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| [IDF] Investigation Description File | |||||||||||||||
| # MAGE-TAB template submission sheet for SysMO-DB, adapted for JenAge RNA-Seq experiments - Version 3beta - 07/03/2012 | |||||||||||||||
| # This section contains the top-level information for your experiment (cells with yellow background must be filled in) | |||||||||||||||
| Investigation Title | Effects of mild stress on ageing in a multi-species approach | ||||||||||||||
| Experiment Class | Transcriptomics | ||||||||||||||
| Experiment Description | Determine mRNA levels in organism Caenorhabditis elegans during normal ageing and during ageing with defined perturbations. | ||||||||||||||
| Experimental Design | stimulus_or_stress_design | ||||||||||||||
| Experimental Design Term Source REF | MGED Ontology | ||||||||||||||
| # Default values for filling in data automatically in the SDRF sheet | |||||||||||||||
| # | (Macros must be activated to use default values) | ||||||||||||||
| # Default Organism | |||||||||||||||
| # Default Strain or Line | |||||||||||||||
| # Default Sex | |||||||||||||||
| # Default Age Time Unit | |||||||||||||||
| # Default Treatment Protocol | NO PERTURBATION | ||||||||||||||
| # Default Treatment Substance | none | ||||||||||||||
| # Default Treatment Substance Concentration | 0 | ||||||||||||||
| # Default Treatment Substance Concentration Unit | μg/ml | ||||||||||||||
| # Default Biobank Material Type | organism_part | ||||||||||||||
| # Default Organism Part | |||||||||||||||
| # Default Biobank Storage Protocol | TISSUE STORAGE | ||||||||||||||
| # Default Biobank Storage Location | |||||||||||||||
| # Default RNA Extraction Protocol | RNA EXTRACTION 1.1 | ||||||||||||||
| # Default RNA Concentration Unit | ng/μl | ||||||||||||||
| # Default RNA Volume Unit | μl | ||||||||||||||
| # Default RNA Storage Location | stored at the FLI | ||||||||||||||
| # Default Sequencing Protocol | SOLEXA SEQ | ||||||||||||||
| # Default Sequencing Library Layout | multiplex | ||||||||||||||
| # Default Sequencing Data Acquisition Protocol | SOLEXA DATA ACQUISITION | ||||||||||||||
| # Default Additional Information | |||||||||||||||
| # 'Experimental Factors' used to describe the variables investigated by your experiment - new factors may only be added by the data management team | |||||||||||||||
| Experimental Factor Name | ORGANISM | STRAIN OR LINE | ORGANISM PART | AGE | TREATMENT | ||||||||||
| Experimental Factor Type | organism | strain_or_line | organism_part | age | treatment | ||||||||||
| Experimental Factor Term Source REF | MGED Ontology | MGED Ontology | MGED Ontology | MGED Ontology | |||||||||||
| # Quality control information | |||||||||||||||
| Quality Control Type | biological_replicate | ||||||||||||||
| Quality Control Term Source REF | MGED Ontology | ||||||||||||||
| # Data release information | |||||||||||||||
| Public Release Date | |||||||||||||||
| # Personal information about the data submitter and investigator | |||||||||||||||
| Person Last Name | Marthandan | ||||||||||||||
| Person First Name | Shiva | ||||||||||||||
| Person Mid Initials | SSM | ||||||||||||||
| Person Email | smarthandan@fli-leibniz.de | ||||||||||||||
| Person Phone | 03641 656172 | ||||||||||||||
| Person Address | |||||||||||||||
| Person Affiliation | FLI | ||||||||||||||
| Person Roles | submitter; investigator | ||||||||||||||
| # Publications based on the data described in this file | |||||||||||||||
| PubMed ID | |||||||||||||||
| Publication DOI | |||||||||||||||
| Publication Author List | |||||||||||||||
| Publication Title | |||||||||||||||
| Publication Status | |||||||||||||||
| # Protocols (Standard Operation Procedures, SOPs) - new protocols may only be added by the data management team | |||||||||||||||
| # | Treatment Protocols | Storage Protocols | Extraction Protocols | Sequencing Protocols | Data Acquisition Protocols | ||||||||||
| Protocol Name | NO PERTURBATION | PERTURBATION ROTENONE FISH | PERTURBATION ROTENONE MOUSE | PERTURBATION ROTENONE WORM | PERTURBATION ROTENONE FIBROBLAST | PERTURBATION 2-DEOXYGLUCOSE FISH | PERTURBATION 2-DEOXYGLUCOSE MOUSE | PERTURBATION 2-DEOXYGLUCOSE WORM | PERTURBATION 2-DEOXYGLUCOSE FIBROBLAST | TISSUE STORAGE | NO STORAGE | RNA EXTRACTION 1.1 | SOLEXA SEQ | SOLEXA DATA ACQUISITION | |
| Protocol URI | no_perturbation | perturbation_rotenone_fish | perturbation_rotenone_mouse | perturbation_rotenone_worm | perturbation_rotenone_fibroblast | perturbation_2-DEOXYGLUCOSE_fish | perturbation_2-DEOXYGLUCOSE_mouse | perturbation_2-DEOXYGLUCOSE_worm | perturbation_2-DEOXYGLUCOSE_fibroblast | tissue_storage | no_storage | rna_extraction | solexa_sequencing | solexa_data_acquisition | |
| Protocol Type | grow | grow | grow | grow | grow | grow | grow | grow | grow | store | store | nucleic_acid_extraction | unknown_protocol_type | unknown_protocol_type | |
| Protocol Term Source REF | MGED Ontology | MGED Ontology | MGED Ontology | MGED Ontology | MGED Ontology | MGED Ontology | MGED Ontology | MGED Ontology | MGED Ontology | MGED Ontology | MGED Ontology | MGED Ontology | MGED Ontology | MGED Ontology | |
| Protocol Description | |||||||||||||||
| Protocol Parameters | Substance,Concentration | Substance,Concentration | Substance,Concentration | Substance,Concentration | Substance,Concentration | Substance,Concentration | Substance,Concentration | Substance,Concentration | Substance,Concentration | 260/280;260/230;Concentration;Volume | |||||
| Protocol Hardware | Solexa 1G Genome Analyzer | ||||||||||||||
| Protocol Software | |||||||||||||||
| # Controlled vocabulary sources - new sources may only be added by the data management team | |||||||||||||||
| Term Source Name | MGED Ontology | ||||||||||||||
| Term Source File | http://mged.sourceforge.net/ontologies/MGEDontology.php | ||||||||||||||
| Term Source Version | 1.3.1.1 | ||||||||||||||
| # Filename of the 'SDRF' part belonging to this 'IDF' part (should be set automatically to the name of this file since the 'SDRF' part is another sheet within this file) | |||||||||||||||
| SDRF File | |||||||||||||||
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| [SDRF] Sample and Data Relationship File | |||||||||||||||||||||||||||||||||||||||||||||
| Macros: | |||||||||||||||||||||||||||||||||||||||||||||
| # Source Definition | Treatment | Material | RNA Extraction | Optional | Sequencing | Experimental Factor Values | |||||||||||||||||||||||||||||||||||||||
| # Specimen | Organism | Strain or Line | Sex | Age | Age Time Unit | Treatment Protocol | Substance | Concentration | Unit | Sample Name | Material Type | Term Source | Organism Part | Storage Protocol | Storage Date | Storage Location | Extraction Protocol | 260/280 | 260/230 | Concentration | Unit | Volume | Unit | Extract Name | Material Type | Term Source | Extraction Date | Storage Location | Additional Information | Sequencing Protocol | Assay Name | Technology Type | Library Source | Library Strategy | Library Selection | Library Layout | Data Acquisition Protocol | Data File | Organism | Strain or Line | Age | Age Time Unit | Organism Part | Treatment | |
| Source Name | Characteristics[Organism] | Characteristics[StrainOrLine] | Characteristics[Sex] | Characteristics[Age] | Unit[TimeUnit] | Protocol REF | Parameter[Substance] | Parameter[Concentration] | Unit[ConcentrationUnit] | Sample Name | Material Type | Term Source REF | Characteristics[OrganismPart] | Protocol REF | Date | Comment[MaterialStorageLocation] | Protocol REF | Parameter[260/280] | Parameter[260/230] | Parameter[Concentration] | Unit[ConcentrationUnit] | Parameter[Volume] | Unit[VolumeUnit] | Extract Name | Material Type | Term Source REF | Date | Comment[RNAStorageLocation] | Comment[AdditionalInformation] | Protocol REF | Assay Name | Technology Type | Comment[LIBRARY_SOURCE] | Comment[LIBRARY_STRATEGY] | Comment[LIBRARY_SELECTION] | Comment[LIBRARY_LAYOUT] | Protocol REF | Array Data File | Factor Value[ORGANISM] | Factor Value[STRAIN OR LINE] | Factor Value[AGE] | Unit[TimeUnit] | Factor Value[ORGANISM PART] | Factor Value[TREATMENT] | |
| BRHF1.0 | Homo sapiens | BJ | male | 31 | population doublings | NO PERTURBATION | none | 0 | BRHF1.0 | cell | MGED Ontology | NO STORAGE | no storage | RNA EXTRACTION 1.1 | 1.84 | 2.02 | 200.7 | ng/μl | 60 | μl | BRHF1.0 | total_RNA | MGED Ontology | 2010-10-22T0:0:0+0000 | stored at the FLI | Homo sapiens | BJ | 31 | population doublings | NO PERTURBATION | |||||||||||||||
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| Experimental Design | Experimental Design LINK | Experimental Factor Type | Experimental Factor Type LINK | Quality Control Type | Quality Control Type LINK | Person Affiliation | Publication Status | Protocol Type | Protocol Type LINK | Material Type | Material Type LINK | Sex | Time Unit | Library Layout | Experiment Description | Storage Location | |||||||||
| compound_treatment_design | compound_treatment_design | age | age | biological_replicate | biological_replicate | FLI | in preparation | PCR_amplification | PCR_amplification | cell | cell | female | day | single | Determine mRNA levels in organism Caenorhabditis elegans during normal ageing and during ageing with defined perturbations. | stored in Biobank | |||||||||
| dose_response_design | dose_response_design | organism | organism | technical_replicate | technical_replicate | FSU | submitted | grow | grow | organism_part | organism_part | male | population doublings | multiplex | Determine mRNA levels in organism Danio rerio during normal ageing and during ageing with defined perturbations. | stored at the FLI | |||||||||
| growth_condition_design | growth_condition_design | organism_part | organism_part | HKI | in press | nucleic_acid_extraction | nucleic_acid_extraction | whole_organism | whole_organism | hermaphrodite | hour | multiplexTruSeq | Determine mRNA levels in human blood cells during normal ageing and during ageing with defined perturbations. | stored at the FSU | |||||||||||
| stimulus_or_stress_design | stimulus_or_stress_design | strain_or_line | strain_or_line | UKJ | published | specified_biomaterial_action | specified_biomaterial_action | unknown | minute | Determine mRNA levels in human fibroblast cells during normal ageing and during ageing with defined perturbations. | stored at the HKI | ||||||||||||||
| starvation | starvation | month | Determine mRNA levels in organism Mus musculus during normal ageing and during ageing with defined perturbations. | stored at the UKJ | |||||||||||||||||||||
| store | store | second | Determine mRNA levels in organism Nothobranchius furzeri during normal ageing and during ageing with defined perturbations. | no storage | |||||||||||||||||||||
| unknown_protocol_type | unknown_protocol_type | week | |||||||||||||||||||||||
| year | |||||||||||||||||||||||||
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| # Custom lookup table - always insert new values before the Dummy value and after the first value | |||||||||
| Organism | StrainOrLine | TreatmentSubstance | ConcentrationUnit | OrganismPart | VolumeUnit | ||||
| Caenorhabditis elegans | AB JxTü | 2-Deoxyglucose | mg/ml | all | μl | ||||
| Danio rerio | AB JxTü Tg(flk:mCherry) | none | ng/μl | blood | ml | ||||
| Homo sapiens | AB JxTü Tg(pu.1:GFP) | Rotenone | nM | brain | Dummy unit | ||||
| Mus musculus | AB JxTü Tg(wt1a:GFP) | Dummy substance | μg/ml | liver | |||||
| Nothobranchius furzeri | BJ | μg/μl | muscle | ||||||
| Dummy organism | C57BL/6 | Dummy unit | skin | ||||||
| daf-2 | Dummy part | ||||||||
| GRZ | |||||||||
| HFF | |||||||||
| Human PBMC - Old aged donor | |||||||||
| Human PBMC - Young donor | |||||||||
| IMR-90 | |||||||||
| MRC-5 | |||||||||
| MZM-04/10p | |||||||||
| N2 | |||||||||
| Wi-38 | |||||||||
| wild type (unspecified) | |||||||||
| Dummy strain | |||||||||
