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SDRF
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| [IDF] Investigation Description File | |||||||||
| # MAGE-TAB template Submission sheet for SysMO | |||||||||
| # This section contains the top-level information for your experiment. | |||||||||
| Investigation Title | Title | ||||||||
| Experiment Class (AssayType) | Transcriptomics | ||||||||
| Experiment Description | |||||||||
| Experimental Design | DesignType | ||||||||
| Technology Type | microarray | ||||||||
| # Please create as many Experimental Factors here as you need to | |||||||||
| # describe the variables investigated by your experiment. | |||||||||
| Experimental Factor Name | |||||||||
| Experimental Factor Type | FactorType | ||||||||
| # Quality Control Type examples: dye_swap_quality_control, biological_replicate, technical_replicate | |||||||||
| Quality Control Type | Quality Control Type | ||||||||
| # Dates should be entered in the form YYYY-MM-DD. If you are using MS Excel, | |||||||||
| # it is recommended that you set your spreadsheet to 'text' format throughout | |||||||||
| # to help avoid any unwanted changes made by Excel. | |||||||||
| Public Release Date | YYYY-MM-DD | ||||||||
| # Please list contact details in columns, below: | |||||||||
| Person Last Name | name | ||||||||
| Person First Name | |||||||||
| Person SEEK ID | SEEKID | ||||||||
| SEEK Project | Project | ||||||||
| Person Email | |||||||||
| Person Phone | |||||||||
| Person Address | |||||||||
| Person Affiliation | |||||||||
| Person Roles | Roles | ||||||||
| # Submitter is the same as person responsible in SEEK | |||||||||
| # Please list all publications associated with this submission, in columns: | |||||||||
| PubMed ID | |||||||||
| Publication Author List | |||||||||
| Publication Title | |||||||||
| Publication Status | |||||||||
| # The next section describes the protocols used in your | |||||||||
| # experiment. Please select your own Protocol Names (e.g. 'GROWTH', | |||||||||
| # 'TREATMENT') for use within this spreadsheet, or re-use SOPs from SysMO SEEK by referring to their SOP IDs. Alternatively, you can refer to ArrayExpress | |||||||||
| # protocols by using the assigned ArrayExpress protocol accession numbers in your SDRF | |||||||||
| Protocol (SOP) Name | GROWTH | TREATMENT | EXTRACTION | HYBRIDIZATION | LABELLING | NORMALIZATION | TRANSFORMATION | ||
| SOP ID | id | id | id | id | id | id | id | ||
| Protocol Type | ExperimentalProtocolType | ExperimentalProtocolType | ExperimentalProtocolType | ExperimentalProtocolType | ExperimentalProtocolType | ExperimentalProtocolType | ExperimentalProtocolType | ||
| Protocol Description | <your growth protocol text here> | <your treatment protocol text here> | <your nucleic acid extraction protocol text here> | <your labeling protocol text here> | <your normalization protocol text here> | <your transformation protocol text here> |
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| [SDRF] Sample and Data Relationship File | ||||||||||
| # The SDRF section contains all the information linking your samples | ||||||||||
| # to your data files. Please feel free to add as many new | ||||||||||
| # Characteristics[] or FactorValue[] columns as necessary to | ||||||||||
| # completely describe your experiment. | ||||||||||
| # The first line below has been filled in with example terms, where possible: | ||||||||||
| Source Name | Material Type | organism | age | Units | individual | sex | Characteristics[StrainOrLine] | Characteristics[Genotype] | ||
| # Unique IDs for biosources (experimental starting materials) | # MaterialType term from MGED ontology | # Sample latin species name | # Sample Age value, e.g. 20 years | # Time units for Characteristic | # Sample Individual value | # Sample Sex value | # Sample StrainOrLine value | # Sample Genotype value | ||
| Cell culture 1 | MaterialType | Organism | TimeUnit | Sex | ||||||
| # These next lines describe the extracts and hybridisation identifiers | ||||||||||
| Extract Name | Labeled Extract Name | Label | Hybridization Name | |||||||
| # Unique IDs for extracts (RNA or DNA) | # Unique IDs for labeled extracts | # Labeling dye, e.g. Cy3, biotin, 33P | # Unique IDs for hybs | |||||||
| biotin | ||||||||||
| # Links and descriptions of the Array and the Data files | ||||||||||
| Array Design REF | Comment[Array serial number] | Array Data File | Comment[EXP] | Derived Array Data File | Derived Array Data Matrix File | Comment[CDF] | ||||
| # ArrayExpress array accession, e.g. A-MEXP-27- if it is not an array design already in ArrayExpress, you will require another datasheet containing this | # Array serial number/chip lot | # Unprocessed data file e.g. CEL, GPR (the raw data) | # EXP file where available | # Normalized/processed data | # Final data matrix file(s) | # CDF library file (do not upload CDF unless custom array used) | ||||
