Classification |
Definition |
1.Experimental Description |
A broad overview of the experiment. In MIARE an experiment is classified as one or more assays that answers a biological, technical and/or theoretical question using silencing RNA. |
1.1 Biological, technical and or theoretical question/hypothesis |
A short description of the biological, technical and/or theoretical question/hypothesis asked in the experiment |
1.2 Primary contact information |
Primary contact person for experiment including name, institute, contact address, email, web site |
1.3 Publication |
Reference to publication for experiment (if applicable) |
1.4 Type of silencing RNA reagent |
Description of silencing RNA technology and target gene collection |
1.5 Number of experimental genes targeted for knock down |
Total number of experimental gene targeted for knock down |
1.6 Keywords |
A list of keywords describing the experiment (terms should be referenced to an ontology) |
1.7 Target organism genus and species |
The Organism genus and species from which mRNA transcripts are targeted by silencing RNA reagent (NCBI Taxonomy name) |
2. Experimental Design |
The context of the experiment |
2.1 Number of replicates |
The number of replicates used in the experiment |
2.2 Description of replicates |
Description of the type and stage of replication |
2.3 Assays being conducted |
Description of the type of assays being conducted or reference to a description of the assay |
2.4 Related information |
Reference to related information e.g. a related experiment or website |
3. Sample Description |
Adapted from MIAME v.1.1 : By a sample we understand the biological material (biomaterial), into which the silencing RNA reagent is being delivered. In this section all steps that precede the delivery of silencing reagent are described. We can usually distinguish between the source of the sample (bio-source, e.g., organism, cell type or line), its treatment. |
3.1 Bio-source Properties |
The Bio-source is the original source material before any treatment events. |
3.1.1 Organism genus and species |
The genus and species (and subspecies) of the organism from which the biomaterial is derived (NCBI taxonomy) |
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Include descriptors relevant to the particular sample. For example, for a cell line use the descriptors, organism part, cell type and cell line. For clinical samples, only submit information from which consent and appropriate ethical approval has been obtained . |
3.1.1.1 Animal/plant strain or line |
The strain or line is an animal or plant offspring. For microbes, these are isolates derived from nature or in the laboratory. |
3.1.1.2 Sex |
Term applied to any organism able to undergo sexual reproduction in order to differentiate the individuals or types involved. Sexual reproduction is defined as the ability to exchange genetic material with the potential of recombinant progeny |
3.1.1.3 Age |
The time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise the identifiable point must be specified such as planting (e.g. 3 days post planting) |
3.1.1.4 Development stage |
The developmental stage of the organism's life cycle during which the biomaterial was extracted |
3.1.1.5 Organism part (tissue) |
The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm) |
3.1.1.6 Cell type |
The type of cell used in the experiment if non mixed, if mixed the targeted cell type should be used, example of instances, epithelial, glial etc. |
3.1.1.7 Cell line |
The identifier for the immortalized cell line if one was used to derive the sample (biomaterial) or the animals or plants that have a single ancestral breeding pair or parent as a result of brother x sister or parent x offspring mating |
3.1.1.8 Genetic variation |
The genetic modification introduced into the organism from which the BioMaterial was derived. Examples of genetic variation include specification of a transgene or the gene knocked-out [MGED Ontology Definition] |
3.1.1.9 Individual genetic characteristics |
The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes |
3.1.1.10 Disease state or normal |
The name of the pathology diagnosed in the organism from which the biomaterial was derived. The disease state is normal if no disease has been diagnosed |
3.1.11 Clinical information available (link) |
Provide a link, summary or reference to additional clinical data |
3.1.12 Individual number |
Identifier or number of the individual organism from which the BioMaterial was derived. For patients, the identifier must be approved by Institutional Review Boards (IRB, review and monitor biomedical research involving human subjects) or appropriate body [MGED Ontology Definition |
3.1.3 Contact details for sample |
Organization or individual to contact regarding sample |
3.2 Biomaterial Manipulations |
Information on the treatment applied to the biomaterial |
3.2.1 Growth conditions/ cell culture conditions |
A description of the conditions used to grow organisms or parts of the organism. This includes isolated environments such as cultures. |
3.2.1.1 Manufacturer name |
The manufacturer name of the components in the growth/cell culture medium |
3.2.1.2 Catalogue number |
The catalogue number of the components in the growth/cell culture medium |
3.2.1.3 Name |
The generic name of the components in the growth/cell culture medium |
3.2.1.4 Percentage serum |
The percentage serum used in the cell culture medium |
3.2.2 Separation technique (e.g., none, trimming, microdissection, FACS) |
The technique used to separate tissues or cells from a heterogeneous sample |
4 Pretreatment |
Description of the conditions that are applied prior to the delivery of the silencing reagent |
4.1 Treatment protocol |
Detailed description of pretreatment protocol used or reference to detailed description |
4.2 Treatment type |
The type of manipulation applied to the BioMaterial for the purposes of generating one of the variables under study [MGED Ontology Definition] |
4.3 Compound |
A drug, solvent, chemical, etc., that can be measured [MGED Ontology Definition] |
5. Assay Plate Description |
The plate(s) the assay were performed in |
5.1 Manufacturer |
The name of the manufacturer of the assay plate(s) |
5.2 Catalogue number |
The manufacturer's catalogue number for the assay plate |
5.3 Assay plate type |
Description of assay plate type, e.g. format of assay plate |
5.4 Plate ID |
Unique identifier of assay plate |
5.5 Assay plate layout |
For each position specify the following |
5.5.1 Position |
The plate row and column for specified silencing reagent |
5.5.2 Reagent group role and control type |
The role of the reagent in well and control type e.g. experimental, control type positive or negative. |
5.5.3 Reagent identifier. |
Reagent identifier |
6. Silencing RNA Reagent |
For each silencing RNA reagent (dsRNA that inhibits gene expression through the RNA interference pathway) or pool specify the following |
6.1 Silencing RNA reagent identifier |
Unique ID or catalogue ID of silencing RNA reagent |
6.2 Target gene accession number and version |
Versioned accession number, e.g. RefSeq ID and database name for gene sequence targeted by silencing RNA reagent |
6.3 Offical gene symbol |
Official gene symbol for target of silencing RNA reagent as defined by Entrez Gene |
6.4 Entrez Gene ID |
The Entrez Gene ID for the target of the silencing RNA reagent |
6.5 Silencing RNA reagent sequence(s) |
Silencing RNA reagent sequence, sense or anti-sense, if pool sequences in the pool |
6.6 Number of silencing RNA reagent(s) per well |
Number of combined silencing RNA reagents per well |
6.7 Silencing reagent type |
Type of silencing RNA reagent e.g. chemically synthesized short interfering RNA, vector based short hairpin RNA, etc |
6.8 Modifications to silencing RNA reagent |
Detail of the chemical modification(s) to the silencing reagent including position |
6.9 Reference to vector |
Reference to publication or contact information (if applicable) |
6.10 Silencing RNA reagent library versioning information/release number |
Unique identifier of the silencing RNA reagent library and release number |
6.11 Silencing RNA reagent manufacturer |
Manufacturer of silencing RNA reagent library including contact details |
7. Delivery |
Introduction of silencing reagent into cell |
7.1 Delivery Type |
Describe type of delivery, e.g. reverse transfection, infection, electroporation, intravenous injection, shooting, feeding |
7.2 Delivery Protocol |
Detailed description of delivery protocol used or reference to detailed description. Plus, description of master plate setup from stock plate specifying manual and automated steps. |
7.2.1 Complexing Protocol |
Short description of the complexing protocol (if applicable) |
7.2.2 Time of complex formation |
Time for formation of delivery reagent and silencing reagent complex (if applicable) |
7.3.1 Delivery reagent Type |
The type of reagent used to delivery silencing reagent |
7.3.2 Catalog number of delivery reagent |
The manufacturer's catalog number for the delivery reagent |
7.3.3 Delivery reagent name |
Name for the delivery reagent |
7.3.4 Manufacturer of delivery reagent |
The name of the manufacturer of delivery reagent |
7.5 Final concentration or amount of delivery reagent |
The final concentration or amount of the delivery reagent |
7.6 Final concentration of silencing reagents |
The final concentration of the silencing reagents |
7.7 Number of cells per well in delivery plate |
Number of cells per well in the delivery plate |
8. Assay Plate |
The plate from which the quantitative or qualitative data is acquired |
8.1 Number of cells per well |
Number of cell per well in the assay plate |
8.2 Time to assay point |
Time from delivery of silencing RNA reagent and assay |
8.3 Time of exposure of silencing RNA reagent |
Time between delivery of silencing RNA reagent and media change (if applicable) |
8.4.1 Media changes |
Description of cell culture medium for any media changes (if applicable) |
8.4.2 Media composition |
The composition of the media |
8.4.3 Time of media change |
The time from silencing RNA reagent delivery to media change |
9 Post Treatment |
Description of the conditions that are applied after the delivery of the silencing RNA reagent |
9. 1 Treatment protocol |
Detailed description of post treatment protocol used or reference to detailed description |
9.2 Treatment type |
The type of manipulation applied to the BioMaterial for the purposes of generating one of the variables under study [MGED Ontology Definition] |
9.3 Compound |
A drug, solvent, chemical, etc., that can be measured [MGED Ontology Definition] |
10. Assay |
Description of the assay performed |
10.1 Assay description |
Short description of assay being used to measure the effect of RNA interference |
10.2 Control definition |
Definition of the controls used in the assay including name(s) and description(s) of control(s) |
10.3 Assay protocol |
Detailed description of assay protocol used or reference to assay protocol or reference to standard assay protocol and description of deviations from protocol |
10.4.1 Assay reagent name |
Name of assay reagent |
10.4.2 Assay reagent catalog number |
The catalog number of the assay reagent |
10.4.3 Assay reagent manufacturer |
Manufacturer of assay reagent |
10.5.1 Instrument name |
Name of assay instrument |
10.5.2 Instrument manufacturer |
Manufacturer of assay instrument |
10.5.3 Instrument catalog number |
Catalog number for assay instrument |
10.6 Type of readout |
Description of readout from assay instrument |
10.7 Instrument settings |
Detail of settings for assay instrument |
11. Data Analysis |
Definition of transformation, normalisation and scoring procedures |
11.1 Details of filtering of data |
Data that was excluded from analysis |
11.2 Transformation details |
What methods were used to transform data |
11.3 Reference to analysis script |
Reference to analysis script (if applicable) |
11.4.1 Analysis software name and version |
The name of the analysis software and version number |
11.4.2 Analysis software manufacturer |
The manufacturer of the analysis software |
11.5 Normalisation method |
Description of how the systematic effects were estimated and removed |
11.5.1 Normalization parameters |
A description of what parameters were used to normalize the data |
11.5.2 Controls used to normalize data |
The controls used in the normalization of the data |
11.6 Scoring method |
Description of method used to score the data. E.g., what statistical analysis procedure were the hits were selected by (Z-score, B-score) |
11.7 Quality controls steps |
Description of data quality control procedures applied to the data |
12. Data |
Quantitative or qualitative data |
12.1 Quantitative data |
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12.1.1 Description of quantified data |
A description of how was the data quantified |
12.1.2 Unprocessed quantified data |
The raw unprocessed quantified data with reference to the assay plate layout or plate |
12.1.3 Normalised quantified data |
The normalized quantified data with reference to the assay plate layout or map (optional) |
12.1.4 Scored data |
The scored value for the quantified data with reference to the assay plate layout or map |
12.2 Qualitative data |
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12.2.1 Description of qualitative data |
A description of how the qualitative data was determined |
12.2.2 Qualitative data |
The qualitative data with reference to the assay plate layout or map |