Search results for the GEO ID: GSE11341  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM286407 | GPL96 |
|
Lung cells_Normoxia_rep1
|
Lung Microvascular endothelial cells,normoxia,0hrControl
|
Primary cells
|
All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).
|
| Sample_geo_accession | GSM286407
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | May 05 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs. Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.
| | Sample_growth_protocol_ch1 | Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK). Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).
| | Sample_hyb_protocol | Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm. Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).
| | Sample_scan_protocol | Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).
| | Sample_data_processing | Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median. Genes that were absent in a majority of chips were eliminated from further analyses.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christine,Marie,Costello
| | Sample_contact_phone | 00353 01 7166738
| | Sample_contact_fax | 00353 01 7166892
| | Sample_contact_institute | Conway Institute
| | Sample_contact_address | University College Dublin
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM286nnn/GSM286407/suppl/GSM286407.CEL.gz
| | Sample_series_id | GSE11341
| | Sample_data_row_count | 22283
| | |
|
GSM286408 | GPL96 |
|
Lung cells_24hrHypoxia_rep1
|
Lung Microvascular endothelial cells,hypoxia,24hr
|
Primary cells
|
All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).
|
| Sample_geo_accession | GSM286408
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | May 05 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs. Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.
| | Sample_growth_protocol_ch1 | Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK). Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).
| | Sample_hyb_protocol | Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm. Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).
| | Sample_scan_protocol | Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).
| | Sample_data_processing | Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median. Genes that were absent in a majority of chips were eliminated from further analyses.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christine,Marie,Costello
| | Sample_contact_phone | 00353 01 7166738
| | Sample_contact_fax | 00353 01 7166892
| | Sample_contact_institute | Conway Institute
| | Sample_contact_address | University College Dublin
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM286nnn/GSM286408/suppl/GSM286408.CEL.gz
| | Sample_series_id | GSE11341
| | Sample_data_row_count | 22283
| | |
|
GSM286409 | GPL96 |
|
Lung cells_48hrHypoxia_rep1
|
Lung Microvascular endothelial cells,hypoxia,48hr
|
Primary cells
|
All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).
|
| Sample_geo_accession | GSM286409
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | May 05 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs. Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.
| | Sample_growth_protocol_ch1 | Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK). Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).
| | Sample_hyb_protocol | Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm. Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).
| | Sample_scan_protocol | Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).
| | Sample_data_processing | Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median. Genes that were absent in a majority of chips were eliminated from further analyses.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christine,Marie,Costello
| | Sample_contact_phone | 00353 01 7166738
| | Sample_contact_fax | 00353 01 7166892
| | Sample_contact_institute | Conway Institute
| | Sample_contact_address | University College Dublin
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM286nnn/GSM286409/suppl/GSM286409.CEL.gz
| | Sample_series_id | GSE11341
| | Sample_data_row_count | 22283
| | |
|
GSM286410 | GPL96 |
|
Lung cells_Normoxia_rep2
|
Lung Microvascular endothelial cells,normoxia,0hrControl
|
Primary cells
|
All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).
|
| Sample_geo_accession | GSM286410
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | May 05 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs. Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.
| | Sample_growth_protocol_ch1 | Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK). Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).
| | Sample_hyb_protocol | Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm. Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).
| | Sample_scan_protocol | Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).
| | Sample_data_processing | Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median. Genes that were absent in a majority of chips were eliminated from further analyses.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christine,Marie,Costello
| | Sample_contact_phone | 00353 01 7166738
| | Sample_contact_fax | 00353 01 7166892
| | Sample_contact_institute | Conway Institute
| | Sample_contact_address | University College Dublin
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM286nnn/GSM286410/suppl/GSM286410.CEL.gz
| | Sample_series_id | GSE11341
| | Sample_data_row_count | 22283
| | |
|
GSM286411 | GPL96 |
|
Lung cells_3hrHypoxia_rep2
|
Lung Microvascular endothelial cells,hypoxia,3hr
|
Primary cells
|
All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).
|
| Sample_geo_accession | GSM286411
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | May 05 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs. Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.
| | Sample_growth_protocol_ch1 | Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK). Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).
| | Sample_hyb_protocol | Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm. Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).
| | Sample_scan_protocol | Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).
| | Sample_data_processing | Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median. Genes that were absent in a majority of chips were eliminated from further analyses.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christine,Marie,Costello
| | Sample_contact_phone | 00353 01 7166738
| | Sample_contact_fax | 00353 01 7166892
| | Sample_contact_institute | Conway Institute
| | Sample_contact_address | University College Dublin
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM286nnn/GSM286411/suppl/GSM286411.CEL.gz
| | Sample_series_id | GSE11341
| | Sample_data_row_count | 22283
| | |
|
GSM286412 | GPL96 |
|
Lung cells_24hrHypoxia_rep2
|
Lung Microvascular endothelial cells,hypoxia,24hr
|
Primary cells
|
All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).
|
| Sample_geo_accession | GSM286412
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | May 05 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs. Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.
| | Sample_growth_protocol_ch1 | Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK). Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).
| | Sample_hyb_protocol | Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm. Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).
| | Sample_scan_protocol | Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).
| | Sample_data_processing | Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median. Genes that were absent in a majority of chips were eliminated from further analyses.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christine,Marie,Costello
| | Sample_contact_phone | 00353 01 7166738
| | Sample_contact_fax | 00353 01 7166892
| | Sample_contact_institute | Conway Institute
| | Sample_contact_address | University College Dublin
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM286nnn/GSM286412/suppl/GSM286412.CEL.gz
| | Sample_series_id | GSE11341
| | Sample_data_row_count | 22283
| | |
|
GSM286413 | GPL96 |
|
Lung cells_48hrHypoxia_rep2
|
Lung Microvascular endothelial cells,hypoxia,48hr
|
Primary cells
|
All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).
|
| Sample_geo_accession | GSM286413
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | May 05 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs. Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.
| | Sample_growth_protocol_ch1 | Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK). Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).
| | Sample_hyb_protocol | Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm. Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).
| | Sample_scan_protocol | Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).
| | Sample_data_processing | Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median. Genes that were absent in a majority of chips were eliminated from further analyses.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christine,Marie,Costello
| | Sample_contact_phone | 00353 01 7166738
| | Sample_contact_fax | 00353 01 7166892
| | Sample_contact_institute | Conway Institute
| | Sample_contact_address | University College Dublin
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM286nnn/GSM286413/suppl/GSM286413.CEL.gz
| | Sample_series_id | GSE11341
| | Sample_data_row_count | 22283
| | |
|
GSM286414 | GPL96 |
|
Lung cells_Normoxia_rep3
|
Lung Microvascular endothelial cells,normoxia,0hrControl
|
Primary cells
|
All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).
|
| Sample_geo_accession | GSM286414
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | May 05 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs. Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.
| | Sample_growth_protocol_ch1 | Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK). Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).
| | Sample_hyb_protocol | Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm. Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).
| | Sample_scan_protocol | Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).
| | Sample_data_processing | Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median. Genes that were absent in a majority of chips were eliminated from further analyses.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christine,Marie,Costello
| | Sample_contact_phone | 00353 01 7166738
| | Sample_contact_fax | 00353 01 7166892
| | Sample_contact_institute | Conway Institute
| | Sample_contact_address | University College Dublin
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM286nnn/GSM286414/suppl/GSM286414.CEL.gz
| | Sample_series_id | GSE11341
| | Sample_data_row_count | 22283
| | |
|
GSM286415 | GPL96 |
|
Lung cells_3hrHypoxia_rep3
|
Lung Microvascular endothelial cells,hypoxia,3hr
|
Primary cells
|
All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).
|
| Sample_geo_accession | GSM286415
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | May 05 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs. Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.
| | Sample_growth_protocol_ch1 | Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK). Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).
| | Sample_hyb_protocol | Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm. Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).
| | Sample_scan_protocol | Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).
| | Sample_data_processing | Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median. Genes that were absent in a majority of chips were eliminated from further analyses.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christine,Marie,Costello
| | Sample_contact_phone | 00353 01 7166738
| | Sample_contact_fax | 00353 01 7166892
| | Sample_contact_institute | Conway Institute
| | Sample_contact_address | University College Dublin
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM286nnn/GSM286415/suppl/GSM286415.CEL.gz
| | Sample_series_id | GSE11341
| | Sample_data_row_count | 22283
| | |
|
GSM286416 | GPL96 |
|
Lung cells_24hrHypoxia_rep3
|
Lung Microvascular endothelial cells,hypoxia,24hr
|
Primary cells
|
All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).
|
| Sample_geo_accession | GSM286416
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | May 05 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs. Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.
| | Sample_growth_protocol_ch1 | Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK). Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).
| | Sample_hyb_protocol | Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm. Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).
| | Sample_scan_protocol | Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).
| | Sample_data_processing | Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median. Genes that were absent in a majority of chips were eliminated from further analyses.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christine,Marie,Costello
| | Sample_contact_phone | 00353 01 7166738
| | Sample_contact_fax | 00353 01 7166892
| | Sample_contact_institute | Conway Institute
| | Sample_contact_address | University College Dublin
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM286nnn/GSM286416/suppl/GSM286416.CEL.gz
| | Sample_series_id | GSE11341
| | Sample_data_row_count | 22283
| | |
|
GSM286417 | GPL96 |
|
Lung cells_48hrHypoxia_rep3
|
Lung Microvascular endothelial cells,hypoxia,48hr
|
Primary cells
|
All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).
|
| Sample_geo_accession | GSM286417
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | May 05 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs. Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.
| | Sample_growth_protocol_ch1 | Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK). Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).
| | Sample_hyb_protocol | Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm. Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).
| | Sample_scan_protocol | Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).
| | Sample_data_processing | Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median. Genes that were absent in a majority of chips were eliminated from further analyses.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christine,Marie,Costello
| | Sample_contact_phone | 00353 01 7166738
| | Sample_contact_fax | 00353 01 7166892
| | Sample_contact_institute | Conway Institute
| | Sample_contact_address | University College Dublin
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM286nnn/GSM286417/suppl/GSM286417.CEL.gz
| | Sample_series_id | GSE11341
| | Sample_data_row_count | 22283
| | |
|
GSM286418 | GPL96 |
|
Cardiac cells_Normoxia_rep1
|
Cardiac Microvascular endothelial cells,normoxia,0hrControl
|
Primary cells
|
All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).
|
| Sample_geo_accession | GSM286418
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | May 05 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs. Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.
| | Sample_growth_protocol_ch1 | Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK). Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).
| | Sample_hyb_protocol | Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm. Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).
| | Sample_scan_protocol | Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).
| | Sample_data_processing | Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median. Genes that were absent in a majority of chips were eliminated from further analyses.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christine,Marie,Costello
| | Sample_contact_phone | 00353 01 7166738
| | Sample_contact_fax | 00353 01 7166892
| | Sample_contact_institute | Conway Institute
| | Sample_contact_address | University College Dublin
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM286nnn/GSM286418/suppl/GSM286418.CEL.gz
| | Sample_series_id | GSE11341
| | Sample_data_row_count | 22283
| | |
|
GSM286419 | GPL96 |
|
Cardiac cells_3hrHypoxia_rep1
|
Cardiac Microvascular endothelial cells,hypoxia,3hr
|
Primary cells
|
All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).
|
| Sample_geo_accession | GSM286419
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | May 05 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs. Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.
| | Sample_growth_protocol_ch1 | Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK). Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).
| | Sample_hyb_protocol | Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm. Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).
| | Sample_scan_protocol | Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).
| | Sample_data_processing | Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median. Genes that were absent in a majority of chips were eliminated from further analyses.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christine,Marie,Costello
| | Sample_contact_phone | 00353 01 7166738
| | Sample_contact_fax | 00353 01 7166892
| | Sample_contact_institute | Conway Institute
| | Sample_contact_address | University College Dublin
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM286nnn/GSM286419/suppl/GSM286419.CEL.gz
| | Sample_series_id | GSE11341
| | Sample_data_row_count | 22283
| | |
|
GSM286420 | GPL96 |
|
Cardiac cells_24hrHypoxia_rep1
|
Cardiac Microvascular endothelial cells,hypoxia,24hr
|
Primary cells
|
All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).
|
| Sample_geo_accession | GSM286420
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | May 05 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs. Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.
| | Sample_growth_protocol_ch1 | Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK). Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).
| | Sample_hyb_protocol | Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm. Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).
| | Sample_scan_protocol | Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).
| | Sample_data_processing | Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median. Genes that were absent in a majority of chips were eliminated from further analyses.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christine,Marie,Costello
| | Sample_contact_phone | 00353 01 7166738
| | Sample_contact_fax | 00353 01 7166892
| | Sample_contact_institute | Conway Institute
| | Sample_contact_address | University College Dublin
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM286nnn/GSM286420/suppl/GSM286420.CEL.gz
| | Sample_series_id | GSE11341
| | Sample_data_row_count | 22283
| | |
|
GSM286421 | GPL96 |
|
Cardiac cells_48hrHypoxia_rep1
|
Cardiac Microvascular endothelial cells,hypoxia,48hr
|
Primary cells
|
All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).
|
| Sample_geo_accession | GSM286421
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | May 05 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs. Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.
| | Sample_growth_protocol_ch1 | Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK). Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).
| | Sample_hyb_protocol | Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm. Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).
| | Sample_scan_protocol | Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).
| | Sample_data_processing | Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median. Genes that were absent in a majority of chips were eliminated from further analyses.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christine,Marie,Costello
| | Sample_contact_phone | 00353 01 7166738
| | Sample_contact_fax | 00353 01 7166892
| | Sample_contact_institute | Conway Institute
| | Sample_contact_address | University College Dublin
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM286nnn/GSM286421/suppl/GSM286421.CEL.gz
| | Sample_series_id | GSE11341
| | Sample_data_row_count | 22283
| | |
|
GSM286422 | GPL96 |
|
Cardiac cells_Normoxia_rep2
|
Cardiac Microvascular endothelial cells,normoxia,0hrControl
|
Primary cells
|
All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).
|
| Sample_geo_accession | GSM286422
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | May 05 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs. Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.
| | Sample_growth_protocol_ch1 | Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK). Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).
| | Sample_hyb_protocol | Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm. Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).
| | Sample_scan_protocol | Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).
| | Sample_data_processing | Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median. Genes that were absent in a majority of chips were eliminated from further analyses.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christine,Marie,Costello
| | Sample_contact_phone | 00353 01 7166738
| | Sample_contact_fax | 00353 01 7166892
| | Sample_contact_institute | Conway Institute
| | Sample_contact_address | University College Dublin
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM286nnn/GSM286422/suppl/GSM286422.CEL.gz
| | Sample_series_id | GSE11341
| | Sample_data_row_count | 22283
| | |
|
GSM286423 | GPL96 |
|
Cardiac cells_3hrHypoxia_rep2
|
Cardiac Microvascular endothelial cells,hypoxia,3hr
|
Primary cells
|
All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).
|
| Sample_geo_accession | GSM286423
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | May 05 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs. Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.
| | Sample_growth_protocol_ch1 | Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK). Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).
| | Sample_hyb_protocol | Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm. Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).
| | Sample_scan_protocol | Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).
| | Sample_data_processing | Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median. Genes that were absent in a majority of chips were eliminated from further analyses.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christine,Marie,Costello
| | Sample_contact_phone | 00353 01 7166738
| | Sample_contact_fax | 00353 01 7166892
| | Sample_contact_institute | Conway Institute
| | Sample_contact_address | University College Dublin
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM286nnn/GSM286423/suppl/GSM286423.CEL.gz
| | Sample_series_id | GSE11341
| | Sample_data_row_count | 22283
| | |
|
GSM286424 | GPL96 |
|
Cardiac cells_24hrHypoxia_rep2
|
Cardiac Microvascular endothelial cells,hypoxia,24hr
|
Primary cells
|
All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).
|
| Sample_geo_accession | GSM286424
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | May 05 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs. Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.
| | Sample_growth_protocol_ch1 | Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK). Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).
| | Sample_hyb_protocol | Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm. Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).
| | Sample_scan_protocol | Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).
| | Sample_data_processing | Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median. Genes that were absent in a majority of chips were eliminated from further analyses.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christine,Marie,Costello
| | Sample_contact_phone | 00353 01 7166738
| | Sample_contact_fax | 00353 01 7166892
| | Sample_contact_institute | Conway Institute
| | Sample_contact_address | University College Dublin
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM286nnn/GSM286424/suppl/GSM286424.CEL.gz
| | Sample_series_id | GSE11341
| | Sample_data_row_count | 22283
| | |
|
GSM286425 | GPL96 |
|
Cardiac cells_48hrHypoxia_rep2
|
Cardiac Microvascular endothelial cells,hypoxia,48hr
|
Primary cells
|
All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).
|
| Sample_geo_accession | GSM286425
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | May 05 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs. Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.
| | Sample_growth_protocol_ch1 | Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK). Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).
| | Sample_hyb_protocol | Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm. Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).
| | Sample_scan_protocol | Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).
| | Sample_data_processing | Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median. Genes that were absent in a majority of chips were eliminated from further analyses.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christine,Marie,Costello
| | Sample_contact_phone | 00353 01 7166738
| | Sample_contact_fax | 00353 01 7166892
| | Sample_contact_institute | Conway Institute
| | Sample_contact_address | University College Dublin
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM286nnn/GSM286425/suppl/GSM286425.CEL.gz
| | Sample_series_id | GSE11341
| | Sample_data_row_count | 22283
| | |
|
GSM286426 | GPL96 |
|
Cardiac cells_Normoxia_rep3
|
Cardiac Microvascular endothelial cells,normoxia,0hrControl
|
Primary cells
|
All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).
|
| Sample_geo_accession | GSM286426
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | May 05 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs. Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.
| | Sample_growth_protocol_ch1 | Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK). Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).
| | Sample_hyb_protocol | Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm. Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).
| | Sample_scan_protocol | Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).
| | Sample_data_processing | Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median. Genes that were absent in a majority of chips were eliminated from further analyses.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christine,Marie,Costello
| | Sample_contact_phone | 00353 01 7166738
| | Sample_contact_fax | 00353 01 7166892
| | Sample_contact_institute | Conway Institute
| | Sample_contact_address | University College Dublin
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM286nnn/GSM286426/suppl/GSM286426.CEL.gz
| | Sample_series_id | GSE11341
| | Sample_data_row_count | 22283
| | |
|
GSM286427 | GPL96 |
|
Cardiac cells_3hrHypoxia_rep3
|
Cardiac Microvascular endothelial cells,hypoxia,3hr
|
Primary cells
|
All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).
|
| Sample_geo_accession | GSM286427
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | May 05 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs. Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.
| | Sample_growth_protocol_ch1 | Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK). Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).
| | Sample_hyb_protocol | Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm. Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).
| | Sample_scan_protocol | Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).
| | Sample_data_processing | Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median. Genes that were absent in a majority of chips were eliminated from further analyses.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christine,Marie,Costello
| | Sample_contact_phone | 00353 01 7166738
| | Sample_contact_fax | 00353 01 7166892
| | Sample_contact_institute | Conway Institute
| | Sample_contact_address | University College Dublin
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM286nnn/GSM286427/suppl/GSM286427.CEL.gz
| | Sample_series_id | GSE11341
| | Sample_data_row_count | 22283
| | |
|
GSM286428 | GPL96 |
|
Cardiac cells_24hrHypoxia_rep3
|
Cardiac Microvascular endothelial cells,hypoxia,24hr
|
Primary cells
|
All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).
|
| Sample_geo_accession | GSM286428
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | May 05 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs. Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.
| | Sample_growth_protocol_ch1 | Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK). Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).
| | Sample_hyb_protocol | Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm. Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).
| | Sample_scan_protocol | Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).
| | Sample_data_processing | Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median. Genes that were absent in a majority of chips were eliminated from further analyses.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christine,Marie,Costello
| | Sample_contact_phone | 00353 01 7166738
| | Sample_contact_fax | 00353 01 7166892
| | Sample_contact_institute | Conway Institute
| | Sample_contact_address | University College Dublin
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM286nnn/GSM286428/suppl/GSM286428.CEL.gz
| | Sample_series_id | GSE11341
| | Sample_data_row_count | 22283
| | |
|
GSM286429 | GPL96 |
|
Cardiac cells_48hrHypoxia_rep3
|
Cardiac Microvascular endothelial cells,hypoxia,48hr
|
Primary cells
|
All cells used in these experiments were passage 6-7 and were routinely checked for mycoplasma contamination using the VenorGeM PCR kit (Cambio Ltd, UK.).
|
| Sample_geo_accession | GSM286429
| | Sample_status | Public on Nov 21 2008
| | Sample_submission_date | May 05 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At experiment start, medium was changed and dishes were transferred to the hypoxia chamber (Coy Labs, USA) and cultured in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 3hr, 24hr or 48hrs. Control conditions were achieved by culture in 21% O2, 5% CO2 and 74% N2 in a cell-culture incubator.
| | Sample_growth_protocol_ch1 | Primary human microvascular endothelial cells from lung and cardiac tissue were grown on sterile tissue culture dishes in Endothelial Growth Medium (EGM-2MV; Code: CC-3202) according to the manufacturers instructions (Lonza Bioscience formerly Cambrex, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At experiment end, cell medium was removed, cells washed with PBS and thoroughly lysed in RLT buffer (RNeasy Mini kit, Qiagen, UK). Total RNA extraction, with on-the-column DNase treatment, was carried out using RNeasy Mini Kits (Qiagen Ltd, UK) according to the maunfacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Total RNA (5ug) was reverse transcribed to cDNA (one-cycle cDNA synthesis kit), clean up of double stranded cDNA, biotin labelling of anti-sense cRNA (integrity checked on the Bioanalyzer 2100, Agilent technologies, USA) and clean up and fragmentation of biotinylated cRNA were all carried out according to the manufacturers protocol (Affymetrix, USA).
| | Sample_hyb_protocol | Fragmented cRNA (15ug) was hybridised to chips for 16 hrs at 45ºC in a hybridisation oven (AffyMetrix, USA) with rotation at 60rpm. Immediately following hybridisation, the array underwent automated washing and staining protocol on the automatic fluidics station 400, (AffyMetrix, USA).
| | Sample_scan_protocol | Arrays were scanned on a GeneChip 3000 scanner (AffyMetrix, USA).
| | Sample_data_processing | Affymetrix .cel files were imported and normalised using algorithms of GeneSpring 6.0 software i.e. data was normalised by applying the following data transformation criteria: a) measurements less than 0.01 were set to 0.01, b) per chip: normalised to 50th percentile and c) per gene: normalise to median. Genes that were absent in a majority of chips were eliminated from further analyses.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Christine,Marie,Costello
| | Sample_contact_phone | 00353 01 7166738
| | Sample_contact_fax | 00353 01 7166892
| | Sample_contact_institute | Conway Institute
| | Sample_contact_address | University College Dublin
| | Sample_contact_city | Dublin
| | Sample_contact_zip/postal_code | Dublin 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM286nnn/GSM286429/suppl/GSM286429.CEL.gz
| | Sample_series_id | GSE11341
| | Sample_data_row_count | 22283
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
Enter the group name here: |
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