Search results for the GEO ID: GSE34112  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM842042 | GPL570 |
|
PC3 cells, hypoxia, DMSO rep 1
|
PC3 cells, hypoxia, DMSO rep 1
|
oxygen level: 0.20%
treatment: DMSO
|
Gene expression data from PC3 cells under hypoxic conditions and treated with DMSO
|
| Sample_geo_accession | GSM842042
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 02 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | On Day 0, PC-3 cells were seeded at 2x106 cells/25cm2 flask and left overnight in a 37C incubator, 5% CO2. Next day (day 1) 0.05% DMSO (Sigma–Aldrich, Gillingham, UK), 25µM of NCX1102 (NO-sulindac; donated by NicOx (Sophia Antipolis, France)), and 25µM of sulindac (NicOx) was prepared in DMSO and added to the corresponding flasks. Flasks were placed in normoxic conditions (21% O2, 37C, 5% CO2) or in hypoxic conditions (0.2% O2, 37C, 95% CO2 & 5% N2) in a PROOX 110 oxygen controller (BioSpherix Ltd., Redfield, NY) for 48hrs.
| | Sample_growth_protocol_ch1 | PC-3 cells were cultured in RPMI 1640 media supplemented with 10% foetal calf serum, 2mM L-glutamine, penicillin 100u/ml, streptomycin 100ug/ml (all from Invitrogen, Paisley, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After 48 hours incubation 700µl of Qiazol lysis reagent (Qiagen, UK) was added. Cell scrapers were used to disrupt the cells and the resulting homogenate was transferred into a 1.5ml eppendorf tube. Total RNA was extracted using the RNeasy Lipid tissue mini kit with an on column DNAse step as directed by the manufacturer (Qiagen, UK). RNA was quantified using the Nanodrop instrument (Labtech Intl, UK). 260/230 and 260/280 ratios were assessed to examine RNA purity and integrity was assessed with the Bioanalyzer instrument (Agilent, UK).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For microarray work reverse transcription of RNA to cDNA was carried out using the Ovation RNA Amplification system v2 (Nugen Technologies Inc, USA). 100ng of total RNA was reverse transcribed as per the manufacturer’s protocol. cDNA was purified using qiaQuick PCR purification kit (Qiagen, UK) and quantified using the Nanodrop instrument. 3.75ug of cDNA was fragmented and labelled with the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, USA) and hybridised to each Affymetrix U133+2 array
| | Sample_hyb_protocol | Labelled cDNA was hybridised to Affymetrix hgu133plus2 arrays using protocols provided by Nugen Inc.
| | Sample_scan_protocol | Arrays were scanned with default settings using an Affymetrix scanner as directed by manufacturer
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further data processing were performed by RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Iain,,Gallagher
| | Sample_contact_email | iaingallagher@gmail.com
| | Sample_contact_phone | 00 44 131 242 6523
| | Sample_contact_laboratory | FU 501
| | Sample_contact_department | Tissue Injury & Repair
| | Sample_contact_institute | Edinburgh University
| | Sample_contact_address | The Chancellor's Building, 49 Little France Crescent
| | Sample_contact_city | Edinburgh
| | Sample_contact_zip/postal_code | EH16 4SB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842042/suppl/GSM842042.CEL.gz
| | Sample_series_id | GSE34112
| | Sample_data_row_count | 54675
| | |
|
GSM842043 | GPL570 |
|
PC3 cells, hypoxia, DMSO rep 2
|
PC3 cells, hypoxia, DMSO rep 2
|
oxygen level: 0.20%
treatment: DMSO
|
Gene expression data from PC3 cells under hypoxic conditions and treated with DMSO
|
| Sample_geo_accession | GSM842043
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 02 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | On Day 0, PC-3 cells were seeded at 2x106 cells/25cm2 flask and left overnight in a 37C incubator, 5% CO2. Next day (day 1) 0.05% DMSO (Sigma–Aldrich, Gillingham, UK), 25µM of NCX1102 (NO-sulindac; donated by NicOx (Sophia Antipolis, France)), and 25µM of sulindac (NicOx) was prepared in DMSO and added to the corresponding flasks. Flasks were placed in normoxic conditions (21% O2, 37C, 5% CO2) or in hypoxic conditions (0.2% O2, 37C, 95% CO2 & 5% N2) in a PROOX 110 oxygen controller (BioSpherix Ltd., Redfield, NY) for 48hrs.
| | Sample_growth_protocol_ch1 | PC-3 cells were cultured in RPMI 1640 media supplemented with 10% foetal calf serum, 2mM L-glutamine, penicillin 100u/ml, streptomycin 100ug/ml (all from Invitrogen, Paisley, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After 48 hours incubation 700µl of Qiazol lysis reagent (Qiagen, UK) was added. Cell scrapers were used to disrupt the cells and the resulting homogenate was transferred into a 1.5ml eppendorf tube. Total RNA was extracted using the RNeasy Lipid tissue mini kit with an on column DNAse step as directed by the manufacturer (Qiagen, UK). RNA was quantified using the Nanodrop instrument (Labtech Intl, UK). 260/230 and 260/280 ratios were assessed to examine RNA purity and integrity was assessed with the Bioanalyzer instrument (Agilent, UK).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For microarray work reverse transcription of RNA to cDNA was carried out using the Ovation RNA Amplification system v2 (Nugen Technologies Inc, USA). 100ng of total RNA was reverse transcribed as per the manufacturer’s protocol. cDNA was purified using qiaQuick PCR purification kit (Qiagen, UK) and quantified using the Nanodrop instrument. 3.75ug of cDNA was fragmented and labelled with the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, USA) and hybridised to each Affymetrix U133+2 array
| | Sample_hyb_protocol | Labelled cDNA was hybridised to Affymetrix hgu133plus2 arrays using protocols provided by Nugen Inc.
| | Sample_scan_protocol | Arrays were scanned with default settings using an Affymetrix scanner as directed by manufacturer
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further data processing were performed by RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Iain,,Gallagher
| | Sample_contact_email | iaingallagher@gmail.com
| | Sample_contact_phone | 00 44 131 242 6523
| | Sample_contact_laboratory | FU 501
| | Sample_contact_department | Tissue Injury & Repair
| | Sample_contact_institute | Edinburgh University
| | Sample_contact_address | The Chancellor's Building, 49 Little France Crescent
| | Sample_contact_city | Edinburgh
| | Sample_contact_zip/postal_code | EH16 4SB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842043/suppl/GSM842043.CEL.gz
| | Sample_series_id | GSE34112
| | Sample_data_row_count | 54675
| | |
|
GSM842044 | GPL570 |
|
PC3 cells, hypoxia, NO-sulindac rep 2b
|
PC3 cells, hypoxia, NO-sulindac rep 2
|
oxygen level: 0.20%
treatment: NO-sulindac
|
Gene expression data from PC3 cells under hypoxic conditions and treated with NO-sulindac
|
| Sample_geo_accession | GSM842044
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 02 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | On Day 0, PC-3 cells were seeded at 2x106 cells/25cm2 flask and left overnight in a 37C incubator, 5% CO2. Next day (day 1) 0.05% DMSO (Sigma–Aldrich, Gillingham, UK), 25µM of NCX1102 (NO-sulindac; donated by NicOx (Sophia Antipolis, France)), and 25µM of sulindac (NicOx) was prepared in DMSO and added to the corresponding flasks. Flasks were placed in normoxic conditions (21% O2, 37C, 5% CO2) or in hypoxic conditions (0.2% O2, 37C, 95% CO2 & 5% N2) in a PROOX 110 oxygen controller (BioSpherix Ltd., Redfield, NY) for 48hrs.
| | Sample_growth_protocol_ch1 | PC-3 cells were cultured in RPMI 1640 media supplemented with 10% foetal calf serum, 2mM L-glutamine, penicillin 100u/ml, streptomycin 100ug/ml (all from Invitrogen, Paisley, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After 48 hours incubation 700µl of Qiazol lysis reagent (Qiagen, UK) was added. Cell scrapers were used to disrupt the cells and the resulting homogenate was transferred into a 1.5ml eppendorf tube. Total RNA was extracted using the RNeasy Lipid tissue mini kit with an on column DNAse step as directed by the manufacturer (Qiagen, UK). RNA was quantified using the Nanodrop instrument (Labtech Intl, UK). 260/230 and 260/280 ratios were assessed to examine RNA purity and integrity was assessed with the Bioanalyzer instrument (Agilent, UK).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For microarray work reverse transcription of RNA to cDNA was carried out using the Ovation RNA Amplification system v2 (Nugen Technologies Inc, USA). 100ng of total RNA was reverse transcribed as per the manufacturer’s protocol. cDNA was purified using qiaQuick PCR purification kit (Qiagen, UK) and quantified using the Nanodrop instrument. 3.75ug of cDNA was fragmented and labelled with the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, USA) and hybridised to each Affymetrix U133+2 array
| | Sample_hyb_protocol | Labelled cDNA was hybridised to Affymetrix hgu133plus2 arrays using protocols provided by Nugen Inc.
| | Sample_scan_protocol | Arrays were scanned with default settings using an Affymetrix scanner as directed by manufacturer
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further data processing were performed by RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Iain,,Gallagher
| | Sample_contact_email | iaingallagher@gmail.com
| | Sample_contact_phone | 00 44 131 242 6523
| | Sample_contact_laboratory | FU 501
| | Sample_contact_department | Tissue Injury & Repair
| | Sample_contact_institute | Edinburgh University
| | Sample_contact_address | The Chancellor's Building, 49 Little France Crescent
| | Sample_contact_city | Edinburgh
| | Sample_contact_zip/postal_code | EH16 4SB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842044/suppl/GSM842044.CEL.gz
| | Sample_series_id | GSE34112
| | Sample_data_row_count | 54675
| | |
|
GSM842045 | GPL570 |
|
PC3 cells, hypoxia, NO-sulindac rep 2
|
PC3 cells, hypoxia, NO-sulindac rep 2
|
oxygen level: 0.20%
treatment: NO-sulindac
|
Gene expression data from PC3 cells under hypoxic conditions and treated with NO-sulindac
|
| Sample_geo_accession | GSM842045
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 02 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | On Day 0, PC-3 cells were seeded at 2x106 cells/25cm2 flask and left overnight in a 37C incubator, 5% CO2. Next day (day 1) 0.05% DMSO (Sigma–Aldrich, Gillingham, UK), 25µM of NCX1102 (NO-sulindac; donated by NicOx (Sophia Antipolis, France)), and 25µM of sulindac (NicOx) was prepared in DMSO and added to the corresponding flasks. Flasks were placed in normoxic conditions (21% O2, 37C, 5% CO2) or in hypoxic conditions (0.2% O2, 37C, 95% CO2 & 5% N2) in a PROOX 110 oxygen controller (BioSpherix Ltd., Redfield, NY) for 48hrs.
| | Sample_growth_protocol_ch1 | PC-3 cells were cultured in RPMI 1640 media supplemented with 10% foetal calf serum, 2mM L-glutamine, penicillin 100u/ml, streptomycin 100ug/ml (all from Invitrogen, Paisley, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After 48 hours incubation 700µl of Qiazol lysis reagent (Qiagen, UK) was added. Cell scrapers were used to disrupt the cells and the resulting homogenate was transferred into a 1.5ml eppendorf tube. Total RNA was extracted using the RNeasy Lipid tissue mini kit with an on column DNAse step as directed by the manufacturer (Qiagen, UK). RNA was quantified using the Nanodrop instrument (Labtech Intl, UK). 260/230 and 260/280 ratios were assessed to examine RNA purity and integrity was assessed with the Bioanalyzer instrument (Agilent, UK).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For microarray work reverse transcription of RNA to cDNA was carried out using the Ovation RNA Amplification system v2 (Nugen Technologies Inc, USA). 100ng of total RNA was reverse transcribed as per the manufacturer’s protocol. cDNA was purified using qiaQuick PCR purification kit (Qiagen, UK) and quantified using the Nanodrop instrument. 3.75ug of cDNA was fragmented and labelled with the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, USA) and hybridised to each Affymetrix U133+2 array
| | Sample_hyb_protocol | Labelled cDNA was hybridised to Affymetrix hgu133plus2 arrays using protocols provided by Nugen Inc.
| | Sample_scan_protocol | Arrays were scanned with default settings using an Affymetrix scanner as directed by manufacturer
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further data processing were performed by RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Iain,,Gallagher
| | Sample_contact_email | iaingallagher@gmail.com
| | Sample_contact_phone | 00 44 131 242 6523
| | Sample_contact_laboratory | FU 501
| | Sample_contact_department | Tissue Injury & Repair
| | Sample_contact_institute | Edinburgh University
| | Sample_contact_address | The Chancellor's Building, 49 Little France Crescent
| | Sample_contact_city | Edinburgh
| | Sample_contact_zip/postal_code | EH16 4SB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842045/suppl/GSM842045.CEL.gz
| | Sample_series_id | GSE34112
| | Sample_data_row_count | 54675
| | |
|
GSM842046 | GPL570 |
|
PC3 cells, hypoxia, sulindac rep 1
|
PC3 cells, hypoxia, sulindac rep 1
|
oxygen level: 0.20%
treatment: sulindac
|
Gene expression data from PC3 cells under hypoxic conditions and treated with sulindac
|
| Sample_geo_accession | GSM842046
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 02 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | On Day 0, PC-3 cells were seeded at 2x106 cells/25cm2 flask and left overnight in a 37C incubator, 5% CO2. Next day (day 1) 0.05% DMSO (Sigma–Aldrich, Gillingham, UK), 25µM of NCX1102 (NO-sulindac; donated by NicOx (Sophia Antipolis, France)), and 25µM of sulindac (NicOx) was prepared in DMSO and added to the corresponding flasks. Flasks were placed in normoxic conditions (21% O2, 37C, 5% CO2) or in hypoxic conditions (0.2% O2, 37C, 95% CO2 & 5% N2) in a PROOX 110 oxygen controller (BioSpherix Ltd., Redfield, NY) for 48hrs.
| | Sample_growth_protocol_ch1 | PC-3 cells were cultured in RPMI 1640 media supplemented with 10% foetal calf serum, 2mM L-glutamine, penicillin 100u/ml, streptomycin 100ug/ml (all from Invitrogen, Paisley, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After 48 hours incubation 700µl of Qiazol lysis reagent (Qiagen, UK) was added. Cell scrapers were used to disrupt the cells and the resulting homogenate was transferred into a 1.5ml eppendorf tube. Total RNA was extracted using the RNeasy Lipid tissue mini kit with an on column DNAse step as directed by the manufacturer (Qiagen, UK). RNA was quantified using the Nanodrop instrument (Labtech Intl, UK). 260/230 and 260/280 ratios were assessed to examine RNA purity and integrity was assessed with the Bioanalyzer instrument (Agilent, UK).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For microarray work reverse transcription of RNA to cDNA was carried out using the Ovation RNA Amplification system v2 (Nugen Technologies Inc, USA). 100ng of total RNA was reverse transcribed as per the manufacturer’s protocol. cDNA was purified using qiaQuick PCR purification kit (Qiagen, UK) and quantified using the Nanodrop instrument. 3.75ug of cDNA was fragmented and labelled with the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, USA) and hybridised to each Affymetrix U133+2 array
| | Sample_hyb_protocol | Labelled cDNA was hybridised to Affymetrix hgu133plus2 arrays using protocols provided by Nugen Inc.
| | Sample_scan_protocol | Arrays were scanned with default settings using an Affymetrix scanner as directed by manufacturer
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further data processing were performed by RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Iain,,Gallagher
| | Sample_contact_email | iaingallagher@gmail.com
| | Sample_contact_phone | 00 44 131 242 6523
| | Sample_contact_laboratory | FU 501
| | Sample_contact_department | Tissue Injury & Repair
| | Sample_contact_institute | Edinburgh University
| | Sample_contact_address | The Chancellor's Building, 49 Little France Crescent
| | Sample_contact_city | Edinburgh
| | Sample_contact_zip/postal_code | EH16 4SB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842046/suppl/GSM842046.CEL.gz
| | Sample_series_id | GSE34112
| | Sample_data_row_count | 54675
| | |
|
GSM842047 | GPL570 |
|
PC3 cells, hypoxia, sulindac rep 2
|
PC3 cells, hypoxia, sulindac rep 2
|
oxygen level: 0.20%
treatment: sulindac
|
Gene expression data from PC3 cells under hypoxic conditions and treated with sulindac
|
| Sample_geo_accession | GSM842047
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 02 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | On Day 0, PC-3 cells were seeded at 2x106 cells/25cm2 flask and left overnight in a 37C incubator, 5% CO2. Next day (day 1) 0.05% DMSO (Sigma–Aldrich, Gillingham, UK), 25µM of NCX1102 (NO-sulindac; donated by NicOx (Sophia Antipolis, France)), and 25µM of sulindac (NicOx) was prepared in DMSO and added to the corresponding flasks. Flasks were placed in normoxic conditions (21% O2, 37C, 5% CO2) or in hypoxic conditions (0.2% O2, 37C, 95% CO2 & 5% N2) in a PROOX 110 oxygen controller (BioSpherix Ltd., Redfield, NY) for 48hrs.
| | Sample_growth_protocol_ch1 | PC-3 cells were cultured in RPMI 1640 media supplemented with 10% foetal calf serum, 2mM L-glutamine, penicillin 100u/ml, streptomycin 100ug/ml (all from Invitrogen, Paisley, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After 48 hours incubation 700µl of Qiazol lysis reagent (Qiagen, UK) was added. Cell scrapers were used to disrupt the cells and the resulting homogenate was transferred into a 1.5ml eppendorf tube. Total RNA was extracted using the RNeasy Lipid tissue mini kit with an on column DNAse step as directed by the manufacturer (Qiagen, UK). RNA was quantified using the Nanodrop instrument (Labtech Intl, UK). 260/230 and 260/280 ratios were assessed to examine RNA purity and integrity was assessed with the Bioanalyzer instrument (Agilent, UK).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For microarray work reverse transcription of RNA to cDNA was carried out using the Ovation RNA Amplification system v2 (Nugen Technologies Inc, USA). 100ng of total RNA was reverse transcribed as per the manufacturer’s protocol. cDNA was purified using qiaQuick PCR purification kit (Qiagen, UK) and quantified using the Nanodrop instrument. 3.75ug of cDNA was fragmented and labelled with the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, USA) and hybridised to each Affymetrix U133+2 array
| | Sample_hyb_protocol | Labelled cDNA was hybridised to Affymetrix hgu133plus2 arrays using protocols provided by Nugen Inc.
| | Sample_scan_protocol | Arrays were scanned with default settings using an Affymetrix scanner as directed by manufacturer
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further data processing were performed by RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Iain,,Gallagher
| | Sample_contact_email | iaingallagher@gmail.com
| | Sample_contact_phone | 00 44 131 242 6523
| | Sample_contact_laboratory | FU 501
| | Sample_contact_department | Tissue Injury & Repair
| | Sample_contact_institute | Edinburgh University
| | Sample_contact_address | The Chancellor's Building, 49 Little France Crescent
| | Sample_contact_city | Edinburgh
| | Sample_contact_zip/postal_code | EH16 4SB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842047/suppl/GSM842047.CEL.gz
| | Sample_series_id | GSE34112
| | Sample_data_row_count | 54675
| | |
|
GSM842048 | GPL570 |
|
PC3 cells, normoxia, no treatment rep 1
|
PC3 cells, normoxia, no treatment rep 1
|
oxygen level: 21.00%
treatment: none
|
Gene expression data from PC3 cells under normoxic conditions with no treatment
|
| Sample_geo_accession | GSM842048
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 02 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | On Day 0, PC-3 cells were seeded at 2x106 cells/25cm2 flask and left overnight in a 37C incubator, 5% CO2. Next day (day 1) 0.05% DMSO (Sigma–Aldrich, Gillingham, UK), 25µM of NCX1102 (NO-sulindac; donated by NicOx (Sophia Antipolis, France)), and 25µM of sulindac (NicOx) was prepared in DMSO and added to the corresponding flasks. Flasks were placed in normoxic conditions (21% O2, 37C, 5% CO2) or in hypoxic conditions (0.2% O2, 37C, 95% CO2 & 5% N2) in a PROOX 110 oxygen controller (BioSpherix Ltd., Redfield, NY) for 48hrs.
| | Sample_growth_protocol_ch1 | PC-3 cells were cultured in RPMI 1640 media supplemented with 10% foetal calf serum, 2mM L-glutamine, penicillin 100u/ml, streptomycin 100ug/ml (all from Invitrogen, Paisley, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After 48 hours incubation 700µl of Qiazol lysis reagent (Qiagen, UK) was added. Cell scrapers were used to disrupt the cells and the resulting homogenate was transferred into a 1.5ml eppendorf tube. Total RNA was extracted using the RNeasy Lipid tissue mini kit with an on column DNAse step as directed by the manufacturer (Qiagen, UK). RNA was quantified using the Nanodrop instrument (Labtech Intl, UK). 260/230 and 260/280 ratios were assessed to examine RNA purity and integrity was assessed with the Bioanalyzer instrument (Agilent, UK).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For microarray work reverse transcription of RNA to cDNA was carried out using the Ovation RNA Amplification system v2 (Nugen Technologies Inc, USA). 100ng of total RNA was reverse transcribed as per the manufacturer’s protocol. cDNA was purified using qiaQuick PCR purification kit (Qiagen, UK) and quantified using the Nanodrop instrument. 3.75ug of cDNA was fragmented and labelled with the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, USA) and hybridised to each Affymetrix U133+2 array
| | Sample_hyb_protocol | Labelled cDNA was hybridised to Affymetrix hgu133plus2 arrays using protocols provided by Nugen Inc.
| | Sample_scan_protocol | Arrays were scanned with default settings using an Affymetrix scanner as directed by manufacturer
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further data processing were performed by RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Iain,,Gallagher
| | Sample_contact_email | iaingallagher@gmail.com
| | Sample_contact_phone | 00 44 131 242 6523
| | Sample_contact_laboratory | FU 501
| | Sample_contact_department | Tissue Injury & Repair
| | Sample_contact_institute | Edinburgh University
| | Sample_contact_address | The Chancellor's Building, 49 Little France Crescent
| | Sample_contact_city | Edinburgh
| | Sample_contact_zip/postal_code | EH16 4SB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842048/suppl/GSM842048.CEL.gz
| | Sample_series_id | GSE34112
| | Sample_data_row_count | 54675
| | |
|
GSM842049 | GPL570 |
|
PC3 cells, normoxia, no treatment rep 2
|
PC3 cells, normoxia, no treatment rep 2
|
oxygen level: 21.00%
treatment: none
|
Gene expression data from PC3 cells under normoxic conditions with no treatment
|
| Sample_geo_accession | GSM842049
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 02 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | On Day 0, PC-3 cells were seeded at 2x106 cells/25cm2 flask and left overnight in a 37C incubator, 5% CO2. Next day (day 1) 0.05% DMSO (Sigma–Aldrich, Gillingham, UK), 25µM of NCX1102 (NO-sulindac; donated by NicOx (Sophia Antipolis, France)), and 25µM of sulindac (NicOx) was prepared in DMSO and added to the corresponding flasks. Flasks were placed in normoxic conditions (21% O2, 37C, 5% CO2) or in hypoxic conditions (0.2% O2, 37C, 95% CO2 & 5% N2) in a PROOX 110 oxygen controller (BioSpherix Ltd., Redfield, NY) for 48hrs.
| | Sample_growth_protocol_ch1 | PC-3 cells were cultured in RPMI 1640 media supplemented with 10% foetal calf serum, 2mM L-glutamine, penicillin 100u/ml, streptomycin 100ug/ml (all from Invitrogen, Paisley, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After 48 hours incubation 700µl of Qiazol lysis reagent (Qiagen, UK) was added. Cell scrapers were used to disrupt the cells and the resulting homogenate was transferred into a 1.5ml eppendorf tube. Total RNA was extracted using the RNeasy Lipid tissue mini kit with an on column DNAse step as directed by the manufacturer (Qiagen, UK). RNA was quantified using the Nanodrop instrument (Labtech Intl, UK). 260/230 and 260/280 ratios were assessed to examine RNA purity and integrity was assessed with the Bioanalyzer instrument (Agilent, UK).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For microarray work reverse transcription of RNA to cDNA was carried out using the Ovation RNA Amplification system v2 (Nugen Technologies Inc, USA). 100ng of total RNA was reverse transcribed as per the manufacturer’s protocol. cDNA was purified using qiaQuick PCR purification kit (Qiagen, UK) and quantified using the Nanodrop instrument. 3.75ug of cDNA was fragmented and labelled with the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, USA) and hybridised to each Affymetrix U133+2 array
| | Sample_hyb_protocol | Labelled cDNA was hybridised to Affymetrix hgu133plus2 arrays using protocols provided by Nugen Inc.
| | Sample_scan_protocol | Arrays were scanned with default settings using an Affymetrix scanner as directed by manufacturer
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further data processing were performed by RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Iain,,Gallagher
| | Sample_contact_email | iaingallagher@gmail.com
| | Sample_contact_phone | 00 44 131 242 6523
| | Sample_contact_laboratory | FU 501
| | Sample_contact_department | Tissue Injury & Repair
| | Sample_contact_institute | Edinburgh University
| | Sample_contact_address | The Chancellor's Building, 49 Little France Crescent
| | Sample_contact_city | Edinburgh
| | Sample_contact_zip/postal_code | EH16 4SB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842049/suppl/GSM842049.CEL.gz
| | Sample_series_id | GSE34112
| | Sample_data_row_count | 54675
| | |
|
GSM842050 | GPL570 |
|
PC3 cells, normoxia, DMSO rep 1
|
PC3 cells, normoxia, DMSO rep 1
|
oxygen level: 21.00%
treatment: DMSO
|
Gene expression data from PC3 cells under normoxic conditions treated with DMSO
|
| Sample_geo_accession | GSM842050
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 02 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | On Day 0, PC-3 cells were seeded at 2x106 cells/25cm2 flask and left overnight in a 37C incubator, 5% CO2. Next day (day 1) 0.05% DMSO (Sigma–Aldrich, Gillingham, UK), 25µM of NCX1102 (NO-sulindac; donated by NicOx (Sophia Antipolis, France)), and 25µM of sulindac (NicOx) was prepared in DMSO and added to the corresponding flasks. Flasks were placed in normoxic conditions (21% O2, 37C, 5% CO2) or in hypoxic conditions (0.2% O2, 37C, 95% CO2 & 5% N2) in a PROOX 110 oxygen controller (BioSpherix Ltd., Redfield, NY) for 48hrs.
| | Sample_growth_protocol_ch1 | PC-3 cells were cultured in RPMI 1640 media supplemented with 10% foetal calf serum, 2mM L-glutamine, penicillin 100u/ml, streptomycin 100ug/ml (all from Invitrogen, Paisley, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After 48 hours incubation 700µl of Qiazol lysis reagent (Qiagen, UK) was added. Cell scrapers were used to disrupt the cells and the resulting homogenate was transferred into a 1.5ml eppendorf tube. Total RNA was extracted using the RNeasy Lipid tissue mini kit with an on column DNAse step as directed by the manufacturer (Qiagen, UK). RNA was quantified using the Nanodrop instrument (Labtech Intl, UK). 260/230 and 260/280 ratios were assessed to examine RNA purity and integrity was assessed with the Bioanalyzer instrument (Agilent, UK).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For microarray work reverse transcription of RNA to cDNA was carried out using the Ovation RNA Amplification system v2 (Nugen Technologies Inc, USA). 100ng of total RNA was reverse transcribed as per the manufacturer’s protocol. cDNA was purified using qiaQuick PCR purification kit (Qiagen, UK) and quantified using the Nanodrop instrument. 3.75ug of cDNA was fragmented and labelled with the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, USA) and hybridised to each Affymetrix U133+2 array
| | Sample_hyb_protocol | Labelled cDNA was hybridised to Affymetrix hgu133plus2 arrays using protocols provided by Nugen Inc.
| | Sample_scan_protocol | Arrays were scanned with default settings using an Affymetrix scanner as directed by manufacturer
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further data processing were performed by RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Iain,,Gallagher
| | Sample_contact_email | iaingallagher@gmail.com
| | Sample_contact_phone | 00 44 131 242 6523
| | Sample_contact_laboratory | FU 501
| | Sample_contact_department | Tissue Injury & Repair
| | Sample_contact_institute | Edinburgh University
| | Sample_contact_address | The Chancellor's Building, 49 Little France Crescent
| | Sample_contact_city | Edinburgh
| | Sample_contact_zip/postal_code | EH16 4SB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842050/suppl/GSM842050.CEL.gz
| | Sample_series_id | GSE34112
| | Sample_data_row_count | 54675
| | |
|
GSM842051 | GPL570 |
|
PC3 cells, normoxia, DMSO rep 2
|
PC3 cells, normoxia, DMSO rep 2
|
oxygen level: 21.00%
treatment: DMSO
|
Gene expression data from PC3 cells under normoxic conditions treated with DMSO
|
| Sample_geo_accession | GSM842051
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 02 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | On Day 0, PC-3 cells were seeded at 2x106 cells/25cm2 flask and left overnight in a 37C incubator, 5% CO2. Next day (day 1) 0.05% DMSO (Sigma–Aldrich, Gillingham, UK), 25µM of NCX1102 (NO-sulindac; donated by NicOx (Sophia Antipolis, France)), and 25µM of sulindac (NicOx) was prepared in DMSO and added to the corresponding flasks. Flasks were placed in normoxic conditions (21% O2, 37C, 5% CO2) or in hypoxic conditions (0.2% O2, 37C, 95% CO2 & 5% N2) in a PROOX 110 oxygen controller (BioSpherix Ltd., Redfield, NY) for 48hrs.
| | Sample_growth_protocol_ch1 | PC-3 cells were cultured in RPMI 1640 media supplemented with 10% foetal calf serum, 2mM L-glutamine, penicillin 100u/ml, streptomycin 100ug/ml (all from Invitrogen, Paisley, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After 48 hours incubation 700µl of Qiazol lysis reagent (Qiagen, UK) was added. Cell scrapers were used to disrupt the cells and the resulting homogenate was transferred into a 1.5ml eppendorf tube. Total RNA was extracted using the RNeasy Lipid tissue mini kit with an on column DNAse step as directed by the manufacturer (Qiagen, UK). RNA was quantified using the Nanodrop instrument (Labtech Intl, UK). 260/230 and 260/280 ratios were assessed to examine RNA purity and integrity was assessed with the Bioanalyzer instrument (Agilent, UK).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For microarray work reverse transcription of RNA to cDNA was carried out using the Ovation RNA Amplification system v2 (Nugen Technologies Inc, USA). 100ng of total RNA was reverse transcribed as per the manufacturer’s protocol. cDNA was purified using qiaQuick PCR purification kit (Qiagen, UK) and quantified using the Nanodrop instrument. 3.75ug of cDNA was fragmented and labelled with the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, USA) and hybridised to each Affymetrix U133+2 array
| | Sample_hyb_protocol | Labelled cDNA was hybridised to Affymetrix hgu133plus2 arrays using protocols provided by Nugen Inc.
| | Sample_scan_protocol | Arrays were scanned with default settings using an Affymetrix scanner as directed by manufacturer
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further data processing were performed by RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Iain,,Gallagher
| | Sample_contact_email | iaingallagher@gmail.com
| | Sample_contact_phone | 00 44 131 242 6523
| | Sample_contact_laboratory | FU 501
| | Sample_contact_department | Tissue Injury & Repair
| | Sample_contact_institute | Edinburgh University
| | Sample_contact_address | The Chancellor's Building, 49 Little France Crescent
| | Sample_contact_city | Edinburgh
| | Sample_contact_zip/postal_code | EH16 4SB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842051/suppl/GSM842051.CEL.gz
| | Sample_series_id | GSE34112
| | Sample_data_row_count | 54675
| | |
|
GSM842052 | GPL570 |
|
PC3 cells, normoxia, NO-sulindac rep 2b
|
PC3 cells, normoxia, NO-sulindac rep 2
|
oxygen level: 21.00%
treatment: NO-sulindac
|
Gene expression data from PC3 cells under normoxic conditions and treated with NO-sulindac
|
| Sample_geo_accession | GSM842052
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 02 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | On Day 0, PC-3 cells were seeded at 2x106 cells/25cm2 flask and left overnight in a 37C incubator, 5% CO2. Next day (day 1) 0.05% DMSO (Sigma–Aldrich, Gillingham, UK), 25µM of NCX1102 (NO-sulindac; donated by NicOx (Sophia Antipolis, France)), and 25µM of sulindac (NicOx) was prepared in DMSO and added to the corresponding flasks. Flasks were placed in normoxic conditions (21% O2, 37C, 5% CO2) or in hypoxic conditions (0.2% O2, 37C, 95% CO2 & 5% N2) in a PROOX 110 oxygen controller (BioSpherix Ltd., Redfield, NY) for 48hrs.
| | Sample_growth_protocol_ch1 | PC-3 cells were cultured in RPMI 1640 media supplemented with 10% foetal calf serum, 2mM L-glutamine, penicillin 100u/ml, streptomycin 100ug/ml (all from Invitrogen, Paisley, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After 48 hours incubation 700µl of Qiazol lysis reagent (Qiagen, UK) was added. Cell scrapers were used to disrupt the cells and the resulting homogenate was transferred into a 1.5ml eppendorf tube. Total RNA was extracted using the RNeasy Lipid tissue mini kit with an on column DNAse step as directed by the manufacturer (Qiagen, UK). RNA was quantified using the Nanodrop instrument (Labtech Intl, UK). 260/230 and 260/280 ratios were assessed to examine RNA purity and integrity was assessed with the Bioanalyzer instrument (Agilent, UK).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For microarray work reverse transcription of RNA to cDNA was carried out using the Ovation RNA Amplification system v2 (Nugen Technologies Inc, USA). 100ng of total RNA was reverse transcribed as per the manufacturer’s protocol. cDNA was purified using qiaQuick PCR purification kit (Qiagen, UK) and quantified using the Nanodrop instrument. 3.75ug of cDNA was fragmented and labelled with the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, USA) and hybridised to each Affymetrix U133+2 array
| | Sample_hyb_protocol | Labelled cDNA was hybridised to Affymetrix hgu133plus2 arrays using protocols provided by Nugen Inc.
| | Sample_scan_protocol | Arrays were scanned with default settings using an Affymetrix scanner as directed by manufacturer
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further data processing were performed by RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Iain,,Gallagher
| | Sample_contact_email | iaingallagher@gmail.com
| | Sample_contact_phone | 00 44 131 242 6523
| | Sample_contact_laboratory | FU 501
| | Sample_contact_department | Tissue Injury & Repair
| | Sample_contact_institute | Edinburgh University
| | Sample_contact_address | The Chancellor's Building, 49 Little France Crescent
| | Sample_contact_city | Edinburgh
| | Sample_contact_zip/postal_code | EH16 4SB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842052/suppl/GSM842052.CEL.gz
| | Sample_series_id | GSE34112
| | Sample_data_row_count | 54675
| | |
|
GSM842053 | GPL570 |
|
PC3 cells, normoxia, NO-sulindac rep 2
|
PC3 cells, normoxia, NO-sulindac rep 2
|
oxygen level: 21.00%
treatment: NO-sulindac
|
Gene expression data from PC3 cells under normoxic conditions and treated with NO-sulindac
|
| Sample_geo_accession | GSM842053
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 02 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | On Day 0, PC-3 cells were seeded at 2x106 cells/25cm2 flask and left overnight in a 37C incubator, 5% CO2. Next day (day 1) 0.05% DMSO (Sigma–Aldrich, Gillingham, UK), 25µM of NCX1102 (NO-sulindac; donated by NicOx (Sophia Antipolis, France)), and 25µM of sulindac (NicOx) was prepared in DMSO and added to the corresponding flasks. Flasks were placed in normoxic conditions (21% O2, 37C, 5% CO2) or in hypoxic conditions (0.2% O2, 37C, 95% CO2 & 5% N2) in a PROOX 110 oxygen controller (BioSpherix Ltd., Redfield, NY) for 48hrs.
| | Sample_growth_protocol_ch1 | PC-3 cells were cultured in RPMI 1640 media supplemented with 10% foetal calf serum, 2mM L-glutamine, penicillin 100u/ml, streptomycin 100ug/ml (all from Invitrogen, Paisley, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After 48 hours incubation 700µl of Qiazol lysis reagent (Qiagen, UK) was added. Cell scrapers were used to disrupt the cells and the resulting homogenate was transferred into a 1.5ml eppendorf tube. Total RNA was extracted using the RNeasy Lipid tissue mini kit with an on column DNAse step as directed by the manufacturer (Qiagen, UK). RNA was quantified using the Nanodrop instrument (Labtech Intl, UK). 260/230 and 260/280 ratios were assessed to examine RNA purity and integrity was assessed with the Bioanalyzer instrument (Agilent, UK).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For microarray work reverse transcription of RNA to cDNA was carried out using the Ovation RNA Amplification system v2 (Nugen Technologies Inc, USA). 100ng of total RNA was reverse transcribed as per the manufacturer’s protocol. cDNA was purified using qiaQuick PCR purification kit (Qiagen, UK) and quantified using the Nanodrop instrument. 3.75ug of cDNA was fragmented and labelled with the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, USA) and hybridised to each Affymetrix U133+2 array
| | Sample_hyb_protocol | Labelled cDNA was hybridised to Affymetrix hgu133plus2 arrays using protocols provided by Nugen Inc.
| | Sample_scan_protocol | Arrays were scanned with default settings using an Affymetrix scanner as directed by manufacturer
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further data processing were performed by RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Iain,,Gallagher
| | Sample_contact_email | iaingallagher@gmail.com
| | Sample_contact_phone | 00 44 131 242 6523
| | Sample_contact_laboratory | FU 501
| | Sample_contact_department | Tissue Injury & Repair
| | Sample_contact_institute | Edinburgh University
| | Sample_contact_address | The Chancellor's Building, 49 Little France Crescent
| | Sample_contact_city | Edinburgh
| | Sample_contact_zip/postal_code | EH16 4SB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842053/suppl/GSM842053.CEL.gz
| | Sample_series_id | GSE34112
| | Sample_data_row_count | 54675
| | |
|
GSM842054 | GPL570 |
|
PC3 cells, normoxia, sulindac rep 1
|
PC3 cells, normoxia, sulindac rep 1
|
oxygen level: 21.00%
treatment: sulindac
|
Gene expression data from PC3 cells under normoxic conditions and treated with sulindac
|
| Sample_geo_accession | GSM842054
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 02 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | On Day 0, PC-3 cells were seeded at 2x106 cells/25cm2 flask and left overnight in a 37C incubator, 5% CO2. Next day (day 1) 0.05% DMSO (Sigma–Aldrich, Gillingham, UK), 25µM of NCX1102 (NO-sulindac; donated by NicOx (Sophia Antipolis, France)), and 25µM of sulindac (NicOx) was prepared in DMSO and added to the corresponding flasks. Flasks were placed in normoxic conditions (21% O2, 37C, 5% CO2) or in hypoxic conditions (0.2% O2, 37C, 95% CO2 & 5% N2) in a PROOX 110 oxygen controller (BioSpherix Ltd., Redfield, NY) for 48hrs.
| | Sample_growth_protocol_ch1 | PC-3 cells were cultured in RPMI 1640 media supplemented with 10% foetal calf serum, 2mM L-glutamine, penicillin 100u/ml, streptomycin 100ug/ml (all from Invitrogen, Paisley, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After 48 hours incubation 700µl of Qiazol lysis reagent (Qiagen, UK) was added. Cell scrapers were used to disrupt the cells and the resulting homogenate was transferred into a 1.5ml eppendorf tube. Total RNA was extracted using the RNeasy Lipid tissue mini kit with an on column DNAse step as directed by the manufacturer (Qiagen, UK). RNA was quantified using the Nanodrop instrument (Labtech Intl, UK). 260/230 and 260/280 ratios were assessed to examine RNA purity and integrity was assessed with the Bioanalyzer instrument (Agilent, UK).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For microarray work reverse transcription of RNA to cDNA was carried out using the Ovation RNA Amplification system v2 (Nugen Technologies Inc, USA). 100ng of total RNA was reverse transcribed as per the manufacturer’s protocol. cDNA was purified using qiaQuick PCR purification kit (Qiagen, UK) and quantified using the Nanodrop instrument. 3.75ug of cDNA was fragmented and labelled with the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, USA) and hybridised to each Affymetrix U133+2 array
| | Sample_hyb_protocol | Labelled cDNA was hybridised to Affymetrix hgu133plus2 arrays using protocols provided by Nugen Inc.
| | Sample_scan_protocol | Arrays were scanned with default settings using an Affymetrix scanner as directed by manufacturer
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further data processing were performed by RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Iain,,Gallagher
| | Sample_contact_email | iaingallagher@gmail.com
| | Sample_contact_phone | 00 44 131 242 6523
| | Sample_contact_laboratory | FU 501
| | Sample_contact_department | Tissue Injury & Repair
| | Sample_contact_institute | Edinburgh University
| | Sample_contact_address | The Chancellor's Building, 49 Little France Crescent
| | Sample_contact_city | Edinburgh
| | Sample_contact_zip/postal_code | EH16 4SB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842054/suppl/GSM842054.CEL.gz
| | Sample_series_id | GSE34112
| | Sample_data_row_count | 54675
| | |
|
GSM842055 | GPL570 |
|
PC3 cells, normoxia, sulindac rep 2
|
PC3 cells, normoxia, sulindac rep 2
|
oxygen level: 21.00%
treatment: sulindac
|
Gene expression data from PC3 cells under normoxic conditions and treated with sulindac
|
| Sample_geo_accession | GSM842055
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 02 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | On Day 0, PC-3 cells were seeded at 2x106 cells/25cm2 flask and left overnight in a 37C incubator, 5% CO2. Next day (day 1) 0.05% DMSO (Sigma–Aldrich, Gillingham, UK), 25µM of NCX1102 (NO-sulindac; donated by NicOx (Sophia Antipolis, France)), and 25µM of sulindac (NicOx) was prepared in DMSO and added to the corresponding flasks. Flasks were placed in normoxic conditions (21% O2, 37C, 5% CO2) or in hypoxic conditions (0.2% O2, 37C, 95% CO2 & 5% N2) in a PROOX 110 oxygen controller (BioSpherix Ltd., Redfield, NY) for 48hrs.
| | Sample_growth_protocol_ch1 | PC-3 cells were cultured in RPMI 1640 media supplemented with 10% foetal calf serum, 2mM L-glutamine, penicillin 100u/ml, streptomycin 100ug/ml (all from Invitrogen, Paisley, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After 48 hours incubation 700µl of Qiazol lysis reagent (Qiagen, UK) was added. Cell scrapers were used to disrupt the cells and the resulting homogenate was transferred into a 1.5ml eppendorf tube. Total RNA was extracted using the RNeasy Lipid tissue mini kit with an on column DNAse step as directed by the manufacturer (Qiagen, UK). RNA was quantified using the Nanodrop instrument (Labtech Intl, UK). 260/230 and 260/280 ratios were assessed to examine RNA purity and integrity was assessed with the Bioanalyzer instrument (Agilent, UK).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For microarray work reverse transcription of RNA to cDNA was carried out using the Ovation RNA Amplification system v2 (Nugen Technologies Inc, USA). 100ng of total RNA was reverse transcribed as per the manufacturer’s protocol. cDNA was purified using qiaQuick PCR purification kit (Qiagen, UK) and quantified using the Nanodrop instrument. 3.75ug of cDNA was fragmented and labelled with the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, USA) and hybridised to each Affymetrix U133+2 array
| | Sample_hyb_protocol | Labelled cDNA was hybridised to Affymetrix hgu133plus2 arrays using protocols provided by Nugen Inc.
| | Sample_scan_protocol | Arrays were scanned with default settings using an Affymetrix scanner as directed by manufacturer
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further data processing were performed by RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Iain,,Gallagher
| | Sample_contact_email | iaingallagher@gmail.com
| | Sample_contact_phone | 00 44 131 242 6523
| | Sample_contact_laboratory | FU 501
| | Sample_contact_department | Tissue Injury & Repair
| | Sample_contact_institute | Edinburgh University
| | Sample_contact_address | The Chancellor's Building, 49 Little France Crescent
| | Sample_contact_city | Edinburgh
| | Sample_contact_zip/postal_code | EH16 4SB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842055/suppl/GSM842055.CEL.gz
| | Sample_series_id | GSE34112
| | Sample_data_row_count | 54675
| | |
|
GSM842056 | GPL570 |
|
PC3 cells, hypoxia, no treatment rep 1
|
PC3 cells, hypoxia, no treatment rep 1
|
oxygen level: 0.20%
treatment: none
|
Gene expression data from PC3 cells under hypoxic conditionswith no treatment
|
| Sample_geo_accession | GSM842056
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 02 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | On Day 0, PC-3 cells were seeded at 2x106 cells/25cm2 flask and left overnight in a 37C incubator, 5% CO2. Next day (day 1) 0.05% DMSO (Sigma–Aldrich, Gillingham, UK), 25µM of NCX1102 (NO-sulindac; donated by NicOx (Sophia Antipolis, France)), and 25µM of sulindac (NicOx) was prepared in DMSO and added to the corresponding flasks. Flasks were placed in normoxic conditions (21% O2, 37C, 5% CO2) or in hypoxic conditions (0.2% O2, 37C, 95% CO2 & 5% N2) in a PROOX 110 oxygen controller (BioSpherix Ltd., Redfield, NY) for 48hrs.
| | Sample_growth_protocol_ch1 | PC-3 cells were cultured in RPMI 1640 media supplemented with 10% foetal calf serum, 2mM L-glutamine, penicillin 100u/ml, streptomycin 100ug/ml (all from Invitrogen, Paisley, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After 48 hours incubation 700µl of Qiazol lysis reagent (Qiagen, UK) was added. Cell scrapers were used to disrupt the cells and the resulting homogenate was transferred into a 1.5ml eppendorf tube. Total RNA was extracted using the RNeasy Lipid tissue mini kit with an on column DNAse step as directed by the manufacturer (Qiagen, UK). RNA was quantified using the Nanodrop instrument (Labtech Intl, UK). 260/230 and 260/280 ratios were assessed to examine RNA purity and integrity was assessed with the Bioanalyzer instrument (Agilent, UK).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For microarray work reverse transcription of RNA to cDNA was carried out using the Ovation RNA Amplification system v2 (Nugen Technologies Inc, USA). 100ng of total RNA was reverse transcribed as per the manufacturer’s protocol. cDNA was purified using qiaQuick PCR purification kit (Qiagen, UK) and quantified using the Nanodrop instrument. 3.75ug of cDNA was fragmented and labelled with the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, USA) and hybridised to each Affymetrix U133+2 array
| | Sample_hyb_protocol | Labelled cDNA was hybridised to Affymetrix hgu133plus2 arrays using protocols provided by Nugen Inc.
| | Sample_scan_protocol | Arrays were scanned with default settings using an Affymetrix scanner as directed by manufacturer
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further data processing were performed by RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Iain,,Gallagher
| | Sample_contact_email | iaingallagher@gmail.com
| | Sample_contact_phone | 00 44 131 242 6523
| | Sample_contact_laboratory | FU 501
| | Sample_contact_department | Tissue Injury & Repair
| | Sample_contact_institute | Edinburgh University
| | Sample_contact_address | The Chancellor's Building, 49 Little France Crescent
| | Sample_contact_city | Edinburgh
| | Sample_contact_zip/postal_code | EH16 4SB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842056/suppl/GSM842056.CEL.gz
| | Sample_series_id | GSE34112
| | Sample_data_row_count | 54675
| | |
|
GSM842057 | GPL570 |
|
PC3 cells, hypoxia, no treatment rep 2
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PC3 cells, hypoxia, no treatment rep 2
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oxygen level: 0.20%
treatment: none
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Gene expression data from PC3 cells under hypoxic conditionswith no treatment
|
| Sample_geo_accession | GSM842057
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 02 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | On Day 0, PC-3 cells were seeded at 2x106 cells/25cm2 flask and left overnight in a 37C incubator, 5% CO2. Next day (day 1) 0.05% DMSO (Sigma–Aldrich, Gillingham, UK), 25µM of NCX1102 (NO-sulindac; donated by NicOx (Sophia Antipolis, France)), and 25µM of sulindac (NicOx) was prepared in DMSO and added to the corresponding flasks. Flasks were placed in normoxic conditions (21% O2, 37C, 5% CO2) or in hypoxic conditions (0.2% O2, 37C, 95% CO2 & 5% N2) in a PROOX 110 oxygen controller (BioSpherix Ltd., Redfield, NY) for 48hrs.
| | Sample_growth_protocol_ch1 | PC-3 cells were cultured in RPMI 1640 media supplemented with 10% foetal calf serum, 2mM L-glutamine, penicillin 100u/ml, streptomycin 100ug/ml (all from Invitrogen, Paisley, UK).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | After 48 hours incubation 700µl of Qiazol lysis reagent (Qiagen, UK) was added. Cell scrapers were used to disrupt the cells and the resulting homogenate was transferred into a 1.5ml eppendorf tube. Total RNA was extracted using the RNeasy Lipid tissue mini kit with an on column DNAse step as directed by the manufacturer (Qiagen, UK). RNA was quantified using the Nanodrop instrument (Labtech Intl, UK). 260/230 and 260/280 ratios were assessed to examine RNA purity and integrity was assessed with the Bioanalyzer instrument (Agilent, UK).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For microarray work reverse transcription of RNA to cDNA was carried out using the Ovation RNA Amplification system v2 (Nugen Technologies Inc, USA). 100ng of total RNA was reverse transcribed as per the manufacturer’s protocol. cDNA was purified using qiaQuick PCR purification kit (Qiagen, UK) and quantified using the Nanodrop instrument. 3.75ug of cDNA was fragmented and labelled with the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, USA) and hybridised to each Affymetrix U133+2 array
| | Sample_hyb_protocol | Labelled cDNA was hybridised to Affymetrix hgu133plus2 arrays using protocols provided by Nugen Inc.
| | Sample_scan_protocol | Arrays were scanned with default settings using an Affymetrix scanner as directed by manufacturer
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further data processing were performed by RMA.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Iain,,Gallagher
| | Sample_contact_email | iaingallagher@gmail.com
| | Sample_contact_phone | 00 44 131 242 6523
| | Sample_contact_laboratory | FU 501
| | Sample_contact_department | Tissue Injury & Repair
| | Sample_contact_institute | Edinburgh University
| | Sample_contact_address | The Chancellor's Building, 49 Little France Crescent
| | Sample_contact_city | Edinburgh
| | Sample_contact_zip/postal_code | EH16 4SB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842057/suppl/GSM842057.CEL.gz
| | Sample_series_id | GSE34112
| | Sample_data_row_count | 54675
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