{ "id": "13227547204752", "status": "described", "provenance": { "desc_version": "4", "data_version": "1", "uploaded": { "by": "Alexandra Pokhilko", "date": "2011-12-01T15:52:00" }, "modified": [ { "by": "Tomasz Zielinski", "date": "2014-10-17T15:48:13", "version": "4.1" }, { "by": "Tomasz Zielinski", "date": "2014-10-17T15:47:37", "version": "3.1" }, { "by": "SYSTEM USER", "date": "2014-09-15T16:54:06" }, { "by": "SYSTEM USER", "date": "2014-09-08T18:30:40" }, { "by": "Andrew Millar", "date": "2012-06-19T23:22:21" }, { "by": "Andrew Millar", "date": "2012-06-19T23:21:54" }, { "by": "Andrew Millar", "date": "2012-03-12T21:05:46" }, { "by": "Andrew Millar", "date": "2012-03-12T21:05:34" }, { "by": "Alexandra Pokhilko", "date": "2011-12-02T14:20:36" }, { "by": "Alexandra Pokhilko", "date": "2011-12-01T15:57:31" }, { "by": "Alexandra Pokhilko", "date": "2011-12-01T15:52:00" }, { "by": "Alexandra Pokhilko", "date": "2011-12-01T15:52:00" } ] }, "description_file": { "id": "0", "file_type": "description file", "original_name": "description file", "version": [ { "id": "2", "file_type": "description file", "content_type": "text/xml", "original_name": "description file", "local_name": "13227547204752_dsc.2.xml", "local_path": "/disk/data/robust/prod-biodare/Robust/Storage/13227547204752/13227547204752_dsc.2.xml", "uploaded": { "by": "Andrew Millar", "date": "2012-06-19T23:21:54" } }, { "id": "1", "file_type": "description file", "content_type": "text/xml", "original_name": "description file", "local_name": "13227547204752_dsc.1.xml", "local_path": "/disk/data/robust/prod-biodare/Robust/Storage/13227547204752/13227547204752_dsc.1.xml", "uploaded": { "by": "Alexandra Pokhilko", "date": "2011-12-01T15:57:31" } }, { "id": "0", "file_type": "description file", "content_type": "text/xml", "original_name": "description file", "local_name": "13227547204752_dsc.xml", "local_path": "/disk/data/robust/prod-biodare/Robust/Storage/13227547204752/13227547204752_dsc.xml", "uploaded": { "by": "Alexandra Pokhilko", "date": "2011-12-01T15:52:00" } } ] }, "pedro_file": { "id": "0", "file_type": "pedro file", "original_name": "pedro file", "version": [ { "id": "1", "file_type": "pedro file", "content_type": "text/xml", "original_name": "Ito2007_wt_LD_PRR9_proteinv2.xml", "local_name": "Ito2007_wt_LD_PRR9_proteinv2.xml", "local_path": "/disk/data/robust/prod-biodare/Robust/Storage/13227547204752/Ito2007_wt_LD_PRR9_proteinv2.xml", "uploaded": { "by": "Andrew Millar", "date": "2012-06-19T23:21:54", "version": "2" } }, { "id": "0", "file_type": "pedro file", "content_type": "application/octet-stream", "original_name": "Ito2007_wt_LD_PRR9_protein.xml", "local_name": "Ito2007_wt_LD_PRR9_protein.xml", "local_path": "/disk/data/robust/prod-biodare/Robust/Storage/13227547204752/Ito2007_wt_LD_PRR9_protein.xml", "uploaded": { "by": "Alexandra Pokhilko", "date": "2011-12-01T15:52:00", "version": "1" } } ] }, "bibliographyFile": { "id": "0", "file_type": "BIBLIOGRAPHY", "original_name": "13227547204752_bibl.xml", "version": [ { "id": "4", "file_type": "BIBLIOGRAPHY", "content_type": "text/plain", "original_name": "13227547204752_bibl.xml", "local_name": "13227547204752_bibl.1.xml", "local_path": "/disk/data/robust/biodare3_prod/Robust/Storage/13227547204752/13227547204752_bibl.1.xml", "uploaded": { "by": "Tomasz Zielinski", "date": "2014-10-17T15:48:13", "version": "4" } }, { "id": "3", "file_type": "BIBLIOGRAPHY", "content_type": "text/plain", "original_name": "13227547204752_bibl.xml", "local_name": "13227547204752_bibl.xml", "local_path": "/disk/data/robust/biodare3_prod/Robust/Storage/13227547204752/13227547204752_bibl.xml", "uploaded": { "by": "Tomasz Zielinski", "date": "2014-10-17T15:47:37", "version": "3" } } ] }, "data_file": { "id": "0", "file_type": "data file", "original_name": "Ito2007_wt_LD_PRR9_protein.xls", "version": { "id": "0", "file_type": "data file", "content_type": "application/vnd.ms-excel", "original_name": "Ito2007_wt_LD_PRR9_protein.xls", "local_name": "Ito2007_wt_LD_PRR9_protein.xls", "local_path": "/disk/data/robust/prod-biodare/Robust/Storage/13227547204752/Ito2007_wt_LD_PRR9_protein.xls", "uploaded": { "by": "Alexandra Pokhilko", "date": "2011-12-01T15:57:31", "version": "1" }, "parameter": [ { "name": "error_type", "value": "none" }, { "name": "first_data_col", "value": "2" }, { "name": "first_data_row", "value": "3" }, { "name": "time_col", "value": "1" } ] } }, "std_raw_file": { "id": "0", "file_type": "data file", "original_name": "STANDARD_RAWDATAFILE.txt", "version": { "id": "0", "file_type": "data file", "content_type": "text/plain", "original_name": "STANDARD_RAWDATAFILE.txt", "local_name": "STANDARD_RAWDATAFILE.txt", "local_path": "/disk/data/robust/prod-biodare/Robust/Storage/13227547204752/STANDARD_RAWDATAFILE.txt", "uploaded": { "by": "Alexandra Pokhilko", "date": "2011-12-01T15:57:31" }, "parameter": [ { "name": "error_type", "value": "none" }, { "name": "first_data_col", "value": "2" }, { "name": "first_data_row", "value": "3" }, { "name": "time_col", "value": "1" } ] } }, "numeric_file": { "id": "0", "file_type": "data file", "original_name": "STANDARD_DATAFILE.txt", "version": { "id": "0", "file_type": "data file", "content_type": "text/plain", "original_name": "STANDARD_DATAFILE.txt", "local_name": "STANDARD_DATAFILE.txt", "local_path": "/disk/data/robust/prod-biodare/Robust/Storage/13227547204752/STANDARD_DATAFILE.txt", "uploaded": { "by": "Alexandra Pokhilko", "date": "2011-12-01T15:57:31" }, "parameter": [ { "name": "error_type", "value": "none" }, { "name": "first_data_col", "value": "2" }, { "name": "first_data_row", "value": "3" }, { "name": "time_col", "value": "1" } ] } }, "user_file": { "id": "0", "file_type": "user file", "original_name": "Ito PRR9 PCP 07.pdf", "version": { "id": "0", "file_type": "data file", "content_type": "application/pdf", "original_name": "Ito PRR9 PCP 07.pdf", "local_name": "Ito PRR9 PCP 07.pdf", "local_path": "/disk/data/robust/prod-biodare/Robust/Storage/13227547204752/Ito PRR9 PCP 07.pdf", "uploaded": { "by": "Andrew Millar", "date": "2012-06-19T23:22:21" } } }, "security": { "owner": "andrew", "supervisor": "andrew", "allowedToRead": [ "edinburgh", "millar", "public", "robust", "timet" ], "allowedToWrite": [ "edinburgh", "millar" ] }, "open_access_info": { "grantedBy": "andrew", "grantedOn": "2012-06-19T23:22:21", "licence": "CC_BY", "comment": "System generated on 17-Oct-2014" }, "desc": { "experiment_type": "Literature data", "id": "13227547204752", "status": "described", "name": "Ito 2007 wt LD PRR9 protein", "purpose": "PRR9 mRNA and protein were measured under the same conditions. This file has PRR9 protein only.", "comments": "This PRR9 protein profile rises more slowly than the FLAG-tagged PRR9 protein in Nakamichi Plant Cell 2010.", "pubmed_id": "17890242", "provenance": { "site": "Mizuno T", "author": "Ito S", "start_date": "2007-11-01" }, "growth_condition": { "name": "LD standard", "medium": "not entered", "stratification": "3 days at 4C", "duration": "10.0", "temperature_conditions": { "label": "const. 20.0C", "env_conditions": { "type": "constant_temp", "label": "const. 20.0C", "duration": "10", "env_day": { "type": "constant_temp", "label": "constant temperature", "duration": "10", "cycle_length": "24", "base_value": "20.0", "second_value": "20.0" } } }, "light_conditions": { "label": "W: LD 12:00:12:00", "light_channel": { "spectrum": "white", "intensity": "70", "source": "LED", "env_conditions": { "type": "diurnal_light", "label": "LD 12:00:12:00", "duration": "10", "env_day": { "type": "diurnal_light", "label": "diurnal light", "duration": "10", "cycle_length": "24", "base_value": "0.0", "second_value": "100.0", "env_period": { "start_time": "0:00", "duration": "12:00" } } } } } }, "experimental_condition": { "name": "12:12", "medium": "not entered", "duration": "1.0", "temperature_conditions": { "label": "const. 20.0C", "env_conditions": { "type": "constant_temp", "label": "const. 20.0C", "duration": "1", "env_day": { "type": "constant_temp", "label": "constant temperature", "duration": "1", "cycle_length": "24", "base_value": "20.0", "second_value": "20.0" } } }, "light_conditions": { "label": "W: LD 12:00:12:00", "light_channel": { "spectrum": "white", "intensity": "40", "source": "LED", "env_conditions": { "type": "diurnal_light", "label": "LD 12:00:12:00", "duration": "1", "env_day": { "type": "diurnal_light", "label": "diurnal light", "duration": "1", "cycle_length": "24", "base_value": "0.0", "second_value": "100.0", "env_period": { "start_time": "0:00", "duration": "12:00" } } } } } }, "measurement": { "technique": "Western blot", "equipment": "TAP-tagged protein", "description": "Literature data from: ''\n\t by: .\n\t \n\t These protein samples were separated by 10% SDS–PAGE and transferred onto a PVDF membrane (for each examination, 80 μg of total protein was used). The protein A domains of the TAP-tag were detected with a PAP (peroxidase–anti-peroxidase) antibody (Sigma). Immunoreactive bands were detected by the ECL plus Western blotting system (Amersham Pharmacia Biotech, USA)." }, "sample_preparation": { "method": "Plants were ground to a fine powder in liquid nitrogen. Crude protein extracts were prepared in 2 vols. of SDS loading buffer (2% SDS, 175 mM Tris–HCl pH 8.0, 0.6 mM EDTA pH 8.0, 3.2% 2-mercaptoethanol, 25% glycerol, 0.008% bromophenol blue). Extracts were immediately boiled for 10 min and the supernatant collected after centrifugation at 6,000×g for 10 min." }, "samples": { "sample": { "sample_id": "1", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "0", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "Wild Type", "line": "unknown" }, "marker": "PRR9", "growth_cond_name": "LD standard", "experiment_cond_name": "12:12", "ignored": "false" } } }, "pedro": { "@xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance", "@xsi:schemaLocation": "/Q:/communal/DataDescription/models/literature/model/full_literature.xsd", "name": "Ito 2007 wt LD PRR9 protein", "purpose": "PRR9 mRNA and protein were measured under the same conditions. This file has PRR9 protein only.", "comments": "This PRR9 protein profile rises more slowly than the FLAG-tagged PRR9 protein in Nakamichi Plant Cell 2010.", "pubmed_id": "17890242", "provenance": { "pub_title": "Rhythmic and light-inducible appearance of clock-associated pseudo-response regulator protein PRR9 through programmed degradation in the dark in Arabidopsis thaliana.", "first_author": "Ito S", "group": "Mizuno T", "pub_date": "2007-11-01" }, "growth_condition": { "name": "LD standard", "stratification": "3 days at 4C", "duration": "10", "temperature_conditions": { "constant_temp": { "cycle_length": "24", "base_temp": "20" } }, "light_conditions": { "light_channel": { "spectrum": "white", "intensity": "70", "source": "LED", "diurnal_light": { "cycle_length": "24", "start_time": "0", "duration": "12" } } } }, "experimental_condition": { "name": "12:12", "duration": "1", "temperature_conditions": { "constant_temp": { "cycle_length": "24", "base_temp": "20" } }, "light_conditions": { "light_channel": { "spectrum": "white", "intensity": "40", "source": "LED", "diurnal_light": { "cycle_length": "24", "start_time": "0", "duration": "12" } } } }, "measurement": { "technique": "Western blot", "equipment": "TAP-tagged protein", "description": "These protein samples were separated by 10% SDS–PAGE and transferred onto a PVDF membrane (for each examination, 80 μg of total protein was used). The protein A domains of the TAP-tag were detected with a PAP (peroxidase–anti-peroxidase) antibody (Sigma). Immunoreactive bands were detected by the ECL plus Western blotting system (Amersham Pharmacia Biotech, USA)." }, "sample_preparation": { "method": "Plants were ground to a fine powder in liquid nitrogen. Crude protein extracts were prepared in 2 vols. of SDS loading buffer (2% SDS, 175 mM Tris–HCl pH 8.0, 0.6 mM EDTA pH 8.0, 3.2% 2-mercaptoethanol, 25% glycerol, 0.008% bromophenol blue). Extracts were immediately boiled for 10 min and the supernatant collected after centrifugation at 6,000×g for 10 min." }, "samples": { "sample": { "sample_id": "1", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "Wild Type" }, "marker": "PRR9", "growth_cond_name": "LD standard", "experiment_cond_name": "12:12" } } }, "biblio": { "principal": "Mizuno T", "institution": "Nagoya University", "author": [ "Ito S", "Nakamichi N", "Kiba T", "Yamashino T" ], "curator": "Alexandra Pokhilko" } }