Search results for the GEO ID: GSE17046  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM426440 | GPL96 |
|
donorF1_IRA860J/cm2_24hpostincubation_biolrep1
|
human dermal fibroblasts IRA irradiated with 860J/cm2
|
cell type: primary human dermal fibroblasts
passage: between 5-10
donor: F1
|
no additional description
|
| Sample_geo_accession | GSM426440
| | Sample_status | Public on Jul 10 2010
| | Sample_submission_date | Jul 10 2009
| | Sample_last_update_date | Jul 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | We used a waterfiltered Hydrosun 500 H 500 IRA lamp (Hydrosun Medizintechnik GmbH, Müllheim, Germany) with an emission in the range of 760-1400 nm leading to an irradiance of 360 mW/cm2 at a distance of 20 cm measured through Hydrosun HBM1 irradiance measuring device (Hydrosun). IRA irradiation lasted 40 min leading to a total dose of 860 J/cm2. The culture dishes were placed on a cooled plate connected to thermostated bath (Thermo Haake GmbH, Karlsruhe, Germany) to maintain temperatures below 37°C during IRA irradiation. For irradiation, medium was replaced by phosphate-buffered saline (37°C, Gibco). Control cells were held on a 37°C thermostated plate under similar conditions without irradiation. Following the treatment cells were cultivated for 24 hours with serum free MEM culture medium at 37°C.
| | Sample_growth_protocol_ch1 | Human dermal fibroblasts were isolated from foreskin of different donors. Cells cultivated in Eagle’s minimum essential medium with Earle’s salts (MEM, PAA Laboratories Pasching, Austria) supplemented with 10% fetal bovine serum (Gibco, Karlsruhe Germany), 1% antibiotics/antimycotics (penicillin, streptomycin, amphotericin B), 1% glutamine (Gibco) and were cultivated on 100 mm plastic culture dishes (Greiner, Solingen, Germany) at 37°C in humidified air with 5% CO2. Cells were used between passages five and ten, grown to 100% confluency before treatment. At least 24 hours before IRA irradiation media was changed to serum-free MEM.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany) according to the manufacturers instruction. RNA quality and purity were assessed using an Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA). The RNA was then utilized to synthesize first- and second-strand cDNA by using the Affymetrix One-Cycle cDNA Synthesis Kit (Affymetrix UK Ltd, High Wycombe,UK) with an subsequent clean up with the GeneChip Sample Cleanup Kit (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The in vitro transcription into biotinylated cRNA was performed with the IVT Labeling Kit (Affymetrix) according to the manufacturers protocols.
| | Sample_hyb_protocol | After purification, fragmentation and a further quality and purity control with the Agilent Bioanalyzer 2100 system 9 µg of the labeled cRNA were hybridized on the Affymetrix HG-U133A Microarray according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_scan_protocol | The hybridized arrays were scanned using Microarray Suite (MAS) Software (Affymetrix) according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_data_processing | The raw data containing .cel-files were normalised in the free statistical software R Version 2.0.1 with the BioCconductor affy-package using the robust multichip average (RMA) method. A separate normalisation procedure for array samples of each of the three different fibroblast cells lead to better results regarding how often commonly regulated genes were found in total and therefore was used for this study.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,,Calles
| | Sample_contact_email | calles@uni-duesseldorf.de
| | Sample_contact_phone | +49 211 3389 324
| | Sample_contact_laboratory | AG Schroeder
| | Sample_contact_department | Molecular Ageing Research/Cellbiology
| | Sample_contact_institute | Institut fuer umweltmedizinische Forschung (IUF)
| | Sample_contact_address | Auf'm Hennekamp 50
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM426nnn/GSM426440/suppl/GSM426440.CEL.gz
| | Sample_series_id | GSE17046
| | Sample_data_row_count | 22283
| | |
|
GSM426478 | GPL96 |
|
donorF1_IRA860J/cm2_24hpostincubation_biolrep2
|
human dermal fibroblasts IRA irradiated with 860J/cm2
|
cell type: primary human dermal fibroblasts
passage: between 5-10
donor: F1
|
no additional description
|
| Sample_geo_accession | GSM426478
| | Sample_status | Public on Jul 10 2010
| | Sample_submission_date | Jul 10 2009
| | Sample_last_update_date | Jul 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | We used a waterfiltered Hydrosun 500 H 500 IRA lamp (Hydrosun Medizintechnik GmbH, Müllheim, Germany) with an emission in the range of 760-1400 nm leading to an irradiance of 360 mW/cm2 at a distance of 20 cm measured through Hydrosun HBM1 irradiance measuring device (Hydrosun). IRA irradiation lasted 40 min leading to a total dose of 860 J/cm2. The culture dishes were placed on a cooled plate connected to thermostated bath (Thermo Haake GmbH, Karlsruhe, Germany) to maintain temperatures below 37°C during IRA irradiation. For irradiation, medium was replaced by phosphate-buffered saline (37°C, Gibco). Control cells were held on a 37°C thermostated plate under similar conditions without irradiation. Following the treatment cells were cultivated for 24 hours with serum free MEM culture medium at 37°C.
| | Sample_growth_protocol_ch1 | Human dermal fibroblasts were isolated from foreskin of different donors. Cells cultivated in Eagle’s minimum essential medium with Earle’s salts (MEM, PAA Laboratories Pasching, Austria) supplemented with 10% fetal bovine serum (Gibco, Karlsruhe Germany), 1% antibiotics/antimycotics (penicillin, streptomycin, amphotericin B), 1% glutamine (Gibco) and were cultivated on 100 mm plastic culture dishes (Greiner, Solingen, Germany) at 37°C in humidified air with 5% CO2. Cells were used between passages five and ten, grown to 100% confluency before treatment. At least 24 hours before IRA irradiation media was changed to serum-free MEM.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany) according to the manufacturers instruction. RNA quality and purity were assessed using an Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA). The RNA was then utilized to synthesize first- and second-strand cDNA by using the Affymetrix One-Cycle cDNA Synthesis Kit (Affymetrix UK Ltd, High Wycombe,UK) with an subsequent clean up with the GeneChip Sample Cleanup Kit (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The in vitro transcription into biotinylated cRNA was performed with the IVT Labeling Kit (Affymetrix) according to the manufacturers protocols.
| | Sample_hyb_protocol | After purification, fragmentation and a further quality and purity control with the Agilent Bioanalyzer 2100 system 9 µg of the labeled cRNA were hybridized on the Affymetrix HG-U133A Microarray according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_scan_protocol | The hybridized arrays were scanned using Microarray Suite (MAS) Software (Affymetrix) according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_data_processing | The raw data containing .cel-files were normalised in the free statistical software R Version 2.0.1 with the BioCconductor affy-package using the robust multichip average (RMA) method. A separate normalisation procedure for array samples of each of the three different fibroblast cells lead to better results regarding how often commonly regulated genes were found in total and therefore was used for this study.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,,Calles
| | Sample_contact_email | calles@uni-duesseldorf.de
| | Sample_contact_phone | +49 211 3389 324
| | Sample_contact_laboratory | AG Schroeder
| | Sample_contact_department | Molecular Ageing Research/Cellbiology
| | Sample_contact_institute | Institut fuer umweltmedizinische Forschung (IUF)
| | Sample_contact_address | Auf'm Hennekamp 50
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM426nnn/GSM426478/suppl/GSM426478.CEL.gz
| | Sample_series_id | GSE17046
| | Sample_data_row_count | 22283
| | |
|
GSM426479 | GPL96 |
|
donorF1_IRA860J/cm2_24hpostincubation_biolrep3
|
human dermal fibroblasts IRA irradiated with 860J/cm2
|
cell type: primary human dermal fibroblasts
passage: between 5-10
donor: F1
|
no additional description
|
| Sample_geo_accession | GSM426479
| | Sample_status | Public on Jul 10 2010
| | Sample_submission_date | Jul 10 2009
| | Sample_last_update_date | Jul 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | We used a waterfiltered Hydrosun 500 H 500 IRA lamp (Hydrosun Medizintechnik GmbH, Müllheim, Germany) with an emission in the range of 760-1400 nm leading to an irradiance of 360 mW/cm2 at a distance of 20 cm measured through Hydrosun HBM1 irradiance measuring device (Hydrosun). IRA irradiation lasted 40 min leading to a total dose of 860 J/cm2. The culture dishes were placed on a cooled plate connected to thermostated bath (Thermo Haake GmbH, Karlsruhe, Germany) to maintain temperatures below 37°C during IRA irradiation. For irradiation, medium was replaced by phosphate-buffered saline (37°C, Gibco). Control cells were held on a 37°C thermostated plate under similar conditions without irradiation. Following the treatment cells were cultivated for 24 hours with serum free MEM culture medium at 37°C.
| | Sample_growth_protocol_ch1 | Human dermal fibroblasts were isolated from foreskin of different donors. Cells cultivated in Eagle’s minimum essential medium with Earle’s salts (MEM, PAA Laboratories Pasching, Austria) supplemented with 10% fetal bovine serum (Gibco, Karlsruhe Germany), 1% antibiotics/antimycotics (penicillin, streptomycin, amphotericin B), 1% glutamine (Gibco) and were cultivated on 100 mm plastic culture dishes (Greiner, Solingen, Germany) at 37°C in humidified air with 5% CO2. Cells were used between passages five and ten, grown to 100% confluency before treatment. At least 24 hours before IRA irradiation media was changed to serum-free MEM.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany) according to the manufacturers instruction. RNA quality and purity were assessed using an Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA). The RNA was then utilized to synthesize first- and second-strand cDNA by using the Affymetrix One-Cycle cDNA Synthesis Kit (Affymetrix UK Ltd, High Wycombe,UK) with an subsequent clean up with the GeneChip Sample Cleanup Kit (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The in vitro transcription into biotinylated cRNA was performed with the IVT Labeling Kit (Affymetrix) according to the manufacturers protocols.
| | Sample_hyb_protocol | After purification, fragmentation and a further quality and purity control with the Agilent Bioanalyzer 2100 system 9 µg of the labeled cRNA were hybridized on the Affymetrix HG-U133A Microarray according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_scan_protocol | The hybridized arrays were scanned using Microarray Suite (MAS) Software (Affymetrix) according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_data_processing | The raw data containing .cel-files were normalised in the free statistical software R Version 2.0.1 with the BioCconductor affy-package using the robust multichip average (RMA) method. A separate normalisation procedure for array samples of each of the three different fibroblast cells lead to better results regarding how often commonly regulated genes were found in total and therefore was used for this study.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,,Calles
| | Sample_contact_email | calles@uni-duesseldorf.de
| | Sample_contact_phone | +49 211 3389 324
| | Sample_contact_laboratory | AG Schroeder
| | Sample_contact_department | Molecular Ageing Research/Cellbiology
| | Sample_contact_institute | Institut fuer umweltmedizinische Forschung (IUF)
| | Sample_contact_address | Auf'm Hennekamp 50
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM426nnn/GSM426479/suppl/GSM426479.CEL.gz
| | Sample_series_id | GSE17046
| | Sample_data_row_count | 22283
| | |
|
GSM426482 | GPL96 |
|
donorF1_shamtreated_24hpostincubation_biolrep1
|
human dermal fibroblasts sham treated control
|
cell type: primary human dermal fibroblasts
passage: between 5-10
donor: F1
|
no additional description
|
| Sample_geo_accession | GSM426482
| | Sample_status | Public on Jul 10 2010
| | Sample_submission_date | Jul 10 2009
| | Sample_last_update_date | Jul 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | We used a waterfiltered Hydrosun 500 H 500 IRA lamp (Hydrosun Medizintechnik GmbH, Müllheim, Germany) with an emission in the range of 760-1400 nm leading to an irradiance of 360 mW/cm2 at a distance of 20 cm measured through Hydrosun HBM1 irradiance measuring device (Hydrosun). IRA irradiation lasted 40 min leading to a total dose of 860 J/cm2. The culture dishes were placed on a cooled plate connected to thermostated bath (Thermo Haake GmbH, Karlsruhe, Germany) to maintain temperatures below 37°C during IRA irradiation. For irradiation, medium was replaced by phosphate-buffered saline (37°C, Gibco). Control cells were held on a 37°C thermostated plate under similar conditions without irradiation. Following the treatment cells were cultivated for 24 hours with serum free MEM culture medium at 37°C.
| | Sample_growth_protocol_ch1 | Human dermal fibroblasts were isolated from foreskin of different donors. Cells cultivated in Eagle’s minimum essential medium with Earle’s salts (MEM, PAA Laboratories Pasching, Austria) supplemented with 10% fetal bovine serum (Gibco, Karlsruhe Germany), 1% antibiotics/antimycotics (penicillin, streptomycin, amphotericin B), 1% glutamine (Gibco) and were cultivated on 100 mm plastic culture dishes (Greiner, Solingen, Germany) at 37°C in humidified air with 5% CO2. Cells were used between passages five and ten, grown to 100% confluency before treatment. At least 24 hours before IRA irradiation media was changed to serum-free MEM.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany) according to the manufacturers instruction. RNA quality and purity were assessed using an Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA). The RNA was then utilized to synthesize first- and second-strand cDNA by using the Affymetrix One-Cycle cDNA Synthesis Kit (Affymetrix UK Ltd, High Wycombe,UK) with an subsequent clean up with the GeneChip Sample Cleanup Kit (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The in vitro transcription into biotinylated cRNA was performed with the IVT Labeling Kit (Affymetrix) according to the manufacturers protocols.
| | Sample_hyb_protocol | After purification, fragmentation and a further quality and purity control with the Agilent Bioanalyzer 2100 system 9 µg of the labeled cRNA were hybridized on the Affymetrix HG-U133A Microarray according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_scan_protocol | The hybridized arrays were scanned using Microarray Suite (MAS) Software (Affymetrix) according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_data_processing | The raw data containing .cel-files were normalised in the free statistical software R Version 2.0.1 with the BioCconductor affy-package using the robust multichip average (RMA) method. A separate normalisation procedure for array samples of each of the three different fibroblast cells lead to better results regarding how often commonly regulated genes were found in total and therefore was used for this study.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,,Calles
| | Sample_contact_email | calles@uni-duesseldorf.de
| | Sample_contact_phone | +49 211 3389 324
| | Sample_contact_laboratory | AG Schroeder
| | Sample_contact_department | Molecular Ageing Research/Cellbiology
| | Sample_contact_institute | Institut fuer umweltmedizinische Forschung (IUF)
| | Sample_contact_address | Auf'm Hennekamp 50
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM426nnn/GSM426482/suppl/GSM426482.CEL.gz
| | Sample_series_id | GSE17046
| | Sample_data_row_count | 22283
| | |
|
GSM426483 | GPL96 |
|
donorF1_shamtreated_24hpostincubation_biolrep2
|
human dermal fibroblasts sham treated control
|
cell type: primary human dermal fibroblasts
passage: between 5-10
donor: F1
|
no additional description
|
| Sample_geo_accession | GSM426483
| | Sample_status | Public on Jul 10 2010
| | Sample_submission_date | Jul 10 2009
| | Sample_last_update_date | Jul 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | We used a waterfiltered Hydrosun 500 H 500 IRA lamp (Hydrosun Medizintechnik GmbH, Müllheim, Germany) with an emission in the range of 760-1400 nm leading to an irradiance of 360 mW/cm2 at a distance of 20 cm measured through Hydrosun HBM1 irradiance measuring device (Hydrosun). IRA irradiation lasted 40 min leading to a total dose of 860 J/cm2. The culture dishes were placed on a cooled plate connected to thermostated bath (Thermo Haake GmbH, Karlsruhe, Germany) to maintain temperatures below 37°C during IRA irradiation. For irradiation, medium was replaced by phosphate-buffered saline (37°C, Gibco). Control cells were held on a 37°C thermostated plate under similar conditions without irradiation. Following the treatment cells were cultivated for 24 hours with serum free MEM culture medium at 37°C.
| | Sample_growth_protocol_ch1 | Human dermal fibroblasts were isolated from foreskin of different donors. Cells cultivated in Eagle’s minimum essential medium with Earle’s salts (MEM, PAA Laboratories Pasching, Austria) supplemented with 10% fetal bovine serum (Gibco, Karlsruhe Germany), 1% antibiotics/antimycotics (penicillin, streptomycin, amphotericin B), 1% glutamine (Gibco) and were cultivated on 100 mm plastic culture dishes (Greiner, Solingen, Germany) at 37°C in humidified air with 5% CO2. Cells were used between passages five and ten, grown to 100% confluency before treatment. At least 24 hours before IRA irradiation media was changed to serum-free MEM.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany) according to the manufacturers instruction. RNA quality and purity were assessed using an Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA). The RNA was then utilized to synthesize first- and second-strand cDNA by using the Affymetrix One-Cycle cDNA Synthesis Kit (Affymetrix UK Ltd, High Wycombe,UK) with an subsequent clean up with the GeneChip Sample Cleanup Kit (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The in vitro transcription into biotinylated cRNA was performed with the IVT Labeling Kit (Affymetrix) according to the manufacturers protocols.
| | Sample_hyb_protocol | After purification, fragmentation and a further quality and purity control with the Agilent Bioanalyzer 2100 system 9 µg of the labeled cRNA were hybridized on the Affymetrix HG-U133A Microarray according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_scan_protocol | The hybridized arrays were scanned using Microarray Suite (MAS) Software (Affymetrix) according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_data_processing | The raw data containing .cel-files were normalised in the free statistical software R Version 2.0.1 with the BioCconductor affy-package using the robust multichip average (RMA) method. A separate normalisation procedure for array samples of each of the three different fibroblast cells lead to better results regarding how often commonly regulated genes were found in total and therefore was used for this study.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,,Calles
| | Sample_contact_email | calles@uni-duesseldorf.de
| | Sample_contact_phone | +49 211 3389 324
| | Sample_contact_laboratory | AG Schroeder
| | Sample_contact_department | Molecular Ageing Research/Cellbiology
| | Sample_contact_institute | Institut fuer umweltmedizinische Forschung (IUF)
| | Sample_contact_address | Auf'm Hennekamp 50
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM426nnn/GSM426483/suppl/GSM426483.CEL.gz
| | Sample_series_id | GSE17046
| | Sample_data_row_count | 22283
| | |
|
GSM426484 | GPL96 |
|
donorF1_shamtreated_24hpostincubation_biolrep3
|
human dermal fibroblasts sham treated control
|
cell type: primary human dermal fibroblasts
passage: between 5-10
donor: F1
|
no additional description
|
| Sample_geo_accession | GSM426484
| | Sample_status | Public on Jul 10 2010
| | Sample_submission_date | Jul 10 2009
| | Sample_last_update_date | Jul 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | We used a waterfiltered Hydrosun 500 H 500 IRA lamp (Hydrosun Medizintechnik GmbH, Müllheim, Germany) with an emission in the range of 760-1400 nm leading to an irradiance of 360 mW/cm2 at a distance of 20 cm measured through Hydrosun HBM1 irradiance measuring device (Hydrosun). IRA irradiation lasted 40 min leading to a total dose of 860 J/cm2. The culture dishes were placed on a cooled plate connected to thermostated bath (Thermo Haake GmbH, Karlsruhe, Germany) to maintain temperatures below 37°C during IRA irradiation. For irradiation, medium was replaced by phosphate-buffered saline (37°C, Gibco). Control cells were held on a 37°C thermostated plate under similar conditions without irradiation. Following the treatment cells were cultivated for 24 hours with serum free MEM culture medium at 37°C.
| | Sample_growth_protocol_ch1 | Human dermal fibroblasts were isolated from foreskin of different donors. Cells cultivated in Eagle’s minimum essential medium with Earle’s salts (MEM, PAA Laboratories Pasching, Austria) supplemented with 10% fetal bovine serum (Gibco, Karlsruhe Germany), 1% antibiotics/antimycotics (penicillin, streptomycin, amphotericin B), 1% glutamine (Gibco) and were cultivated on 100 mm plastic culture dishes (Greiner, Solingen, Germany) at 37°C in humidified air with 5% CO2. Cells were used between passages five and ten, grown to 100% confluency before treatment. At least 24 hours before IRA irradiation media was changed to serum-free MEM.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany) according to the manufacturers instruction. RNA quality and purity were assessed using an Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA). The RNA was then utilized to synthesize first- and second-strand cDNA by using the Affymetrix One-Cycle cDNA Synthesis Kit (Affymetrix UK Ltd, High Wycombe,UK) with an subsequent clean up with the GeneChip Sample Cleanup Kit (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The in vitro transcription into biotinylated cRNA was performed with the IVT Labeling Kit (Affymetrix) according to the manufacturers protocols.
| | Sample_hyb_protocol | After purification, fragmentation and a further quality and purity control with the Agilent Bioanalyzer 2100 system 9 µg of the labeled cRNA were hybridized on the Affymetrix HG-U133A Microarray according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_scan_protocol | The hybridized arrays were scanned using Microarray Suite (MAS) Software (Affymetrix) according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_data_processing | The raw data containing .cel-files were normalised in the free statistical software R Version 2.0.1 with the BioCconductor affy-package using the robust multichip average (RMA) method. A separate normalisation procedure for array samples of each of the three different fibroblast cells lead to better results regarding how often commonly regulated genes were found in total and therefore was used for this study.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,,Calles
| | Sample_contact_email | calles@uni-duesseldorf.de
| | Sample_contact_phone | +49 211 3389 324
| | Sample_contact_laboratory | AG Schroeder
| | Sample_contact_department | Molecular Ageing Research/Cellbiology
| | Sample_contact_institute | Institut fuer umweltmedizinische Forschung (IUF)
| | Sample_contact_address | Auf'm Hennekamp 50
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM426nnn/GSM426484/suppl/GSM426484.CEL.gz
| | Sample_series_id | GSE17046
| | Sample_data_row_count | 22283
| | |
|
GSM426485 | GPL96 |
|
donorF2_IRA860J/cm2_24hpostincubation_biolrep1
|
human dermal fibroblasts IRA irradiated with 860J/cm2
|
cell type: primary human dermal fibroblasts
passage: between 5-10
donor: F2
|
no additional description
|
| Sample_geo_accession | GSM426485
| | Sample_status | Public on Jul 10 2010
| | Sample_submission_date | Jul 10 2009
| | Sample_last_update_date | Jul 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | We used a waterfiltered Hydrosun 500 H 500 IRA lamp (Hydrosun Medizintechnik GmbH, Müllheim, Germany) with an emission in the range of 760-1400 nm leading to an irradiance of 360 mW/cm2 at a distance of 20 cm measured through Hydrosun HBM1 irradiance measuring device (Hydrosun). IRA irradiation lasted 40 min leading to a total dose of 860 J/cm2. The culture dishes were placed on a cooled plate connected to thermostated bath (Thermo Haake GmbH, Karlsruhe, Germany) to maintain temperatures below 37°C during IRA irradiation. For irradiation, medium was replaced by phosphate-buffered saline (37°C, Gibco). Control cells were held on a 37°C thermostated plate under similar conditions without irradiation. Following the treatment cells were cultivated for 24 hours with serum free MEM culture medium at 37°C.
| | Sample_growth_protocol_ch1 | Human dermal fibroblasts were isolated from foreskin of different donors. Cells cultivated in Eagle’s minimum essential medium with Earle’s salts (MEM, PAA Laboratories Pasching, Austria) supplemented with 10% fetal bovine serum (Gibco, Karlsruhe Germany), 1% antibiotics/antimycotics (penicillin, streptomycin, amphotericin B), 1% glutamine (Gibco) and were cultivated on 100 mm plastic culture dishes (Greiner, Solingen, Germany) at 37°C in humidified air with 5% CO2. Cells were used between passages five and ten, grown to 100% confluency before treatment. At least 24 hours before IRA irradiation media was changed to serum-free MEM.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany) according to the manufacturers instruction. RNA quality and purity were assessed using an Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA). The RNA was then utilized to synthesize first- and second-strand cDNA by using the Affymetrix One-Cycle cDNA Synthesis Kit (Affymetrix UK Ltd, High Wycombe,UK) with an subsequent clean up with the GeneChip Sample Cleanup Kit (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The in vitro transcription into biotinylated cRNA was performed with the IVT Labeling Kit (Affymetrix) according to the manufacturers protocols.
| | Sample_hyb_protocol | After purification, fragmentation and a further quality and purity control with the Agilent Bioanalyzer 2100 system 9 µg of the labeled cRNA were hybridized on the Affymetrix HG-U133A Microarray according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_scan_protocol | The hybridized arrays were scanned using Microarray Suite (MAS) Software (Affymetrix) according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_data_processing | The raw data containing .cel-files were normalised in the free statistical software R Version 2.0.1 with the BioCconductor affy-package using the robust multichip average (RMA) method. A separate normalisation procedure for array samples of each of the three different fibroblast cells lead to better results regarding how often commonly regulated genes were found in total and therefore was used for this study.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,,Calles
| | Sample_contact_email | calles@uni-duesseldorf.de
| | Sample_contact_phone | +49 211 3389 324
| | Sample_contact_laboratory | AG Schroeder
| | Sample_contact_department | Molecular Ageing Research/Cellbiology
| | Sample_contact_institute | Institut fuer umweltmedizinische Forschung (IUF)
| | Sample_contact_address | Auf'm Hennekamp 50
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM426nnn/GSM426485/suppl/GSM426485.CEL.gz
| | Sample_series_id | GSE17046
| | Sample_data_row_count | 22283
| | |
|
GSM426486 | GPL96 |
|
donorF2_IRA860J/cm2_24hpostincubation_biolrep2
|
human dermal fibroblasts IRA irradiated with 860J/cm2
|
cell type: primary human dermal fibroblasts
passage: between 5-10
donor: F2
|
no additional description
|
| Sample_geo_accession | GSM426486
| | Sample_status | Public on Jul 10 2010
| | Sample_submission_date | Jul 10 2009
| | Sample_last_update_date | Jul 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | We used a waterfiltered Hydrosun 500 H 500 IRA lamp (Hydrosun Medizintechnik GmbH, Müllheim, Germany) with an emission in the range of 760-1400 nm leading to an irradiance of 360 mW/cm2 at a distance of 20 cm measured through Hydrosun HBM1 irradiance measuring device (Hydrosun). IRA irradiation lasted 40 min leading to a total dose of 860 J/cm2. The culture dishes were placed on a cooled plate connected to thermostated bath (Thermo Haake GmbH, Karlsruhe, Germany) to maintain temperatures below 37°C during IRA irradiation. For irradiation, medium was replaced by phosphate-buffered saline (37°C, Gibco). Control cells were held on a 37°C thermostated plate under similar conditions without irradiation. Following the treatment cells were cultivated for 24 hours with serum free MEM culture medium at 37°C.
| | Sample_growth_protocol_ch1 | Human dermal fibroblasts were isolated from foreskin of different donors. Cells cultivated in Eagle’s minimum essential medium with Earle’s salts (MEM, PAA Laboratories Pasching, Austria) supplemented with 10% fetal bovine serum (Gibco, Karlsruhe Germany), 1% antibiotics/antimycotics (penicillin, streptomycin, amphotericin B), 1% glutamine (Gibco) and were cultivated on 100 mm plastic culture dishes (Greiner, Solingen, Germany) at 37°C in humidified air with 5% CO2. Cells were used between passages five and ten, grown to 100% confluency before treatment. At least 24 hours before IRA irradiation media was changed to serum-free MEM.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany) according to the manufacturers instruction. RNA quality and purity were assessed using an Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA). The RNA was then utilized to synthesize first- and second-strand cDNA by using the Affymetrix One-Cycle cDNA Synthesis Kit (Affymetrix UK Ltd, High Wycombe,UK) with an subsequent clean up with the GeneChip Sample Cleanup Kit (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The in vitro transcription into biotinylated cRNA was performed with the IVT Labeling Kit (Affymetrix) according to the manufacturers protocols.
| | Sample_hyb_protocol | After purification, fragmentation and a further quality and purity control with the Agilent Bioanalyzer 2100 system 9 µg of the labeled cRNA were hybridized on the Affymetrix HG-U133A Microarray according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_scan_protocol | The hybridized arrays were scanned using Microarray Suite (MAS) Software (Affymetrix) according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_data_processing | The raw data containing .cel-files were normalised in the free statistical software R Version 2.0.1 with the BioCconductor affy-package using the robust multichip average (RMA) method. A separate normalisation procedure for array samples of each of the three different fibroblast cells lead to better results regarding how often commonly regulated genes were found in total and therefore was used for this study.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,,Calles
| | Sample_contact_email | calles@uni-duesseldorf.de
| | Sample_contact_phone | +49 211 3389 324
| | Sample_contact_laboratory | AG Schroeder
| | Sample_contact_department | Molecular Ageing Research/Cellbiology
| | Sample_contact_institute | Institut fuer umweltmedizinische Forschung (IUF)
| | Sample_contact_address | Auf'm Hennekamp 50
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM426nnn/GSM426486/suppl/GSM426486.CEL.gz
| | Sample_series_id | GSE17046
| | Sample_data_row_count | 22283
| | |
|
GSM426487 | GPL96 |
|
donorF2_IRA860J/cm2_24hpostincubation_biolrep3
|
human dermal fibroblasts IRA irradiated with 860J/cm2
|
cell type: primary human dermal fibroblasts
passage: between 5-10
donor: F2
|
no additional description
|
| Sample_geo_accession | GSM426487
| | Sample_status | Public on Jul 10 2010
| | Sample_submission_date | Jul 10 2009
| | Sample_last_update_date | Jul 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | We used a waterfiltered Hydrosun 500 H 500 IRA lamp (Hydrosun Medizintechnik GmbH, Müllheim, Germany) with an emission in the range of 760-1400 nm leading to an irradiance of 360 mW/cm2 at a distance of 20 cm measured through Hydrosun HBM1 irradiance measuring device (Hydrosun). IRA irradiation lasted 40 min leading to a total dose of 860 J/cm2. The culture dishes were placed on a cooled plate connected to thermostated bath (Thermo Haake GmbH, Karlsruhe, Germany) to maintain temperatures below 37°C during IRA irradiation. For irradiation, medium was replaced by phosphate-buffered saline (37°C, Gibco). Control cells were held on a 37°C thermostated plate under similar conditions without irradiation. Following the treatment cells were cultivated for 24 hours with serum free MEM culture medium at 37°C.
| | Sample_growth_protocol_ch1 | Human dermal fibroblasts were isolated from foreskin of different donors. Cells cultivated in Eagle’s minimum essential medium with Earle’s salts (MEM, PAA Laboratories Pasching, Austria) supplemented with 10% fetal bovine serum (Gibco, Karlsruhe Germany), 1% antibiotics/antimycotics (penicillin, streptomycin, amphotericin B), 1% glutamine (Gibco) and were cultivated on 100 mm plastic culture dishes (Greiner, Solingen, Germany) at 37°C in humidified air with 5% CO2. Cells were used between passages five and ten, grown to 100% confluency before treatment. At least 24 hours before IRA irradiation media was changed to serum-free MEM.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany) according to the manufacturers instruction. RNA quality and purity were assessed using an Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA). The RNA was then utilized to synthesize first- and second-strand cDNA by using the Affymetrix One-Cycle cDNA Synthesis Kit (Affymetrix UK Ltd, High Wycombe,UK) with an subsequent clean up with the GeneChip Sample Cleanup Kit (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The in vitro transcription into biotinylated cRNA was performed with the IVT Labeling Kit (Affymetrix) according to the manufacturers protocols.
| | Sample_hyb_protocol | After purification, fragmentation and a further quality and purity control with the Agilent Bioanalyzer 2100 system 9 µg of the labeled cRNA were hybridized on the Affymetrix HG-U133A Microarray according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_scan_protocol | The hybridized arrays were scanned using Microarray Suite (MAS) Software (Affymetrix) according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_data_processing | The raw data containing .cel-files were normalised in the free statistical software R Version 2.0.1 with the BioCconductor affy-package using the robust multichip average (RMA) method. A separate normalisation procedure for array samples of each of the three different fibroblast cells lead to better results regarding how often commonly regulated genes were found in total and therefore was used for this study.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,,Calles
| | Sample_contact_email | calles@uni-duesseldorf.de
| | Sample_contact_phone | +49 211 3389 324
| | Sample_contact_laboratory | AG Schroeder
| | Sample_contact_department | Molecular Ageing Research/Cellbiology
| | Sample_contact_institute | Institut fuer umweltmedizinische Forschung (IUF)
| | Sample_contact_address | Auf'm Hennekamp 50
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM426nnn/GSM426487/suppl/GSM426487.CEL.gz
| | Sample_series_id | GSE17046
| | Sample_data_row_count | 22283
| | |
|
GSM426488 | GPL96 |
|
donorF2_shamtreated_24hpostincubation_biolrep1
|
human dermal fibroblasts sham treated control
|
cell type: primary human dermal fibroblasts
passage: between 5-10
donor: F2
|
no additional description
|
| Sample_geo_accession | GSM426488
| | Sample_status | Public on Jul 10 2010
| | Sample_submission_date | Jul 10 2009
| | Sample_last_update_date | Jul 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | We used a waterfiltered Hydrosun 500 H 500 IRA lamp (Hydrosun Medizintechnik GmbH, Müllheim, Germany) with an emission in the range of 760-1400 nm leading to an irradiance of 360 mW/cm2 at a distance of 20 cm measured through Hydrosun HBM1 irradiance measuring device (Hydrosun). IRA irradiation lasted 40 min leading to a total dose of 860 J/cm2. The culture dishes were placed on a cooled plate connected to thermostated bath (Thermo Haake GmbH, Karlsruhe, Germany) to maintain temperatures below 37°C during IRA irradiation. For irradiation, medium was replaced by phosphate-buffered saline (37°C, Gibco). Control cells were held on a 37°C thermostated plate under similar conditions without irradiation. Following the treatment cells were cultivated for 24 hours with serum free MEM culture medium at 37°C.
| | Sample_growth_protocol_ch1 | Human dermal fibroblasts were isolated from foreskin of different donors. Cells cultivated in Eagle’s minimum essential medium with Earle’s salts (MEM, PAA Laboratories Pasching, Austria) supplemented with 10% fetal bovine serum (Gibco, Karlsruhe Germany), 1% antibiotics/antimycotics (penicillin, streptomycin, amphotericin B), 1% glutamine (Gibco) and were cultivated on 100 mm plastic culture dishes (Greiner, Solingen, Germany) at 37°C in humidified air with 5% CO2. Cells were used between passages five and ten, grown to 100% confluency before treatment. At least 24 hours before IRA irradiation media was changed to serum-free MEM.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany) according to the manufacturers instruction. RNA quality and purity were assessed using an Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA). The RNA was then utilized to synthesize first- and second-strand cDNA by using the Affymetrix One-Cycle cDNA Synthesis Kit (Affymetrix UK Ltd, High Wycombe,UK) with an subsequent clean up with the GeneChip Sample Cleanup Kit (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The in vitro transcription into biotinylated cRNA was performed with the IVT Labeling Kit (Affymetrix) according to the manufacturers protocols.
| | Sample_hyb_protocol | After purification, fragmentation and a further quality and purity control with the Agilent Bioanalyzer 2100 system 9 µg of the labeled cRNA were hybridized on the Affymetrix HG-U133A Microarray according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_scan_protocol | The hybridized arrays were scanned using Microarray Suite (MAS) Software (Affymetrix) according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_data_processing | The raw data containing .cel-files were normalised in the free statistical software R Version 2.0.1 with the BioCconductor affy-package using the robust multichip average (RMA) method. A separate normalisation procedure for array samples of each of the three different fibroblast cells lead to better results regarding how often commonly regulated genes were found in total and therefore was used for this study.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,,Calles
| | Sample_contact_email | calles@uni-duesseldorf.de
| | Sample_contact_phone | +49 211 3389 324
| | Sample_contact_laboratory | AG Schroeder
| | Sample_contact_department | Molecular Ageing Research/Cellbiology
| | Sample_contact_institute | Institut fuer umweltmedizinische Forschung (IUF)
| | Sample_contact_address | Auf'm Hennekamp 50
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM426nnn/GSM426488/suppl/GSM426488.CEL.gz
| | Sample_series_id | GSE17046
| | Sample_data_row_count | 22283
| | |
|
GSM426489 | GPL96 |
|
donorF2_shamtreated_24hpostincubation_biolrep2
|
human dermal fibroblasts sham treated control
|
cell type: primary human dermal fibroblasts
passage: between 5-10
donor: F2
|
no additional description
|
| Sample_geo_accession | GSM426489
| | Sample_status | Public on Jul 10 2010
| | Sample_submission_date | Jul 10 2009
| | Sample_last_update_date | Jul 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | We used a waterfiltered Hydrosun 500 H 500 IRA lamp (Hydrosun Medizintechnik GmbH, Müllheim, Germany) with an emission in the range of 760-1400 nm leading to an irradiance of 360 mW/cm2 at a distance of 20 cm measured through Hydrosun HBM1 irradiance measuring device (Hydrosun). IRA irradiation lasted 40 min leading to a total dose of 860 J/cm2. The culture dishes were placed on a cooled plate connected to thermostated bath (Thermo Haake GmbH, Karlsruhe, Germany) to maintain temperatures below 37°C during IRA irradiation. For irradiation, medium was replaced by phosphate-buffered saline (37°C, Gibco). Control cells were held on a 37°C thermostated plate under similar conditions without irradiation. Following the treatment cells were cultivated for 24 hours with serum free MEM culture medium at 37°C.
| | Sample_growth_protocol_ch1 | Human dermal fibroblasts were isolated from foreskin of different donors. Cells cultivated in Eagle’s minimum essential medium with Earle’s salts (MEM, PAA Laboratories Pasching, Austria) supplemented with 10% fetal bovine serum (Gibco, Karlsruhe Germany), 1% antibiotics/antimycotics (penicillin, streptomycin, amphotericin B), 1% glutamine (Gibco) and were cultivated on 100 mm plastic culture dishes (Greiner, Solingen, Germany) at 37°C in humidified air with 5% CO2. Cells were used between passages five and ten, grown to 100% confluency before treatment. At least 24 hours before IRA irradiation media was changed to serum-free MEM.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany) according to the manufacturers instruction. RNA quality and purity were assessed using an Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA). The RNA was then utilized to synthesize first- and second-strand cDNA by using the Affymetrix One-Cycle cDNA Synthesis Kit (Affymetrix UK Ltd, High Wycombe,UK) with an subsequent clean up with the GeneChip Sample Cleanup Kit (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The in vitro transcription into biotinylated cRNA was performed with the IVT Labeling Kit (Affymetrix) according to the manufacturers protocols.
| | Sample_hyb_protocol | After purification, fragmentation and a further quality and purity control with the Agilent Bioanalyzer 2100 system 9 µg of the labeled cRNA were hybridized on the Affymetrix HG-U133A Microarray according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_scan_protocol | The hybridized arrays were scanned using Microarray Suite (MAS) Software (Affymetrix) according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_data_processing | The raw data containing .cel-files were normalised in the free statistical software R Version 2.0.1 with the BioCconductor affy-package using the robust multichip average (RMA) method. A separate normalisation procedure for array samples of each of the three different fibroblast cells lead to better results regarding how often commonly regulated genes were found in total and therefore was used for this study.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,,Calles
| | Sample_contact_email | calles@uni-duesseldorf.de
| | Sample_contact_phone | +49 211 3389 324
| | Sample_contact_laboratory | AG Schroeder
| | Sample_contact_department | Molecular Ageing Research/Cellbiology
| | Sample_contact_institute | Institut fuer umweltmedizinische Forschung (IUF)
| | Sample_contact_address | Auf'm Hennekamp 50
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM426nnn/GSM426489/suppl/GSM426489.CEL.gz
| | Sample_series_id | GSE17046
| | Sample_data_row_count | 22283
| | |
|
GSM426490 | GPL96 |
|
donorF2_shamtreated_24hpostincubation_biolrep3
|
human dermal fibroblasts sham treated control
|
cell type: primary human dermal fibroblasts
passage: between 5-10
donor: F2
|
no additional description
|
| Sample_geo_accession | GSM426490
| | Sample_status | Public on Jul 10 2010
| | Sample_submission_date | Jul 10 2009
| | Sample_last_update_date | Jul 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | We used a waterfiltered Hydrosun 500 H 500 IRA lamp (Hydrosun Medizintechnik GmbH, Müllheim, Germany) with an emission in the range of 760-1400 nm leading to an irradiance of 360 mW/cm2 at a distance of 20 cm measured through Hydrosun HBM1 irradiance measuring device (Hydrosun). IRA irradiation lasted 40 min leading to a total dose of 860 J/cm2. The culture dishes were placed on a cooled plate connected to thermostated bath (Thermo Haake GmbH, Karlsruhe, Germany) to maintain temperatures below 37°C during IRA irradiation. For irradiation, medium was replaced by phosphate-buffered saline (37°C, Gibco). Control cells were held on a 37°C thermostated plate under similar conditions without irradiation. Following the treatment cells were cultivated for 24 hours with serum free MEM culture medium at 37°C.
| | Sample_growth_protocol_ch1 | Human dermal fibroblasts were isolated from foreskin of different donors. Cells cultivated in Eagle’s minimum essential medium with Earle’s salts (MEM, PAA Laboratories Pasching, Austria) supplemented with 10% fetal bovine serum (Gibco, Karlsruhe Germany), 1% antibiotics/antimycotics (penicillin, streptomycin, amphotericin B), 1% glutamine (Gibco) and were cultivated on 100 mm plastic culture dishes (Greiner, Solingen, Germany) at 37°C in humidified air with 5% CO2. Cells were used between passages five and ten, grown to 100% confluency before treatment. At least 24 hours before IRA irradiation media was changed to serum-free MEM.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany) according to the manufacturers instruction. RNA quality and purity were assessed using an Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA). The RNA was then utilized to synthesize first- and second-strand cDNA by using the Affymetrix One-Cycle cDNA Synthesis Kit (Affymetrix UK Ltd, High Wycombe,UK) with an subsequent clean up with the GeneChip Sample Cleanup Kit (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The in vitro transcription into biotinylated cRNA was performed with the IVT Labeling Kit (Affymetrix) according to the manufacturers protocols.
| | Sample_hyb_protocol | After purification, fragmentation and a further quality and purity control with the Agilent Bioanalyzer 2100 system 9 µg of the labeled cRNA were hybridized on the Affymetrix HG-U133A Microarray according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_scan_protocol | The hybridized arrays were scanned using Microarray Suite (MAS) Software (Affymetrix) according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_data_processing | The raw data containing .cel-files were normalised in the free statistical software R Version 2.0.1 with the BioCconductor affy-package using the robust multichip average (RMA) method. A separate normalisation procedure for array samples of each of the three different fibroblast cells lead to better results regarding how often commonly regulated genes were found in total and therefore was used for this study.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,,Calles
| | Sample_contact_email | calles@uni-duesseldorf.de
| | Sample_contact_phone | +49 211 3389 324
| | Sample_contact_laboratory | AG Schroeder
| | Sample_contact_department | Molecular Ageing Research/Cellbiology
| | Sample_contact_institute | Institut fuer umweltmedizinische Forschung (IUF)
| | Sample_contact_address | Auf'm Hennekamp 50
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM426nnn/GSM426490/suppl/GSM426490.CEL.gz
| | Sample_series_id | GSE17046
| | Sample_data_row_count | 22283
| | |
|
GSM426491 | GPL96 |
|
donorF3_IRA860J/cm2_24hpostincubation_biolrep1
|
human dermal fibroblasts IRA irradiated with 860J/cm2
|
cell type: primary human dermal fibroblasts
passage: between 5-10
donor: F3
|
no additional description
|
| Sample_geo_accession | GSM426491
| | Sample_status | Public on Jul 10 2010
| | Sample_submission_date | Jul 10 2009
| | Sample_last_update_date | Jul 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | We used a waterfiltered Hydrosun 500 H 500 IRA lamp (Hydrosun Medizintechnik GmbH, Müllheim, Germany) with an emission in the range of 760-1400 nm leading to an irradiance of 360 mW/cm2 at a distance of 20 cm measured through Hydrosun HBM1 irradiance measuring device (Hydrosun). IRA irradiation lasted 40 min leading to a total dose of 860 J/cm2. The culture dishes were placed on a cooled plate connected to thermostated bath (Thermo Haake GmbH, Karlsruhe, Germany) to maintain temperatures below 37°C during IRA irradiation. For irradiation, medium was replaced by phosphate-buffered saline (37°C, Gibco). Control cells were held on a 37°C thermostated plate under similar conditions without irradiation. Following the treatment cells were cultivated for 24 hours with serum free MEM culture medium at 37°C.
| | Sample_growth_protocol_ch1 | Human dermal fibroblasts were isolated from foreskin of different donors. Cells cultivated in Eagle’s minimum essential medium with Earle’s salts (MEM, PAA Laboratories Pasching, Austria) supplemented with 10% fetal bovine serum (Gibco, Karlsruhe Germany), 1% antibiotics/antimycotics (penicillin, streptomycin, amphotericin B), 1% glutamine (Gibco) and were cultivated on 100 mm plastic culture dishes (Greiner, Solingen, Germany) at 37°C in humidified air with 5% CO2. Cells were used between passages five and ten, grown to 100% confluency before treatment. At least 24 hours before IRA irradiation media was changed to serum-free MEM.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany) according to the manufacturers instruction. RNA quality and purity were assessed using an Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA). The RNA was then utilized to synthesize first- and second-strand cDNA by using the Affymetrix One-Cycle cDNA Synthesis Kit (Affymetrix UK Ltd, High Wycombe,UK) with an subsequent clean up with the GeneChip Sample Cleanup Kit (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The in vitro transcription into biotinylated cRNA was performed with the IVT Labeling Kit (Affymetrix) according to the manufacturers protocols.
| | Sample_hyb_protocol | After purification, fragmentation and a further quality and purity control with the Agilent Bioanalyzer 2100 system 9 µg of the labeled cRNA were hybridized on the Affymetrix HG-U133A Microarray according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_scan_protocol | The hybridized arrays were scanned using Microarray Suite (MAS) Software (Affymetrix) according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_data_processing | The raw data containing .cel-files were normalised in the free statistical software R Version 2.0.1 with the BioCconductor affy-package using the robust multichip average (RMA) method. A separate normalisation procedure for array samples of each of the three different fibroblast cells lead to better results regarding how often commonly regulated genes were found in total and therefore was used for this study.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,,Calles
| | Sample_contact_email | calles@uni-duesseldorf.de
| | Sample_contact_phone | +49 211 3389 324
| | Sample_contact_laboratory | AG Schroeder
| | Sample_contact_department | Molecular Ageing Research/Cellbiology
| | Sample_contact_institute | Institut fuer umweltmedizinische Forschung (IUF)
| | Sample_contact_address | Auf'm Hennekamp 50
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM426nnn/GSM426491/suppl/GSM426491.CEL.gz
| | Sample_series_id | GSE17046
| | Sample_data_row_count | 22283
| | |
|
GSM426492 | GPL96 |
|
donorF3_IRA860J/cm2_24hpostincubation_biolrep2
|
human dermal fibroblasts IRA irradiated with 860J/cm2
|
cell type: primary human dermal fibroblasts
passage: between 5-10
donor: F3
|
no additional description
|
| Sample_geo_accession | GSM426492
| | Sample_status | Public on Jul 10 2010
| | Sample_submission_date | Jul 10 2009
| | Sample_last_update_date | Jul 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | We used a waterfiltered Hydrosun 500 H 500 IRA lamp (Hydrosun Medizintechnik GmbH, Müllheim, Germany) with an emission in the range of 760-1400 nm leading to an irradiance of 360 mW/cm2 at a distance of 20 cm measured through Hydrosun HBM1 irradiance measuring device (Hydrosun). IRA irradiation lasted 40 min leading to a total dose of 860 J/cm2. The culture dishes were placed on a cooled plate connected to thermostated bath (Thermo Haake GmbH, Karlsruhe, Germany) to maintain temperatures below 37°C during IRA irradiation. For irradiation, medium was replaced by phosphate-buffered saline (37°C, Gibco). Control cells were held on a 37°C thermostated plate under similar conditions without irradiation. Following the treatment cells were cultivated for 24 hours with serum free MEM culture medium at 37°C.
| | Sample_growth_protocol_ch1 | Human dermal fibroblasts were isolated from foreskin of different donors. Cells cultivated in Eagle’s minimum essential medium with Earle’s salts (MEM, PAA Laboratories Pasching, Austria) supplemented with 10% fetal bovine serum (Gibco, Karlsruhe Germany), 1% antibiotics/antimycotics (penicillin, streptomycin, amphotericin B), 1% glutamine (Gibco) and were cultivated on 100 mm plastic culture dishes (Greiner, Solingen, Germany) at 37°C in humidified air with 5% CO2. Cells were used between passages five and ten, grown to 100% confluency before treatment. At least 24 hours before IRA irradiation media was changed to serum-free MEM.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany) according to the manufacturers instruction. RNA quality and purity were assessed using an Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA). The RNA was then utilized to synthesize first- and second-strand cDNA by using the Affymetrix One-Cycle cDNA Synthesis Kit (Affymetrix UK Ltd, High Wycombe,UK) with an subsequent clean up with the GeneChip Sample Cleanup Kit (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The in vitro transcription into biotinylated cRNA was performed with the IVT Labeling Kit (Affymetrix) according to the manufacturers protocols.
| | Sample_hyb_protocol | After purification, fragmentation and a further quality and purity control with the Agilent Bioanalyzer 2100 system 9 µg of the labeled cRNA were hybridized on the Affymetrix HG-U133A Microarray according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_scan_protocol | The hybridized arrays were scanned using Microarray Suite (MAS) Software (Affymetrix) according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_data_processing | The raw data containing .cel-files were normalised in the free statistical software R Version 2.0.1 with the BioCconductor affy-package using the robust multichip average (RMA) method. A separate normalisation procedure for array samples of each of the three different fibroblast cells lead to better results regarding how often commonly regulated genes were found in total and therefore was used for this study.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,,Calles
| | Sample_contact_email | calles@uni-duesseldorf.de
| | Sample_contact_phone | +49 211 3389 324
| | Sample_contact_laboratory | AG Schroeder
| | Sample_contact_department | Molecular Ageing Research/Cellbiology
| | Sample_contact_institute | Institut fuer umweltmedizinische Forschung (IUF)
| | Sample_contact_address | Auf'm Hennekamp 50
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM426nnn/GSM426492/suppl/GSM426492.CEL.gz
| | Sample_series_id | GSE17046
| | Sample_data_row_count | 22283
| | |
|
GSM426493 | GPL96 |
|
donorF3_IRA860J/cm2_24hpostincubation_biolrep3
|
human dermal fibroblasts IRA irradiated with 860J/cm2
|
cell type: primary human dermal fibroblasts
passage: between 5-10
donor: F3
|
no additional description
|
| Sample_geo_accession | GSM426493
| | Sample_status | Public on Jul 10 2010
| | Sample_submission_date | Jul 10 2009
| | Sample_last_update_date | Jul 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | We used a waterfiltered Hydrosun 500 H 500 IRA lamp (Hydrosun Medizintechnik GmbH, Müllheim, Germany) with an emission in the range of 760-1400 nm leading to an irradiance of 360 mW/cm2 at a distance of 20 cm measured through Hydrosun HBM1 irradiance measuring device (Hydrosun). IRA irradiation lasted 40 min leading to a total dose of 860 J/cm2. The culture dishes were placed on a cooled plate connected to thermostated bath (Thermo Haake GmbH, Karlsruhe, Germany) to maintain temperatures below 37°C during IRA irradiation. For irradiation, medium was replaced by phosphate-buffered saline (37°C, Gibco). Control cells were held on a 37°C thermostated plate under similar conditions without irradiation. Following the treatment cells were cultivated for 24 hours with serum free MEM culture medium at 37°C.
| | Sample_growth_protocol_ch1 | Human dermal fibroblasts were isolated from foreskin of different donors. Cells cultivated in Eagle’s minimum essential medium with Earle’s salts (MEM, PAA Laboratories Pasching, Austria) supplemented with 10% fetal bovine serum (Gibco, Karlsruhe Germany), 1% antibiotics/antimycotics (penicillin, streptomycin, amphotericin B), 1% glutamine (Gibco) and were cultivated on 100 mm plastic culture dishes (Greiner, Solingen, Germany) at 37°C in humidified air with 5% CO2. Cells were used between passages five and ten, grown to 100% confluency before treatment. At least 24 hours before IRA irradiation media was changed to serum-free MEM.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany) according to the manufacturers instruction. RNA quality and purity were assessed using an Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA). The RNA was then utilized to synthesize first- and second-strand cDNA by using the Affymetrix One-Cycle cDNA Synthesis Kit (Affymetrix UK Ltd, High Wycombe,UK) with an subsequent clean up with the GeneChip Sample Cleanup Kit (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The in vitro transcription into biotinylated cRNA was performed with the IVT Labeling Kit (Affymetrix) according to the manufacturers protocols.
| | Sample_hyb_protocol | After purification, fragmentation and a further quality and purity control with the Agilent Bioanalyzer 2100 system 9 µg of the labeled cRNA were hybridized on the Affymetrix HG-U133A Microarray according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_scan_protocol | The hybridized arrays were scanned using Microarray Suite (MAS) Software (Affymetrix) according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_data_processing | The raw data containing .cel-files were normalised in the free statistical software R Version 2.0.1 with the BioCconductor affy-package using the robust multichip average (RMA) method. A separate normalisation procedure for array samples of each of the three different fibroblast cells lead to better results regarding how often commonly regulated genes were found in total and therefore was used for this study.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,,Calles
| | Sample_contact_email | calles@uni-duesseldorf.de
| | Sample_contact_phone | +49 211 3389 324
| | Sample_contact_laboratory | AG Schroeder
| | Sample_contact_department | Molecular Ageing Research/Cellbiology
| | Sample_contact_institute | Institut fuer umweltmedizinische Forschung (IUF)
| | Sample_contact_address | Auf'm Hennekamp 50
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM426nnn/GSM426493/suppl/GSM426493.CEL.gz
| | Sample_series_id | GSE17046
| | Sample_data_row_count | 22283
| | |
|
GSM426494 | GPL96 |
|
donorF3_shamtreated_24hpostincubation_biolrep1
|
human dermal fibroblasts sham treated control
|
cell type: primary human dermal fibroblasts
passage: between 5-10
donor: F3
|
no additional description
|
| Sample_geo_accession | GSM426494
| | Sample_status | Public on Jul 10 2010
| | Sample_submission_date | Jul 10 2009
| | Sample_last_update_date | Jul 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | We used a waterfiltered Hydrosun 500 H 500 IRA lamp (Hydrosun Medizintechnik GmbH, Müllheim, Germany) with an emission in the range of 760-1400 nm leading to an irradiance of 360 mW/cm2 at a distance of 20 cm measured through Hydrosun HBM1 irradiance measuring device (Hydrosun). IRA irradiation lasted 40 min leading to a total dose of 860 J/cm2. The culture dishes were placed on a cooled plate connected to thermostated bath (Thermo Haake GmbH, Karlsruhe, Germany) to maintain temperatures below 37°C during IRA irradiation. For irradiation, medium was replaced by phosphate-buffered saline (37°C, Gibco). Control cells were held on a 37°C thermostated plate under similar conditions without irradiation. Following the treatment cells were cultivated for 24 hours with serum free MEM culture medium at 37°C.
| | Sample_growth_protocol_ch1 | Human dermal fibroblasts were isolated from foreskin of different donors. Cells cultivated in Eagle’s minimum essential medium with Earle’s salts (MEM, PAA Laboratories Pasching, Austria) supplemented with 10% fetal bovine serum (Gibco, Karlsruhe Germany), 1% antibiotics/antimycotics (penicillin, streptomycin, amphotericin B), 1% glutamine (Gibco) and were cultivated on 100 mm plastic culture dishes (Greiner, Solingen, Germany) at 37°C in humidified air with 5% CO2. Cells were used between passages five and ten, grown to 100% confluency before treatment. At least 24 hours before IRA irradiation media was changed to serum-free MEM.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany) according to the manufacturers instruction. RNA quality and purity were assessed using an Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA). The RNA was then utilized to synthesize first- and second-strand cDNA by using the Affymetrix One-Cycle cDNA Synthesis Kit (Affymetrix UK Ltd, High Wycombe,UK) with an subsequent clean up with the GeneChip Sample Cleanup Kit (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The in vitro transcription into biotinylated cRNA was performed with the IVT Labeling Kit (Affymetrix) according to the manufacturers protocols.
| | Sample_hyb_protocol | After purification, fragmentation and a further quality and purity control with the Agilent Bioanalyzer 2100 system 9 µg of the labeled cRNA were hybridized on the Affymetrix HG-U133A Microarray according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_scan_protocol | The hybridized arrays were scanned using Microarray Suite (MAS) Software (Affymetrix) according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_data_processing | The raw data containing .cel-files were normalised in the free statistical software R Version 2.0.1 with the BioCconductor affy-package using the robust multichip average (RMA) method. A separate normalisation procedure for array samples of each of the three different fibroblast cells lead to better results regarding how often commonly regulated genes were found in total and therefore was used for this study.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,,Calles
| | Sample_contact_email | calles@uni-duesseldorf.de
| | Sample_contact_phone | +49 211 3389 324
| | Sample_contact_laboratory | AG Schroeder
| | Sample_contact_department | Molecular Ageing Research/Cellbiology
| | Sample_contact_institute | Institut fuer umweltmedizinische Forschung (IUF)
| | Sample_contact_address | Auf'm Hennekamp 50
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM426nnn/GSM426494/suppl/GSM426494.CEL.gz
| | Sample_series_id | GSE17046
| | Sample_data_row_count | 22283
| | |
|
GSM426495 | GPL96 |
|
donorF3_shamtreated_24hpostincubation_biolrep2
|
human dermal fibroblasts sham treated control
|
cell type: primary human dermal fibroblasts
passage: between 5-10
donor: F3
|
no additional description
|
| Sample_geo_accession | GSM426495
| | Sample_status | Public on Jul 10 2010
| | Sample_submission_date | Jul 10 2009
| | Sample_last_update_date | Jul 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | We used a waterfiltered Hydrosun 500 H 500 IRA lamp (Hydrosun Medizintechnik GmbH, Müllheim, Germany) with an emission in the range of 760-1400 nm leading to an irradiance of 360 mW/cm2 at a distance of 20 cm measured through Hydrosun HBM1 irradiance measuring device (Hydrosun). IRA irradiation lasted 40 min leading to a total dose of 860 J/cm2. The culture dishes were placed on a cooled plate connected to thermostated bath (Thermo Haake GmbH, Karlsruhe, Germany) to maintain temperatures below 37°C during IRA irradiation. For irradiation, medium was replaced by phosphate-buffered saline (37°C, Gibco). Control cells were held on a 37°C thermostated plate under similar conditions without irradiation. Following the treatment cells were cultivated for 24 hours with serum free MEM culture medium at 37°C.
| | Sample_growth_protocol_ch1 | Human dermal fibroblasts were isolated from foreskin of different donors. Cells cultivated in Eagle’s minimum essential medium with Earle’s salts (MEM, PAA Laboratories Pasching, Austria) supplemented with 10% fetal bovine serum (Gibco, Karlsruhe Germany), 1% antibiotics/antimycotics (penicillin, streptomycin, amphotericin B), 1% glutamine (Gibco) and were cultivated on 100 mm plastic culture dishes (Greiner, Solingen, Germany) at 37°C in humidified air with 5% CO2. Cells were used between passages five and ten, grown to 100% confluency before treatment. At least 24 hours before IRA irradiation media was changed to serum-free MEM.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany) according to the manufacturers instruction. RNA quality and purity were assessed using an Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA). The RNA was then utilized to synthesize first- and second-strand cDNA by using the Affymetrix One-Cycle cDNA Synthesis Kit (Affymetrix UK Ltd, High Wycombe,UK) with an subsequent clean up with the GeneChip Sample Cleanup Kit (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The in vitro transcription into biotinylated cRNA was performed with the IVT Labeling Kit (Affymetrix) according to the manufacturers protocols.
| | Sample_hyb_protocol | After purification, fragmentation and a further quality and purity control with the Agilent Bioanalyzer 2100 system 9 µg of the labeled cRNA were hybridized on the Affymetrix HG-U133A Microarray according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_scan_protocol | The hybridized arrays were scanned using Microarray Suite (MAS) Software (Affymetrix) according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_data_processing | The raw data containing .cel-files were normalised in the free statistical software R Version 2.0.1 with the BioCconductor affy-package using the robust multichip average (RMA) method. A separate normalisation procedure for array samples of each of the three different fibroblast cells lead to better results regarding how often commonly regulated genes were found in total and therefore was used for this study.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,,Calles
| | Sample_contact_email | calles@uni-duesseldorf.de
| | Sample_contact_phone | +49 211 3389 324
| | Sample_contact_laboratory | AG Schroeder
| | Sample_contact_department | Molecular Ageing Research/Cellbiology
| | Sample_contact_institute | Institut fuer umweltmedizinische Forschung (IUF)
| | Sample_contact_address | Auf'm Hennekamp 50
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM426nnn/GSM426495/suppl/GSM426495.CEL.gz
| | Sample_series_id | GSE17046
| | Sample_data_row_count | 22283
| | |
|
GSM426496 | GPL96 |
|
donorF3_shamtreated_24hpostincubation_biolrep3
|
human dermal fibroblasts sham treated control
|
cell type: primary human dermal fibroblasts
passage: between 5-10
donor: F3
|
no additional description
|
| Sample_geo_accession | GSM426496
| | Sample_status | Public on Jul 10 2010
| | Sample_submission_date | Jul 10 2009
| | Sample_last_update_date | Jul 10 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | We used a waterfiltered Hydrosun 500 H 500 IRA lamp (Hydrosun Medizintechnik GmbH, Müllheim, Germany) with an emission in the range of 760-1400 nm leading to an irradiance of 360 mW/cm2 at a distance of 20 cm measured through Hydrosun HBM1 irradiance measuring device (Hydrosun). IRA irradiation lasted 40 min leading to a total dose of 860 J/cm2. The culture dishes were placed on a cooled plate connected to thermostated bath (Thermo Haake GmbH, Karlsruhe, Germany) to maintain temperatures below 37°C during IRA irradiation. For irradiation, medium was replaced by phosphate-buffered saline (37°C, Gibco). Control cells were held on a 37°C thermostated plate under similar conditions without irradiation. Following the treatment cells were cultivated for 24 hours with serum free MEM culture medium at 37°C.
| | Sample_growth_protocol_ch1 | Human dermal fibroblasts were isolated from foreskin of different donors. Cells cultivated in Eagle’s minimum essential medium with Earle’s salts (MEM, PAA Laboratories Pasching, Austria) supplemented with 10% fetal bovine serum (Gibco, Karlsruhe Germany), 1% antibiotics/antimycotics (penicillin, streptomycin, amphotericin B), 1% glutamine (Gibco) and were cultivated on 100 mm plastic culture dishes (Greiner, Solingen, Germany) at 37°C in humidified air with 5% CO2. Cells were used between passages five and ten, grown to 100% confluency before treatment. At least 24 hours before IRA irradiation media was changed to serum-free MEM.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany) according to the manufacturers instruction. RNA quality and purity were assessed using an Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA). The RNA was then utilized to synthesize first- and second-strand cDNA by using the Affymetrix One-Cycle cDNA Synthesis Kit (Affymetrix UK Ltd, High Wycombe,UK) with an subsequent clean up with the GeneChip Sample Cleanup Kit (Affymetrix).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The in vitro transcription into biotinylated cRNA was performed with the IVT Labeling Kit (Affymetrix) according to the manufacturers protocols.
| | Sample_hyb_protocol | After purification, fragmentation and a further quality and purity control with the Agilent Bioanalyzer 2100 system 9 µg of the labeled cRNA were hybridized on the Affymetrix HG-U133A Microarray according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_scan_protocol | The hybridized arrays were scanned using Microarray Suite (MAS) Software (Affymetrix) according to the manufacturers protocols at the Affymetrix core facility of the BMFZ at the Heinrich-Heine University Duesseldorf.
| | Sample_data_processing | The raw data containing .cel-files were normalised in the free statistical software R Version 2.0.1 with the BioCconductor affy-package using the robust multichip average (RMA) method. A separate normalisation procedure for array samples of each of the three different fibroblast cells lead to better results regarding how often commonly regulated genes were found in total and therefore was used for this study.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christian,,Calles
| | Sample_contact_email | calles@uni-duesseldorf.de
| | Sample_contact_phone | +49 211 3389 324
| | Sample_contact_laboratory | AG Schroeder
| | Sample_contact_department | Molecular Ageing Research/Cellbiology
| | Sample_contact_institute | Institut fuer umweltmedizinische Forschung (IUF)
| | Sample_contact_address | Auf'm Hennekamp 50
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM426nnn/GSM426496/suppl/GSM426496.CEL.gz
| | Sample_series_id | GSE17046
| | Sample_data_row_count | 22283
| | |
|
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