incubator. Cells were passaged by removing the DMEM, washing with phosphate-buffered saline (PBS, 10 ml; Gibco), and treating the cultures with 2 ml of 1x trypsin-EDTA (Gibco) for 5 minutes in the incubator. The released cells were then resuspended in supplemented DMEM (8 ml), with 200 µl aliquots removed for cell counting and a 2 ml aliquot was removed for the seeding of a new flask for cell growth containing supplemented DMEM (30 ml). Population doublings were calculated by the following formula: log (N/Ni) x 3.33 (N = number of cells, Ni | initial seeded number of cells). Age-matched young and old cells were harvested under both 3% and 20% oxygen conditions for total RNA extraction and subsequent microarray analysis. The old cells grown under the 20% oxygen condition were senescent.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using TRIzol Reagent (Invitrogen) following the manufacurer's protocol on young (PD 30 at 3% and 20% oxygen), old (PD 53 at 3% oxygen), and senescent (PD 48 at 20% oxygen) Imr90 cells. No more than 5 x 10^6 cells were used for the extractions and were collected at 80% confluency.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Between 1 and 10 µg of total RNA from each sample was used to generate a high fidelity cDNA, which was modified at the 3' end to contain an initiation site for T7 RNA polymerase. Staining was performed in the Affymetrix fluidics module as per the manufacturer's protocol using Streptavidin-phycoerythrin stain (SAPE; Molecular Probes), a fluorescent conjugate used to detect the hybridized target sequences.
| | Sample_hyb_protocol | Hybridization and washing of all arrays were performed in the Affymetrix fluidics module as per the manufacturer's protocol on the Affymetrix Human U133A oligonucleotide Array.
| | Sample_scan_protocol | GeneChips were scanned using the GeneArray Scanner 3000, set to scan each array twice at a factory set PMT level and resolution.
| | Sample_data_processing | The data were analyzed with GeneSpring GX (Agilent Technologies). The RMA aligorithm was used for background subtraction, normalization, and summarization of data. An ANOVA (asymptotic) was used to determine the significance of transcriptional alterations. The data was permuted from all spots randomly 100 times to determine the FDR. The FDR was corrected for multiple testing using the Benjamini-Hochberg approach. The Q-Value cutoff for the experiment was 0.05 with probe sets with Q-values greater than 0.05 considered insignificant expressors across the experiment. Spots showing changes of 2 fold or more across one or more conditions were considered significant.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bernd,Robert,Stab II
| | Sample_contact_email | bstab@vt.edu
| | Sample_contact_laboratory | Dr. Helm's Laboratory
| | Sample_contact_department | Biochemistry
| | Sample_contact_institute | Virginia Tech
| | Sample_contact_address | Life Sciences 1 Washington Str
| | Sample_contact_city | Blacksburg
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 24061
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470494/suppl/GSM470494_20%_Senescent_1.CEL.gz
| | Sample_series_id | GSE19018
| | Sample_data_row_count | 54675
| | |
|
GSM470495 | GPL570 |
|
Senescent cells (PD 48) under 20% oxygen, biological rep2
|
Imr90 cells, senescent (PD 48), 20% oxygen growth conditions
|
cell line: Imr90
oxygen growth conditions: 20%
growth stage: Old
|
Gene expression data of senescent cells grown under 20% oxygen growth conditions
|
| Sample_geo_accession | GSM470495
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 13 2009
| | Sample_last_update_date | Dec 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Treatment was the 3% oxygen growth conditions.
| | Sample_growth_protocol_ch1 = Imr90 (human lung fibroblast) cells were obtained from ATCC at population doubling (PD) 27. Cells were cultured as monolayers in Dubelco's modified medium (DMEM; ATCC) supplemented with 10% (v/v) fetal bovine serum (FBS; Atlanta Biologicals) and 5% carbon dioxide humidified air at 37 ºC. Monolayers were grown to 80% confluency in T-150 flasks with the growth medium (25 ml) changed every 2-3 days. Separate incubators were used for both the 3% and 20% oxygen growth conditions. Nitrogen gas was used to maintain steady levels of 3% oxygen in the 3% oxygen incubator. Cells were passaged by removing the DMEM, washing with phosphate-buffered saline (PBS, 10 ml; Gibco), and treating the cultures with 2 ml of 1x trypsin-EDTA (Gibco) for 5 minutes in the incubator. The released cells were then resuspended in supplemented DMEM (8 ml), with 200 µl aliquots removed for cell counting and a 2 ml aliquot was removed for the seeding of a new flask for cell growth containing supplemented DMEM (30 ml). Population doublings were calculated by the following formula: log (N/Ni) x 3.33 (N = number of cells, Ni | initial seeded number of cells). Age-matched young and old cells were harvested under both 3% and 20% oxygen conditions for total RNA extraction and subsequent microarray analysis. The old cells grown under the 20% oxygen condition were senescent.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using TRIzol Reagent (Invitrogen) following the manufacurer's protocol on young (PD 30 at 3% and 20% oxygen), old (PD 53 at 3% oxygen), and senescent (PD 48 at 20% oxygen) Imr90 cells. No more than 5 x 10^6 cells were used for the extractions and were collected at 80% confluency.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Between 1 and 10 µg of total RNA from each sample was used to generate a high fidelity cDNA, which was modified at the 3' end to contain an initiation site for T7 RNA polymerase. Staining was performed in the Affymetrix fluidics module as per the manufacturer's protocol using Streptavidin-phycoerythrin stain (SAPE; Molecular Probes), a fluorescent conjugate used to detect the hybridized target sequences.
| | Sample_hyb_protocol | Hybridization and washing of all arrays were performed in the Affymetrix fluidics module as per the manufacturer's protocol on the Affymetrix Human U133A oligonucleotide Array.
| | Sample_scan_protocol | GeneChips were scanned using the GeneArray Scanner 3000, set to scan each array twice at a factory set PMT level and resolution.
| | Sample_data_processing | The data were analyzed with GeneSpring GX (Agilent Technologies). The RMA aligorithm was used for background subtraction, normalization, and summarization of data. An ANOVA (asymptotic) was used to determine the significance of transcriptional alterations. The data was permuted from all spots randomly 100 times to determine the FDR. The FDR was corrected for multiple testing using the Benjamini-Hochberg approach. The Q-Value cutoff for the experiment was 0.05 with probe sets with Q-values greater than 0.05 considered insignificant expressors across the experiment. Spots showing changes of 2 fold or more across one or more conditions were considered significant.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bernd,Robert,Stab II
| | Sample_contact_email | bstab@vt.edu
| | Sample_contact_laboratory | Dr. Helm's Laboratory
| | Sample_contact_department | Biochemistry
| | Sample_contact_institute | Virginia Tech
| | Sample_contact_address | Life Sciences 1 Washington Str
| | Sample_contact_city | Blacksburg
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 24061
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470495/suppl/GSM470495_20%_Senescent_2.CEL.gz
| | Sample_series_id | GSE19018
| | Sample_data_row_count | 54675
| | |
|
GSM470496 | GPL570 |
|
Senescent cells (PD 48) under 20% oxygen, biological rep3
|
Imr90 cells, senescent (PD 48), 20% oxygen growth conditions
|
cell line: Imr90
oxygen growth conditions: 20%
growth stage: Old
|
Gene expression data of senescent cells grown under 20% oxygen growth conditions
|
| Sample_geo_accession | GSM470496
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 13 2009
| | Sample_last_update_date | Dec 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Treatment was the 3% oxygen growth conditions.
| | Sample_growth_protocol_ch1 = Imr90 (human lung fibroblast) cells were obtained from ATCC at population doubling (PD) 27. Cells were cultured as monolayers in Dubelco's modified medium (DMEM; ATCC) supplemented with 10% (v/v) fetal bovine serum (FBS; Atlanta Biologicals) and 5% carbon dioxide humidified air at 37 ºC. Monolayers were grown to 80% confluency in T-150 flasks with the growth medium (25 ml) changed every 2-3 days. Separate incubators were used for both the 3% and 20% oxygen growth conditions. Nitrogen gas was used to maintain steady levels of 3% oxygen in the 3% oxygen incubator. Cells were passaged by removing the DMEM, washing with phosphate-buffered saline (PBS, 10 ml; Gibco), and treating the cultures with 2 ml of 1x trypsin-EDTA (Gibco) for 5 minutes in the incubator. The released cells were then resuspended in supplemented DMEM (8 ml), with 200 µl aliquots removed for cell counting and a 2 ml aliquot was removed for the seeding of a new flask for cell growth containing supplemented DMEM (30 ml). Population doublings were calculated by the following formula: log (N/Ni) x 3.33 (N = number of cells, Ni | initial seeded number of cells). Age-matched young and old cells were harvested under both 3% and 20% oxygen conditions for total RNA extraction and subsequent microarray analysis. The old cells grown under the 20% oxygen condition were senescent.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using TRIzol Reagent (Invitrogen) following the manufacurer's protocol on young (PD 30 at 3% and 20% oxygen), old (PD 53 at 3% oxygen), and senescent (PD 48 at 20% oxygen) Imr90 cells. No more than 5 x 10^6 cells were used for the extractions and were collected at 80% confluency.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Between 1 and 10 µg of total RNA from each sample was used to generate a high fidelity cDNA, which was modified at the 3' end to contain an initiation site for T7 RNA polymerase. Staining was performed in the Affymetrix fluidics module as per the manufacturer's protocol using Streptavidin-phycoerythrin stain (SAPE; Molecular Probes), a fluorescent conjugate used to detect the hybridized target sequences.
| | Sample_hyb_protocol | Hybridization and washing of all arrays were performed in the Affymetrix fluidics module as per the manufacturer's protocol on the Affymetrix Human U133A oligonucleotide Array.
| | Sample_scan_protocol | GeneChips were scanned using the GeneArray Scanner 3000, set to scan each array twice at a factory set PMT level and resolution.
| | Sample_data_processing | The data were analyzed with GeneSpring GX (Agilent Technologies). The RMA aligorithm was used for background subtraction, normalization, and summarization of data. An ANOVA (asymptotic) was used to determine the significance of transcriptional alterations. The data was permuted from all spots randomly 100 times to determine the FDR. The FDR was corrected for multiple testing using the Benjamini-Hochberg approach. The Q-Value cutoff for the experiment was 0.05 with probe sets with Q-values greater than 0.05 considered insignificant expressors across the experiment. Spots showing changes of 2 fold or more across one or more conditions were considered significant.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bernd,Robert,Stab II
| | Sample_contact_email | bstab@vt.edu
| | Sample_contact_laboratory | Dr. Helm's Laboratory
| | Sample_contact_department | Biochemistry
| | Sample_contact_institute | Virginia Tech
| | Sample_contact_address | Life Sciences 1 Washington Str
| | Sample_contact_city | Blacksburg
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 24061
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470496/suppl/GSM470496_20%_Senescent_3.CEL.gz
| | Sample_series_id | GSE19018
| | Sample_data_row_count | 54675
| | |
|
GSM470497 | GPL570 |
|
Young cells (PD 30) under 3% oxygen, biological rep1
|
Imr90 cells, young (PD 30), 3% oxygen growth conditions
|
cell line: Imr90
oxygen growth conditions: 3%
growth stage: Young
|
Gene expression data of young cells grown under 3% oxygen growth conditions, age-matched to the young 20% cells
|
| Sample_geo_accession | GSM470497
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 13 2009
| | Sample_last_update_date | Dec 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Treatment was the 3% oxygen growth conditions.
| | Sample_growth_protocol_ch1 = Imr90 (human lung fibroblast) cells were obtained from ATCC at population doubling (PD) 27. Cells were cultured as monolayers in Dubelco's modified medium (DMEM; ATCC) supplemented with 10% (v/v) fetal bovine serum (FBS; Atlanta Biologicals) and 5% carbon dioxide humidified air at 37 ºC. Monolayers were grown to 80% confluency in T-150 flasks with the growth medium (25 ml) changed every 2-3 days. Separate incubators were used for both the 3% and 20% oxygen growth conditions. Nitrogen gas was used to maintain steady levels of 3% oxygen in the 3% oxygen incubator. Cells were passaged by removing the DMEM, washing with phosphate-buffered saline (PBS, 10 ml; Gibco), and treating the cultures with 2 ml of 1x trypsin-EDTA (Gibco) for 5 minutes in the incubator. The released cells were then resuspended in supplemented DMEM (8 ml), with 200 µl aliquots removed for cell counting and a 2 ml aliquot was removed for the seeding of a new flask for cell growth containing supplemented DMEM (30 ml). Population doublings were calculated by the following formula: log (N/Ni) x 3.33 (N = number of cells, Ni | initial seeded number of cells). Age-matched young and old cells were harvested under both 3% and 20% oxygen conditions for total RNA extraction and subsequent microarray analysis. The old cells grown under the 20% oxygen condition were senescent.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using TRIzol Reagent (Invitrogen) following the manufacurer's protocol on young (PD 30 at 3% and 20% oxygen), old (PD 53 at 3% oxygen), and senescent (PD 48 at 20% oxygen) Imr90 cells. No more than 5 x 10^6 cells were used for the extractions and were collected at 80% confluency.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Between 1 and 10 µg of total RNA from each sample was used to generate a high fidelity cDNA, which was modified at the 3' end to contain an initiation site for T7 RNA polymerase. Staining was performed in the Affymetrix fluidics module as per the manufacturer's protocol using Streptavidin-phycoerythrin stain (SAPE; Molecular Probes), a fluorescent conjugate used to detect the hybridized target sequences.
| | Sample_hyb_protocol | Hybridization and washing of all arrays were performed in the Affymetrix fluidics module as per the manufacturer's protocol on the Affymetrix Human U133A oligonucleotide Array.
| | Sample_scan_protocol | GeneChips were scanned using the GeneArray Scanner 3000, set to scan each array twice at a factory set PMT level and resolution.
| | Sample_data_processing | The data were analyzed with GeneSpring GX (Agilent Technologies). The RMA aligorithm was used for background subtraction, normalization, and summarization of data. An ANOVA (asymptotic) was used to determine the significance of transcriptional alterations. The data was permuted from all spots randomly 100 times to determine the FDR. The FDR was corrected for multiple testing using the Benjamini-Hochberg approach. The Q-Value cutoff for the experiment was 0.05 with probe sets with Q-values greater than 0.05 considered insignificant expressors across the experiment. Spots showing changes of 2 fold or more across one or more conditions were considered significant.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bernd,Robert,Stab II
| | Sample_contact_email | bstab@vt.edu
| | Sample_contact_laboratory | Dr. Helm's Laboratory
| | Sample_contact_department | Biochemistry
| | Sample_contact_institute | Virginia Tech
| | Sample_contact_address | Life Sciences 1 Washington Str
| | Sample_contact_city | Blacksburg
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 24061
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470497/suppl/GSM470497_3%_Young_1.CEL.gz
| | Sample_series_id | GSE19018
| | Sample_data_row_count | 54675
| | |
|
GSM470498 | GPL570 |
|
Young cells (PD 30) under 3% oxygen, biological rep2
|
Imr90 cells, young (PD 30), 3% oxygen growth conditions
|
cell line: Imr90
oxygen growth conditions: 3%
growth stage: Young
|
Gene expression data of young cells grown under 3% oxygen growth conditions, age-matched to the young 20% cells
|
| Sample_geo_accession | GSM470498
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 13 2009
| | Sample_last_update_date | Dec 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Treatment was the 3% oxygen growth conditions.
| | Sample_growth_protocol_ch1 = Imr90 (human lung fibroblast) cells were obtained from ATCC at population doubling (PD) 27. Cells were cultured as monolayers in Dubelco's modified medium (DMEM; ATCC) supplemented with 10% (v/v) fetal bovine serum (FBS; Atlanta Biologicals) and 5% carbon dioxide humidified air at 37 ºC. Monolayers were grown to 80% confluency in T-150 flasks with the growth medium (25 ml) changed every 2-3 days. Separate incubators were used for both the 3% and 20% oxygen growth conditions. Nitrogen gas was used to maintain steady levels of 3% oxygen in the 3% oxygen incubator. Cells were passaged by removing the DMEM, washing with phosphate-buffered saline (PBS, 10 ml; Gibco), and treating the cultures with 2 ml of 1x trypsin-EDTA (Gibco) for 5 minutes in the incubator. The released cells were then resuspended in supplemented DMEM (8 ml), with 200 µl aliquots removed for cell counting and a 2 ml aliquot was removed for the seeding of a new flask for cell growth containing supplemented DMEM (30 ml). Population doublings were calculated by the following formula: log (N/Ni) x 3.33 (N = number of cells, Ni | initial seeded number of cells). Age-matched young and old cells were harvested under both 3% and 20% oxygen conditions for total RNA extraction and subsequent microarray analysis. The old cells grown under the 20% oxygen condition were senescent.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using TRIzol Reagent (Invitrogen) following the manufacurer's protocol on young (PD 30 at 3% and 20% oxygen), old (PD 53 at 3% oxygen), and senescent (PD 48 at 20% oxygen) Imr90 cells. No more than 5 x 10^6 cells were used for the extractions and were collected at 80% confluency.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Between 1 and 10 µg of total RNA from each sample was used to generate a high fidelity cDNA, which was modified at the 3' end to contain an initiation site for T7 RNA polymerase. Staining was performed in the Affymetrix fluidics module as per the manufacturer's protocol using Streptavidin-phycoerythrin stain (SAPE; Molecular Probes), a fluorescent conjugate used to detect the hybridized target sequences.
| | Sample_hyb_protocol | Hybridization and washing of all arrays were performed in the Affymetrix fluidics module as per the manufacturer's protocol on the Affymetrix Human U133A oligonucleotide Array.
| | Sample_scan_protocol | GeneChips were scanned using the GeneArray Scanner 3000, set to scan each array twice at a factory set PMT level and resolution.
| | Sample_data_processing | The data were analyzed with GeneSpring GX (Agilent Technologies). The RMA aligorithm was used for background subtraction, normalization, and summarization of data. An ANOVA (asymptotic) was used to determine the significance of transcriptional alterations. The data was permuted from all spots randomly 100 times to determine the FDR. The FDR was corrected for multiple testing using the Benjamini-Hochberg approach. The Q-Value cutoff for the experiment was 0.05 with probe sets with Q-values greater than 0.05 considered insignificant expressors across the experiment. Spots showing changes of 2 fold or more across one or more conditions were considered significant.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bernd,Robert,Stab II
| | Sample_contact_email | bstab@vt.edu
| | Sample_contact_laboratory | Dr. Helm's Laboratory
| | Sample_contact_department | Biochemistry
| | Sample_contact_institute | Virginia Tech
| | Sample_contact_address | Life Sciences 1 Washington Str
| | Sample_contact_city | Blacksburg
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 24061
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470498/suppl/GSM470498_3%_Young_2.CEL.gz
| | Sample_series_id | GSE19018
| | Sample_data_row_count | 54675
| | |
|
GSM470499 | GPL570 |
|
Young cells (PD 30) under 3% oxygen, biological rep3
|
Imr90 cells, young (PD 30), 3% oxygen growth conditions
|
cell line: Imr90
oxygen growth conditions: 3%
growth stage: Young
|
Gene expression data of young cells grown under 3% oxygen growth conditions, age-matched to the young 20% cells
|
| Sample_geo_accession | GSM470499
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 13 2009
| | Sample_last_update_date | Dec 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Treatment was the 3% oxygen growth conditions.
| | Sample_growth_protocol_ch1 = Imr90 (human lung fibroblast) cells were obtained from ATCC at population doubling (PD) 27. Cells were cultured as monolayers in Dubelco's modified medium (DMEM; ATCC) supplemented with 10% (v/v) fetal bovine serum (FBS; Atlanta Biologicals) and 5% carbon dioxide humidified air at 37 ºC. Monolayers were grown to 80% confluency in T-150 flasks with the growth medium (25 ml) changed every 2-3 days. Separate incubators were used for both the 3% and 20% oxygen growth conditions. Nitrogen gas was used to maintain steady levels of 3% oxygen in the 3% oxygen incubator. Cells were passaged by removing the DMEM, washing with phosphate-buffered saline (PBS, 10 ml; Gibco), and treating the cultures with 2 ml of 1x trypsin-EDTA (Gibco) for 5 minutes in the incubator. The released cells were then resuspended in supplemented DMEM (8 ml), with 200 µl aliquots removed for cell counting and a 2 ml aliquot was removed for the seeding of a new flask for cell growth containing supplemented DMEM (30 ml). Population doublings were calculated by the following formula: log (N/Ni) x 3.33 (N = number of cells, Ni | initial seeded number of cells). Age-matched young and old cells were harvested under both 3% and 20% oxygen conditions for total RNA extraction and subsequent microarray analysis. The old cells grown under the 20% oxygen condition were senescent.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using TRIzol Reagent (Invitrogen) following the manufacurer's protocol on young (PD 30 at 3% and 20% oxygen), old (PD 53 at 3% oxygen), and senescent (PD 48 at 20% oxygen) Imr90 cells. No more than 5 x 10^6 cells were used for the extractions and were collected at 80% confluency.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Between 1 and 10 µg of total RNA from each sample was used to generate a high fidelity cDNA, which was modified at the 3' end to contain an initiation site for T7 RNA polymerase. Staining was performed in the Affymetrix fluidics module as per the manufacturer's protocol using Streptavidin-phycoerythrin stain (SAPE; Molecular Probes), a fluorescent conjugate used to detect the hybridized target sequences.
| | Sample_hyb_protocol | Hybridization and washing of all arrays were performed in the Affymetrix fluidics module as per the manufacturer's protocol on the Affymetrix Human U133A oligonucleotide Array.
| | Sample_scan_protocol | GeneChips were scanned using the GeneArray Scanner 3000, set to scan each array twice at a factory set PMT level and resolution.
| | Sample_data_processing | The data were analyzed with GeneSpring GX (Agilent Technologies). The RMA aligorithm was used for background subtraction, normalization, and summarization of data. An ANOVA (asymptotic) was used to determine the significance of transcriptional alterations. The data was permuted from all spots randomly 100 times to determine the FDR. The FDR was corrected for multiple testing using the Benjamini-Hochberg approach. The Q-Value cutoff for the experiment was 0.05 with probe sets with Q-values greater than 0.05 considered insignificant expressors across the experiment. Spots showing changes of 2 fold or more across one or more conditions were considered significant.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bernd,Robert,Stab II
| | Sample_contact_email | bstab@vt.edu
| | Sample_contact_laboratory | Dr. Helm's Laboratory
| | Sample_contact_department | Biochemistry
| | Sample_contact_institute | Virginia Tech
| | Sample_contact_address | Life Sciences 1 Washington Str
| | Sample_contact_city | Blacksburg
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 24061
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470499/suppl/GSM470499_3%_Young_3.CEL.gz
| | Sample_series_id | GSE19018
| | Sample_data_row_count | 54675
| | |
|
GSM470500 | GPL570 |
|
Old cells (nonsenescent; PD 53) under 3% oxygen, biological rep1
|
Imr90 cells, old (nonsenescent; PD 53), 3% oxygen growth conditions
|
cell line: Imr90
oxygen growth conditions: 3%
growth stage: Old
|
Gene expression data of old nonsenescent cells grown under 3% oxygen growth conditions, age matched to the 20% senescent cells
|
| Sample_geo_accession | GSM470500
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 13 2009
| | Sample_last_update_date | Dec 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Treatment was the 3% oxygen growth conditions.
| | Sample_growth_protocol_ch1 = Imr90 (human lung fibroblast) cells were obtained from ATCC at population doubling (PD) 27. Cells were cultured as monolayers in Dubelco's modified medium (DMEM; ATCC) supplemented with 10% (v/v) fetal bovine serum (FBS; Atlanta Biologicals) and 5% carbon dioxide humidified air at 37 ºC. Monolayers were grown to 80% confluency in T-150 flasks with the growth medium (25 ml) changed every 2-3 days. Separate incubators were used for both the 3% and 20% oxygen growth conditions. Nitrogen gas was used to maintain steady levels of 3% oxygen in the 3% oxygen incubator. Cells were passaged by removing the DMEM, washing with phosphate-buffered saline (PBS, 10 ml; Gibco), and treating the cultures with 2 ml of 1x trypsin-EDTA (Gibco) for 5 minutes in the incubator. The released cells were then resuspended in supplemented DMEM (8 ml), with 200 µl aliquots removed for cell counting and a 2 ml aliquot was removed for the seeding of a new flask for cell growth containing supplemented DMEM (30 ml). Population doublings were calculated by the following formula: log (N/Ni) x 3.33 (N = number of cells, Ni | initial seeded number of cells). Age-matched young and old cells were harvested under both 3% and 20% oxygen conditions for total RNA extraction and subsequent microarray analysis. The old cells grown under the 20% oxygen condition were senescent.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using TRIzol Reagent (Invitrogen) following the manufacurer's protocol on young (PD 30 at 3% and 20% oxygen), old (PD 53 at 3% oxygen), and senescent (PD 48 at 20% oxygen) Imr90 cells. No more than 5 x 10^6 cells were used for the extractions and were collected at 80% confluency.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Between 1 and 10 µg of total RNA from each sample was used to generate a high fidelity cDNA, which was modified at the 3' end to contain an initiation site for T7 RNA polymerase. Staining was performed in the Affymetrix fluidics module as per the manufacturer's protocol using Streptavidin-phycoerythrin stain (SAPE; Molecular Probes), a fluorescent conjugate used to detect the hybridized target sequences.
| | Sample_hyb_protocol | Hybridization and washing of all arrays were performed in the Affymetrix fluidics module as per the manufacturer's protocol on the Affymetrix Human U133A oligonucleotide Array.
| | Sample_scan_protocol | GeneChips were scanned using the GeneArray Scanner 3000, set to scan each array twice at a factory set PMT level and resolution.
| | Sample_data_processing | The data were analyzed with GeneSpring GX (Agilent Technologies). The RMA aligorithm was used for background subtraction, normalization, and summarization of data. An ANOVA (asymptotic) was used to determine the significance of transcriptional alterations. The data was permuted from all spots randomly 100 times to determine the FDR. The FDR was corrected for multiple testing using the Benjamini-Hochberg approach. The Q-Value cutoff for the experiment was 0.05 with probe sets with Q-values greater than 0.05 considered insignificant expressors across the experiment. Spots showing changes of 2 fold or more across one or more conditions were considered significant.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bernd,Robert,Stab II
| | Sample_contact_email | bstab@vt.edu
| | Sample_contact_laboratory | Dr. Helm's Laboratory
| | Sample_contact_department | Biochemistry
| | Sample_contact_institute | Virginia Tech
| | Sample_contact_address | Life Sciences 1 Washington Str
| | Sample_contact_city | Blacksburg
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 24061
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470500/suppl/GSM470500_3%_Old_1.CEL.gz
| | Sample_series_id | GSE19018
| | Sample_data_row_count | 54675
| | |
|
GSM470501 | GPL570 |
|
Old cells (nonsenescent; PD 53) under 3% oxygen, biological rep2
|
Imr90 cells, old (nonsenescent; PD 53), 3% oxygen growth conditions
|
cell line: Imr90
oxygen growth conditions: 3%
growth stage: Old
|
Gene expression data of old nonsenescent cells grown under 3% oxygen growth conditions, age matched to the 20% senescent cells
|
| Sample_geo_accession | GSM470501
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 13 2009
| | Sample_last_update_date | Dec 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Treatment was the 3% oxygen growth conditions.
| | Sample_growth_protocol_ch1 = Imr90 (human lung fibroblast) cells were obtained from ATCC at population doubling (PD) 27. Cells were cultured as monolayers in Dubelco's modified medium (DMEM; ATCC) supplemented with 10% (v/v) fetal bovine serum (FBS; Atlanta Biologicals) and 5% carbon dioxide humidified air at 37 ºC. Monolayers were grown to 80% confluency in T-150 flasks with the growth medium (25 ml) changed every 2-3 days. Separate incubators were used for both the 3% and 20% oxygen growth conditions. Nitrogen gas was used to maintain steady levels of 3% oxygen in the 3% oxygen incubator. Cells were passaged by removing the DMEM, washing with phosphate-buffered saline (PBS, 10 ml; Gibco), and treating the cultures with 2 ml of 1x trypsin-EDTA (Gibco) for 5 minutes in the incubator. The released cells were then resuspended in supplemented DMEM (8 ml), with 200 µl aliquots removed for cell counting and a 2 ml aliquot was removed for the seeding of a new flask for cell growth containing supplemented DMEM (30 ml). Population doublings were calculated by the following formula: log (N/Ni) x 3.33 (N = number of cells, Ni | initial seeded number of cells). Age-matched young and old cells were harvested under both 3% and 20% oxygen conditions for total RNA extraction and subsequent microarray analysis. The old cells grown under the 20% oxygen condition were senescent.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using TRIzol Reagent (Invitrogen) following the manufacurer's protocol on young (PD 30 at 3% and 20% oxygen), old (PD 53 at 3% oxygen), and senescent (PD 48 at 20% oxygen) Imr90 cells. No more than 5 x 10^6 cells were used for the extractions and were collected at 80% confluency.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Between 1 and 10 µg of total RNA from each sample was used to generate a high fidelity cDNA, which was modified at the 3' end to contain an initiation site for T7 RNA polymerase. Staining was performed in the Affymetrix fluidics module as per the manufacturer's protocol using Streptavidin-phycoerythrin stain (SAPE; Molecular Probes), a fluorescent conjugate used to detect the hybridized target sequences.
| | Sample_hyb_protocol | Hybridization and washing of all arrays were performed in the Affymetrix fluidics module as per the manufacturer's protocol on the Affymetrix Human U133A oligonucleotide Array.
| | Sample_scan_protocol | GeneChips were scanned using the GeneArray Scanner 3000, set to scan each array twice at a factory set PMT level and resolution.
| | Sample_data_processing | The data were analyzed with GeneSpring GX (Agilent Technologies). The RMA aligorithm was used for background subtraction, normalization, and summarization of data. An ANOVA (asymptotic) was used to determine the significance of transcriptional alterations. The data was permuted from all spots randomly 100 times to determine the FDR. The FDR was corrected for multiple testing using the Benjamini-Hochberg approach. The Q-Value cutoff for the experiment was 0.05 with probe sets with Q-values greater than 0.05 considered insignificant expressors across the experiment. Spots showing changes of 2 fold or more across one or more conditions were considered significant.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bernd,Robert,Stab II
| | Sample_contact_email | bstab@vt.edu
| | Sample_contact_laboratory | Dr. Helm's Laboratory
| | Sample_contact_department | Biochemistry
| | Sample_contact_institute | Virginia Tech
| | Sample_contact_address | Life Sciences 1 Washington Str
| | Sample_contact_city | Blacksburg
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 24061
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470501/suppl/GSM470501_3%_Old_2.CEL.gz
| | Sample_series_id | GSE19018
| | Sample_data_row_count | 54675
| | |
|
GSM470502 | GPL570 |
|
Old cells (nonsenescent; PD 53) under 3% oxygen, biological rep3
|
Imr90 cells, old (nonsenescent; PD 53), 3% oxygen growth conditions
|
cell line: Imr90
oxygen growth conditions: 3%
growth stage: Old
|
Gene expression data of old nonsenescent cells grown under 3% oxygen growth conditions, age matched to the 20% senescent cells
|
| Sample_geo_accession | GSM470502
| | Sample_status | Public on Mar 01 2010
| | Sample_submission_date | Nov 13 2009
| | Sample_last_update_date | Dec 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Treatment was the 3% oxygen growth conditions.
| | Sample_growth_protocol_ch1 = Imr90 (human lung fibroblast) cells were obtained from ATCC at population doubling (PD) 27. Cells were cultured as monolayers in Dubelco's modified medium (DMEM; ATCC) supplemented with 10% (v/v) fetal bovine serum (FBS; Atlanta Biologicals) and 5% carbon dioxide humidified air at 37 ºC. Monolayers were grown to 80% confluency in T-150 flasks with the growth medium (25 ml) changed every 2-3 days. Separate incubators were used for both the 3% and 20% oxygen growth conditions. Nitrogen gas was used to maintain steady levels of 3% oxygen in the 3% oxygen incubator. Cells were passaged by removing the DMEM, washing with phosphate-buffered saline (PBS, 10 ml; Gibco), and treating the cultures with 2 ml of 1x trypsin-EDTA (Gibco) for 5 minutes in the incubator. The released cells were then resuspended in supplemented DMEM (8 ml), with 200 µl aliquots removed for cell counting and a 2 ml aliquot was removed for the seeding of a new flask for cell growth containing supplemented DMEM (30 ml). Population doublings were calculated by the following formula: log (N/Ni) x 3.33 (N = number of cells, Ni | initial seeded number of cells). Age-matched young and old cells were harvested under both 3% and 20% oxygen conditions for total RNA extraction and subsequent microarray analysis. The old cells grown under the 20% oxygen condition were senescent.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using TRIzol Reagent (Invitrogen) following the manufacurer's protocol on young (PD 30 at 3% and 20% oxygen), old (PD 53 at 3% oxygen), and senescent (PD 48 at 20% oxygen) Imr90 cells. No more than 5 x 10^6 cells were used for the extractions and were collected at 80% confluency.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Between 1 and 10 µg of total RNA from each sample was used to generate a high fidelity cDNA, which was modified at the 3' end to contain an initiation site for T7 RNA polymerase. Staining was performed in the Affymetrix fluidics module as per the manufacturer's protocol using Streptavidin-phycoerythrin stain (SAPE; Molecular Probes), a fluorescent conjugate used to detect the hybridized target sequences.
| | Sample_hyb_protocol | Hybridization and washing of all arrays were performed in the Affymetrix fluidics module as per the manufacturer's protocol on the Affymetrix Human U133A oligonucleotide Array.
| | Sample_scan_protocol | GeneChips were scanned using the GeneArray Scanner 3000, set to scan each array twice at a factory set PMT level and resolution.
| | Sample_data_processing | The data were analyzed with GeneSpring GX (Agilent Technologies). The RMA aligorithm was used for background subtraction, normalization, and summarization of data. An ANOVA (asymptotic) was used to determine the significance of transcriptional alterations. The data was permuted from all spots randomly 100 times to determine the FDR. The FDR was corrected for multiple testing using the Benjamini-Hochberg approach. The Q-Value cutoff for the experiment was 0.05 with probe sets with Q-values greater than 0.05 considered insignificant expressors across the experiment. Spots showing changes of 2 fold or more across one or more conditions were considered significant.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bernd,Robert,Stab II
| | Sample_contact_email | bstab@vt.edu
| | Sample_contact_laboratory | Dr. Helm's Laboratory
| | Sample_contact_department | Biochemistry
| | Sample_contact_institute | Virginia Tech
| | Sample_contact_address | Life Sciences 1 Washington Str
| | Sample_contact_city | Blacksburg
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 24061
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM470nnn/GSM470502/suppl/GSM470502_3%_Old_3.CEL.gz
| | Sample_series_id | GSE19018
| | Sample_data_row_count | 54675
| | |
|
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