Search results for the GEO ID: GSE13034  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM326530 | GPL339 |
|
MEF_WT_con_rep1
|
WT MEF control
|
Genotype: HtrA2 wild type, Treatment vehicle 4hrs
|
Gene expression data from WT MEFs treated for 4hrs with vehicle
|
| Sample_geo_accession | GSM326530
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Oct 03 2008
| | Sample_last_update_date | Oct 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | MEFs at passage 4 were subjected to treatment with vehicle (control) or 1 μM rotenone (rot) for 4 hrs.
| | Sample_growth_protocol_ch1 | Primary MEFs derived from WT and HtrA2 KO mice were cultured in DMEM supplemented with 10% FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s instructions, whereby 600 μl RLT buffer / 30 μg of tissue were first homogenized by pipetting or using a glass dounce homogenizer, before further disruption in a QIAshredder column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA. A complete description of all procedures is available online at http://www.affymetrix.com/support/technical/manual/expression_manual.affx and at http://bioinformatics.picr.man.ac.uk/mbcf/One_Cycle_Target_Prep_Protocol_PICR_v1-0.pdf
| | Sample_hyb_protocol | The standard PICR hybridisation protocol was followed for hybridisation RNA labelled using the 1-cycle protocol to standard GeneChips with 11mciron featrue sizes (http://bioinformatics.picr.man.ac.uk/mbcf/downloads/_HYBRIDISATION_PROTOCOLS/PICR%20One%20Cycle%2011uM%20feature.pdf). This is derived from the Affymetrix Standard Eukaryote Sample Preparation Protocol (section 2, chapter 3) of the GeneChip Expression Analysis Technical Manual (version April 2004) (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 running GCOS software.
| | Sample_data_processing | Probe signals were quantile normalized and probeset signal intensity estimates generated using RMA.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kristina,,Klupsch
| | Sample_contact_laboratory | Signal Transduction Laboratory
| | Sample_contact_department | London Research Institute
| | Sample_contact_institute | Cancer Research UK
| | Sample_contact_address | 44 Lincoln's Inn Fields
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC2A 3PX
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM326nnn/GSM326530/suppl/GSM326530.CEL.gz
| | Sample_series_id | GSE13034
| | Sample_series_id | GSE13035
| | Sample_data_row_count | 22690
| | |
|
GSM326531 | GPL339 |
|
MEF_WT_con_rep2
|
WT MEF control
|
Genotype: HtrA2 wild type, Treatment vehicle 4hrs
|
Gene expression data from WT MEFs treated for 4hrs with vehicle
|
| Sample_geo_accession | GSM326531
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Oct 03 2008
| | Sample_last_update_date | Oct 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | MEFs at passage 4 were subjected to treatment with vehicle (control) or 1 μM rotenone (rot) for 4 hrs.
| | Sample_growth_protocol_ch1 | Primary MEFs derived from WT and HtrA2 KO mice were cultured in DMEM supplemented with 10% FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s instructions, whereby 600 μl RLT buffer / 30 μg of tissue were first homogenized by pipetting or using a glass dounce homogenizer, before further disruption in a QIAshredder column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA. A complete description of all procedures is available online at http://www.affymetrix.com/support/technical/manual/expression_manual.affx and at http://bioinformatics.picr.man.ac.uk/mbcf/One_Cycle_Target_Prep_Protocol_PICR_v1-0.pdf
| | Sample_hyb_protocol | The standard PICR hybridisation protocol was followed for hybridisation RNA labelled using the 1-cycle protocol to standard GeneChips with 11mciron featrue sizes (http://bioinformatics.picr.man.ac.uk/mbcf/downloads/_HYBRIDISATION_PROTOCOLS/PICR%20One%20Cycle%2011uM%20feature.pdf). This is derived from the Affymetrix Standard Eukaryote Sample Preparation Protocol (section 2, chapter 3) of the GeneChip Expression Analysis Technical Manual (version April 2004) (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 running GCOS software.
| | Sample_data_processing | Probe signals were quantile normalized and probeset signal intensity estimates generated using RMA.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kristina,,Klupsch
| | Sample_contact_laboratory | Signal Transduction Laboratory
| | Sample_contact_department | London Research Institute
| | Sample_contact_institute | Cancer Research UK
| | Sample_contact_address | 44 Lincoln's Inn Fields
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC2A 3PX
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM326nnn/GSM326531/suppl/GSM326531.CEL.gz
| | Sample_series_id | GSE13034
| | Sample_series_id | GSE13035
| | Sample_data_row_count | 22690
| | |
|
GSM326532 | GPL339 |
|
MEF_WT_con_rep3
|
WT MEF control
|
Genotype: HtrA2 wild type, Treatment vehicle 4hrs
|
Gene expression data from WT MEFs treated for 4hrs with vehicle
|
| Sample_geo_accession | GSM326532
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Oct 03 2008
| | Sample_last_update_date | Oct 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | MEFs at passage 4 were subjected to treatment with vehicle (control) or 1 μM rotenone (rot) for 4 hrs.
| | Sample_growth_protocol_ch1 | Primary MEFs derived from WT and HtrA2 KO mice were cultured in DMEM supplemented with 10% FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s instructions, whereby 600 μl RLT buffer / 30 μg of tissue were first homogenized by pipetting or using a glass dounce homogenizer, before further disruption in a QIAshredder column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA. A complete description of all procedures is available online at http://www.affymetrix.com/support/technical/manual/expression_manual.affx and at http://bioinformatics.picr.man.ac.uk/mbcf/One_Cycle_Target_Prep_Protocol_PICR_v1-0.pdf
| | Sample_hyb_protocol | The standard PICR hybridisation protocol was followed for hybridisation RNA labelled using the 1-cycle protocol to standard GeneChips with 11mciron featrue sizes (http://bioinformatics.picr.man.ac.uk/mbcf/downloads/_HYBRIDISATION_PROTOCOLS/PICR%20One%20Cycle%2011uM%20feature.pdf). This is derived from the Affymetrix Standard Eukaryote Sample Preparation Protocol (section 2, chapter 3) of the GeneChip Expression Analysis Technical Manual (version April 2004) (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 running GCOS software.
| | Sample_data_processing | Probe signals were quantile normalized and probeset signal intensity estimates generated using RMA.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kristina,,Klupsch
| | Sample_contact_laboratory | Signal Transduction Laboratory
| | Sample_contact_department | London Research Institute
| | Sample_contact_institute | Cancer Research UK
| | Sample_contact_address | 44 Lincoln's Inn Fields
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC2A 3PX
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM326nnn/GSM326532/suppl/GSM326532.CEL.gz
| | Sample_series_id | GSE13034
| | Sample_series_id | GSE13035
| | Sample_data_row_count | 22690
| | |
|
GSM326533 | GPL339 |
|
MEF_WT_rot_rep1
|
WT MEF rotenone
|
Genotype: HtrA2 knockout, Treatment: 1uM rotenone 4hrs
|
Gene expression data from WT MEFs treated for 4hrs with 1uM rotenone
|
| Sample_geo_accession | GSM326533
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Oct 03 2008
| | Sample_last_update_date | Oct 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | MEFs at passage 4 were subjected to treatment with vehicle (control) or 1 μM rotenone (rot) for 4 hrs.
| | Sample_growth_protocol_ch1 | Primary MEFs derived from WT and HtrA2 KO mice were cultured in DMEM supplemented with 10% FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s instructions, whereby 600 μl RLT buffer / 30 μg of tissue were first homogenized by pipetting or using a glass dounce homogenizer, before further disruption in a QIAshredder column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA. A complete description of all procedures is available online at http://www.affymetrix.com/support/technical/manual/expression_manual.affx and at http://bioinformatics.picr.man.ac.uk/mbcf/One_Cycle_Target_Prep_Protocol_PICR_v1-0.pdf
| | Sample_hyb_protocol | The standard PICR hybridisation protocol was followed for hybridisation RNA labelled using the 1-cycle protocol to standard GeneChips with 11mciron featrue sizes (http://bioinformatics.picr.man.ac.uk/mbcf/downloads/_HYBRIDISATION_PROTOCOLS/PICR%20One%20Cycle%2011uM%20feature.pdf). This is derived from the Affymetrix Standard Eukaryote Sample Preparation Protocol (section 2, chapter 3) of the GeneChip Expression Analysis Technical Manual (version April 2004) (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 running GCOS software.
| | Sample_data_processing | Probe signals were quantile normalized and probeset signal intensity estimates generated using RMA.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kristina,,Klupsch
| | Sample_contact_laboratory | Signal Transduction Laboratory
| | Sample_contact_department | London Research Institute
| | Sample_contact_institute | Cancer Research UK
| | Sample_contact_address | 44 Lincoln's Inn Fields
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC2A 3PX
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM326nnn/GSM326533/suppl/GSM326533.CEL.gz
| | Sample_series_id | GSE13034
| | Sample_series_id | GSE13035
| | Sample_data_row_count | 22690
| | |
|
GSM326534 | GPL339 |
|
MEF_WT_rot_rep2
|
WT MEF rotenone
|
Genotype: HtrA2 knockout, Treatment: 1uM rotenone 4hrs
|
Gene expression data from WT MEFs treated for 4hrs with 1uM rotenone
|
| Sample_geo_accession | GSM326534
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Oct 03 2008
| | Sample_last_update_date | Oct 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | MEFs at passage 4 were subjected to treatment with vehicle (control) or 1 μM rotenone (rot) for 4 hrs.
| | Sample_growth_protocol_ch1 | Primary MEFs derived from WT and HtrA2 KO mice were cultured in DMEM supplemented with 10% FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s instructions, whereby 600 μl RLT buffer / 30 μg of tissue were first homogenized by pipetting or using a glass dounce homogenizer, before further disruption in a QIAshredder column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA. A complete description of all procedures is available online at http://www.affymetrix.com/support/technical/manual/expression_manual.affx and at http://bioinformatics.picr.man.ac.uk/mbcf/One_Cycle_Target_Prep_Protocol_PICR_v1-0.pdf
| | Sample_hyb_protocol | The standard PICR hybridisation protocol was followed for hybridisation RNA labelled using the 1-cycle protocol to standard GeneChips with 11mciron featrue sizes (http://bioinformatics.picr.man.ac.uk/mbcf/downloads/_HYBRIDISATION_PROTOCOLS/PICR%20One%20Cycle%2011uM%20feature.pdf). This is derived from the Affymetrix Standard Eukaryote Sample Preparation Protocol (section 2, chapter 3) of the GeneChip Expression Analysis Technical Manual (version April 2004) (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 running GCOS software.
| | Sample_data_processing | Probe signals were quantile normalized and probeset signal intensity estimates generated using RMA.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kristina,,Klupsch
| | Sample_contact_laboratory | Signal Transduction Laboratory
| | Sample_contact_department | London Research Institute
| | Sample_contact_institute | Cancer Research UK
| | Sample_contact_address | 44 Lincoln's Inn Fields
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC2A 3PX
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM326nnn/GSM326534/suppl/GSM326534.CEL.gz
| | Sample_series_id | GSE13034
| | Sample_series_id | GSE13035
| | Sample_data_row_count | 22690
| | |
|
GSM326535 | GPL339 |
|
MEF_WT_rot_rep3
|
WT MEF rotenone
|
Genotype: HtrA2 knockout, Treatment: 1uM rotenone 4hrs
|
Gene expression data from WT MEFs treated for 4hrs with 1uM rotenone
|
| Sample_geo_accession | GSM326535
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Oct 03 2008
| | Sample_last_update_date | Oct 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | MEFs at passage 4 were subjected to treatment with vehicle (control) or 1 μM rotenone (rot) for 4 hrs.
| | Sample_growth_protocol_ch1 | Primary MEFs derived from WT and HtrA2 KO mice were cultured in DMEM supplemented with 10% FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s instructions, whereby 600 μl RLT buffer / 30 μg of tissue were first homogenized by pipetting or using a glass dounce homogenizer, before further disruption in a QIAshredder column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA. A complete description of all procedures is available online at http://www.affymetrix.com/support/technical/manual/expression_manual.affx and at http://bioinformatics.picr.man.ac.uk/mbcf/One_Cycle_Target_Prep_Protocol_PICR_v1-0.pdf
| | Sample_hyb_protocol | The standard PICR hybridisation protocol was followed for hybridisation RNA labelled using the 1-cycle protocol to standard GeneChips with 11mciron featrue sizes (http://bioinformatics.picr.man.ac.uk/mbcf/downloads/_HYBRIDISATION_PROTOCOLS/PICR%20One%20Cycle%2011uM%20feature.pdf). This is derived from the Affymetrix Standard Eukaryote Sample Preparation Protocol (section 2, chapter 3) of the GeneChip Expression Analysis Technical Manual (version April 2004) (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 running GCOS software.
| | Sample_data_processing | Probe signals were quantile normalized and probeset signal intensity estimates generated using RMA.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kristina,,Klupsch
| | Sample_contact_laboratory | Signal Transduction Laboratory
| | Sample_contact_department | London Research Institute
| | Sample_contact_institute | Cancer Research UK
| | Sample_contact_address | 44 Lincoln's Inn Fields
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC2A 3PX
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM326nnn/GSM326535/suppl/GSM326535.CEL.gz
| | Sample_series_id | GSE13034
| | Sample_series_id | GSE13035
| | Sample_data_row_count | 22690
| | |
|
GSM326536 | GPL339 |
|
MEF_HtrA2 KO_con_rep1
|
HtrA2 KO control
|
Genotype: HtrA2 knockout, Treatment vehicle 4hrs
|
Gene expression data from HtrA2 KO MEFs treated for 4hrs with vehicle
|
| Sample_geo_accession | GSM326536
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Oct 03 2008
| | Sample_last_update_date | Oct 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | MEFs at passage 4 were subjected to treatment with vehicle (control) or 1 μM rotenone (rot) for 4 hrs.
| | Sample_growth_protocol_ch1 | Primary MEFs derived from WT and HtrA2 KO mice were cultured in DMEM supplemented with 10% FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s instructions, whereby 600 μl RLT buffer / 30 μg of tissue were first homogenized by pipetting or using a glass dounce homogenizer, before further disruption in a QIAshredder column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA. A complete description of all procedures is available online at http://www.affymetrix.com/support/technical/manual/expression_manual.affx and at http://bioinformatics.picr.man.ac.uk/mbcf/One_Cycle_Target_Prep_Protocol_PICR_v1-0.pdf
| | Sample_hyb_protocol | The standard PICR hybridisation protocol was followed for hybridisation RNA labelled using the 1-cycle protocol to standard GeneChips with 11mciron featrue sizes (http://bioinformatics.picr.man.ac.uk/mbcf/downloads/_HYBRIDISATION_PROTOCOLS/PICR%20One%20Cycle%2011uM%20feature.pdf). This is derived from the Affymetrix Standard Eukaryote Sample Preparation Protocol (section 2, chapter 3) of the GeneChip Expression Analysis Technical Manual (version April 2004) (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 running GCOS software.
| | Sample_data_processing | Probe signals were quantile normalized and probeset signal intensity estimates generated using RMA.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kristina,,Klupsch
| | Sample_contact_laboratory | Signal Transduction Laboratory
| | Sample_contact_department | London Research Institute
| | Sample_contact_institute | Cancer Research UK
| | Sample_contact_address | 44 Lincoln's Inn Fields
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC2A 3PX
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM326nnn/GSM326536/suppl/GSM326536.CEL.gz
| | Sample_series_id | GSE13034
| | Sample_series_id | GSE13035
| | Sample_data_row_count | 22690
| | |
|
GSM326537 | GPL339 |
|
MEF_HtrA2 KO_con_rep2
|
HtrA2 KO control
|
Genotype: HtrA2 knockout, Treatment vehicle 4hrs
|
Gene expression data from HtrA2 KO MEFs treated for 4hrs with vehicle
|
| Sample_geo_accession | GSM326537
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Oct 03 2008
| | Sample_last_update_date | Oct 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | MEFs at passage 4 were subjected to treatment with vehicle (control) or 1 μM rotenone (rot) for 4 hrs.
| | Sample_growth_protocol_ch1 | Primary MEFs derived from WT and HtrA2 KO mice were cultured in DMEM supplemented with 10% FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s instructions, whereby 600 μl RLT buffer / 30 μg of tissue were first homogenized by pipetting or using a glass dounce homogenizer, before further disruption in a QIAshredder column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA. A complete description of all procedures is available online at http://www.affymetrix.com/support/technical/manual/expression_manual.affx and at http://bioinformatics.picr.man.ac.uk/mbcf/One_Cycle_Target_Prep_Protocol_PICR_v1-0.pdf
| | Sample_hyb_protocol | The standard PICR hybridisation protocol was followed for hybridisation RNA labelled using the 1-cycle protocol to standard GeneChips with 11mciron featrue sizes (http://bioinformatics.picr.man.ac.uk/mbcf/downloads/_HYBRIDISATION_PROTOCOLS/PICR%20One%20Cycle%2011uM%20feature.pdf). This is derived from the Affymetrix Standard Eukaryote Sample Preparation Protocol (section 2, chapter 3) of the GeneChip Expression Analysis Technical Manual (version April 2004) (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 running GCOS software.
| | Sample_data_processing | Probe signals were quantile normalized and probeset signal intensity estimates generated using RMA.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kristina,,Klupsch
| | Sample_contact_laboratory | Signal Transduction Laboratory
| | Sample_contact_department | London Research Institute
| | Sample_contact_institute | Cancer Research UK
| | Sample_contact_address | 44 Lincoln's Inn Fields
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC2A 3PX
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM326nnn/GSM326537/suppl/GSM326537.CEL.gz
| | Sample_series_id | GSE13034
| | Sample_series_id | GSE13035
| | Sample_data_row_count | 22690
| | |
|
GSM326538 | GPL339 |
|
MEF_HtrA2 KO_con_rep3
|
HtrA2 KO control
|
Genotype: HtrA2 knockout, Treatment vehicle 4hrs
|
Gene expression data from HtrA2 KO MEFs treated for 4hrs with vehicle
|
| Sample_geo_accession | GSM326538
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Oct 03 2008
| | Sample_last_update_date | Oct 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | MEFs at passage 4 were subjected to treatment with vehicle (control) or 1 μM rotenone (rot) for 4 hrs.
| | Sample_growth_protocol_ch1 | Primary MEFs derived from WT and HtrA2 KO mice were cultured in DMEM supplemented with 10% FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s instructions, whereby 600 μl RLT buffer / 30 μg of tissue were first homogenized by pipetting or using a glass dounce homogenizer, before further disruption in a QIAshredder column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA. A complete description of all procedures is available online at http://www.affymetrix.com/support/technical/manual/expression_manual.affx and at http://bioinformatics.picr.man.ac.uk/mbcf/One_Cycle_Target_Prep_Protocol_PICR_v1-0.pdf
| | Sample_hyb_protocol | The standard PICR hybridisation protocol was followed for hybridisation RNA labelled using the 1-cycle protocol to standard GeneChips with 11mciron featrue sizes (http://bioinformatics.picr.man.ac.uk/mbcf/downloads/_HYBRIDISATION_PROTOCOLS/PICR%20One%20Cycle%2011uM%20feature.pdf). This is derived from the Affymetrix Standard Eukaryote Sample Preparation Protocol (section 2, chapter 3) of the GeneChip Expression Analysis Technical Manual (version April 2004) (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 running GCOS software.
| | Sample_data_processing | Probe signals were quantile normalized and probeset signal intensity estimates generated using RMA.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kristina,,Klupsch
| | Sample_contact_laboratory | Signal Transduction Laboratory
| | Sample_contact_department | London Research Institute
| | Sample_contact_institute | Cancer Research UK
| | Sample_contact_address | 44 Lincoln's Inn Fields
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC2A 3PX
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM326nnn/GSM326538/suppl/GSM326538.CEL.gz
| | Sample_series_id | GSE13034
| | Sample_series_id | GSE13035
| | Sample_data_row_count | 22690
| | |
|
GSM326539 | GPL339 |
|
MEF_HtrA2 KO_rot_rep1
|
HtrA2 KO rotenone
|
Genotype: HtrA2 knockout, Treatment: 1uM rotenone 4hrs
|
Gene expression data from HtrA2 KO MEFs treated for 4hrs with 1uM rotenone
|
| Sample_geo_accession | GSM326539
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Oct 03 2008
| | Sample_last_update_date | Oct 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | MEFs at passage 4 were subjected to treatment with vehicle (control) or 1 μM rotenone (rot) for 4 hrs.
| | Sample_growth_protocol_ch1 | Primary MEFs derived from WT and HtrA2 KO mice were cultured in DMEM supplemented with 10% FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s instructions, whereby 600 μl RLT buffer / 30 μg of tissue were first homogenized by pipetting or using a glass dounce homogenizer, before further disruption in a QIAshredder column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA. A complete description of all procedures is available online at http://www.affymetrix.com/support/technical/manual/expression_manual.affx and at http://bioinformatics.picr.man.ac.uk/mbcf/One_Cycle_Target_Prep_Protocol_PICR_v1-0.pdf
| | Sample_hyb_protocol | The standard PICR hybridisation protocol was followed for hybridisation RNA labelled using the 1-cycle protocol to standard GeneChips with 11mciron featrue sizes (http://bioinformatics.picr.man.ac.uk/mbcf/downloads/_HYBRIDISATION_PROTOCOLS/PICR%20One%20Cycle%2011uM%20feature.pdf). This is derived from the Affymetrix Standard Eukaryote Sample Preparation Protocol (section 2, chapter 3) of the GeneChip Expression Analysis Technical Manual (version April 2004) (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 running GCOS software.
| | Sample_data_processing | Probe signals were quantile normalized and probeset signal intensity estimates generated using RMA.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kristina,,Klupsch
| | Sample_contact_laboratory | Signal Transduction Laboratory
| | Sample_contact_department | London Research Institute
| | Sample_contact_institute | Cancer Research UK
| | Sample_contact_address | 44 Lincoln's Inn Fields
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC2A 3PX
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM326nnn/GSM326539/suppl/GSM326539.CEL.gz
| | Sample_series_id | GSE13034
| | Sample_series_id | GSE13035
| | Sample_data_row_count | 22690
| | |
|
GSM326540 | GPL339 |
|
MEF_HtrA2 KO_rot_rep2
|
HtrA2 KO rotenone
|
Genotype: HtrA2 knockout, Treatment: 1uM rotenone 4hrs
|
Gene expression data from HtrA2 KO MEFs treated for 4hrs with 1uM rotenone
|
| Sample_geo_accession | GSM326540
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Oct 03 2008
| | Sample_last_update_date | Oct 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | MEFs at passage 4 were subjected to treatment with vehicle (control) or 1 μM rotenone (rot) for 4 hrs.
| | Sample_growth_protocol_ch1 | Primary MEFs derived from WT and HtrA2 KO mice were cultured in DMEM supplemented with 10% FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s instructions, whereby 600 μl RLT buffer / 30 μg of tissue were first homogenized by pipetting or using a glass dounce homogenizer, before further disruption in a QIAshredder column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA. A complete description of all procedures is available online at http://www.affymetrix.com/support/technical/manual/expression_manual.affx and at http://bioinformatics.picr.man.ac.uk/mbcf/One_Cycle_Target_Prep_Protocol_PICR_v1-0.pdf
| | Sample_hyb_protocol | The standard PICR hybridisation protocol was followed for hybridisation RNA labelled using the 1-cycle protocol to standard GeneChips with 11mciron featrue sizes (http://bioinformatics.picr.man.ac.uk/mbcf/downloads/_HYBRIDISATION_PROTOCOLS/PICR%20One%20Cycle%2011uM%20feature.pdf). This is derived from the Affymetrix Standard Eukaryote Sample Preparation Protocol (section 2, chapter 3) of the GeneChip Expression Analysis Technical Manual (version April 2004) (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 running GCOS software.
| | Sample_data_processing | Probe signals were quantile normalized and probeset signal intensity estimates generated using RMA.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kristina,,Klupsch
| | Sample_contact_laboratory | Signal Transduction Laboratory
| | Sample_contact_department | London Research Institute
| | Sample_contact_institute | Cancer Research UK
| | Sample_contact_address | 44 Lincoln's Inn Fields
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC2A 3PX
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM326nnn/GSM326540/suppl/GSM326540.CEL.gz
| | Sample_series_id | GSE13034
| | Sample_series_id | GSE13035
| | Sample_data_row_count | 22690
| | |
|
GSM326541 | GPL339 |
|
MEF_HtrA2 KO_rot_rep3
|
HtrA2 KO rotenone
|
Genotype: HtrA2 knockout, Treatment: 1uM rotenone 4hrs
|
Gene expression data from HtrA2 KO MEFs treated for 4hrs with 1uM rotenone
|
| Sample_geo_accession | GSM326541
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Oct 03 2008
| | Sample_last_update_date | Oct 09 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | MEFs at passage 4 were subjected to treatment with vehicle (control) or 1 μM rotenone (rot) for 4 hrs.
| | Sample_growth_protocol_ch1 | Primary MEFs derived from WT and HtrA2 KO mice were cultured in DMEM supplemented with 10% FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s instructions, whereby 600 μl RLT buffer / 30 μg of tissue were first homogenized by pipetting or using a glass dounce homogenizer, before further disruption in a QIAshredder column (Qiagen).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA. A complete description of all procedures is available online at http://www.affymetrix.com/support/technical/manual/expression_manual.affx and at http://bioinformatics.picr.man.ac.uk/mbcf/One_Cycle_Target_Prep_Protocol_PICR_v1-0.pdf
| | Sample_hyb_protocol | The standard PICR hybridisation protocol was followed for hybridisation RNA labelled using the 1-cycle protocol to standard GeneChips with 11mciron featrue sizes (http://bioinformatics.picr.man.ac.uk/mbcf/downloads/_HYBRIDISATION_PROTOCOLS/PICR%20One%20Cycle%2011uM%20feature.pdf). This is derived from the Affymetrix Standard Eukaryote Sample Preparation Protocol (section 2, chapter 3) of the GeneChip Expression Analysis Technical Manual (version April 2004) (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip scanner 3000 running GCOS software.
| | Sample_data_processing | Probe signals were quantile normalized and probeset signal intensity estimates generated using RMA.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Kristina,,Klupsch
| | Sample_contact_laboratory | Signal Transduction Laboratory
| | Sample_contact_department | London Research Institute
| | Sample_contact_institute | Cancer Research UK
| | Sample_contact_address | 44 Lincoln's Inn Fields
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | WC2A 3PX
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM326nnn/GSM326541/suppl/GSM326541.CEL.gz
| | Sample_series_id | GSE13034
| | Sample_series_id | GSE13035
| | Sample_data_row_count | 22690
| | |
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