Most recent edit on 2009-04-27 13:40:39 by MiareAdmin
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• Biological, technical, and/or theoretical question/hypothesis.
Deletions:
• Biological, technical, and/or theoretical question/hypothesis
Edited on 2007-04-04 00:54:49 by GraemeGrimes
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Categories
CategoryReportingGuidelines
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Version: 0.6.5
Glossary of Terms
Edited on 2007-02-20 08:17:09 by GraemeGrimes
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Glossary of Terms
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Glossary
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Glossary
Edited on 2007-02-19 08:00:01 by GraemeGrimes
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o Animal/plant strain or line (CV)
o Cell line (CV)
o Genetic variation (e.g., gene knockout, transgenic variation) (CV)
o Disease state or normal (CV)
• Separation technique (e.g., none, trimming, microdissection, FACS) (CV)
• Compound (CV)
• Compound (CV)
Deletions:
o Animal/plant strain or line
o Cell line
o Genetic variation (e.g., gene knockout, transgenic variation)
o Disease state or normal
• Separation technique (e.g., none, trimming, microdissection, FACS)
• Compound
• Compound
Edited on 2007-02-19 06:49:19 by GraemeGrimes
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o Organism part (tissue) (CV)
o Cell type (CV)
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o Organism part (tissue)
o Cell type
Edited on 2007-02-19 06:47:53 by GraemeGrimes
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• Assay plate type (CV)
o Reagent group and control type (CV)
• Modifications to silencing RNA reagent (CV)
• Delivery Type, e.g. reverse transfection, electroporation, shooting etc (CV)
• Delivery protocol
o Delivery reagent type (CV)
o Type of readout (CV)
• Normalisation method (CV)
• Scoring method (CV)
• Quality controls steps (CV)
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• Assay plate type
o Reagent group and control type
• Silencing RNA reagent type
• Modifications to silencing RNA reagent
• Delivery Type, e.g. reverse transfection, electroporation, shooting etc
• Delivery protocol
o Delivery reagent type
• Treatment type
o Type of readout
• Normalisation method
• Scoring method
• Quality controls steps
Edited on 2007-02-19 06:44:46 by GraemeGrimes
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• Type of silencing RNA reagent (CV)
• Keywords (CV)
• Target organism genus and species (CV)
• Description of replicates (CV)
• Assays being conducted (CV)
• Organism genus and species (CV)
o Sex (CV)
o Age (CV)
o Development stage (CV)
• Treatment type (CV)
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• Type of silencing RNA reagent
• Keywords
• Target organism genus and species
• Description of replicates
• Assays being conducted
• Organism genus and species
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Bio-source Properties
Biomaterial Manipulations
Edited on 2007-02-19 06:02:54 by GraemeGrimes
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Assay Plate
Post treatment
Data Analysis
Data
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Assay
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Pretreatment
Assay Plate Description
Silencing RNA Reagent
Edited on 2007-02-19 05:55:37 by GraemeGrimes
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Delivery
Oldest known version of this page was edited on 2007-02-19 05:55:04 by GraemeGrimes []
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Version: 0.6.5
Date: 2006-11-10
The ‘experimental description’ section provides information about the provenance, hypothesis
and key factors in an experiment. MIARE defines an experiment as one or more assays that
answer a biological question using silencing RNA reagents.
• Biological, technical, and/or theoretical question/hypothesis
• Primary contact information
• Publication
• Type of silencing RNA reagent
• Number of experimental genes targeted for knock down
• Keywords
• Target organism genus and species
The ‘experimental design’ section describes factors that apply to the entire experiment. This
section enables a user to evaluate the context of an experiment.
• Number of replicates
• Description of replicates
• Assays being conducted
• Related information e.g., related publications
Sample Description
The ‘sample’ section is adapted from the MIAME 1.1 standards. A ‘sample’ represents the
biological material (or biomaterial) for which the data is established.
Bio-source Properties
• Organism genus and species
• Contact details for sample
• Where descriptors are relevant to the particular sample include
o Animal/plant strain or line
o Sex
o Age
o Development stage
o Organism part (tissue)
o Cell type
o Cell line
o Genetic variation (e.g., gene knockout, transgenic variation)
o Individual genetic characteristics (e.g., disease alleles, polymorphisms)
o Disease state or normal
o Clinical information available
o Individual number (for interrelation of the samples in the experiment)
Biomaterial Manipulations
The ‘biomaterial manipulations’ section is similar to the “sample” sub section from MIAME v1.1.
This section covers manipulations such as cell culture conditions.
• growth conditions/ cell culture conditions
o Manufacturer name
o Catalogue number
o Name
o Percentage serum
• Separation technique (e.g., none, trimming, microdissection, FACS)
Pretreatment
The ‘pretreatment section’ contains a description of the conditions applied prior to the delivery of
the silencing RNA reagent.
• Treatment protocol
• Treatment type
• Compound
Assay Plate Description
The ‘assay plate description’ section contains information on the physical assay plate and the
layout (plate map) of the reagents on the assay plate.
• Manufacturer
• Catalogue number
• Assay plate type
• Plate ID
• Assay plate layout (for each position specify the following)
o Position e.g. row, column
o Reagent group and control type
o Reagent identifier
Silencing RNA Reagent
The ‘silencing RNA reagent’ section describes the RNA reagent, both experimental and control,
used in the study. In addition, it describes the original manufacturer library from which the
silencing RNA reagent where taken (if applicable).
• Silencing RNA reagent identifier
• Target gene accession number and version
• Official gene symbol
• Entrez Gene ID
• Silencing RNA reagent sequence(s)
• Number of silencing RNA reagent(s) per well
• Silencing RNA reagent type
• Modifications to silencing RNA reagent
• Reference to vector
• Silencing RNA reagent library
o Versioning information/release number
o Manufacturer
Delivery
The ‘delivery’ section requires information relating to the delivery of the silencing RNA reagent
into a particular biological sample.
• Delivery Type, e.g. reverse transfection, electroporation, shooting etc
• Delivery protocol
o Complexing Protocol (if applicable)
o Time of complex formation (if applicable)
• Delivery reagent
o Delivery reagent type
o Catalogue number of delivery reagent
o Delivery reagent name
o Manufacturer of delivery reagent
• Final concentration or amount of delivery reagent
• Final concentration of silencing reagent
• Number of cells per well in delivery plate
Assay Plate
The ‘assay plate’ section contains information on conditions within the plate where the assaying
(data acquisition) take place.
• Number of cells per well
• Time to assay point from delivery of silencing RNA reagent
• Time of exposure of silencing RNA reagent (for media changes)
• Media changes
o Media composition
o Time of media change
Post treatment
The ‘post treatment’ section holds a description of the conditions that are applied after the
delivery of the silencing reagent.
• Treatment protocol
• Treatment type
• Compound
Assay
An assay is the process where the effects of RNA interference are measured (data acquisition).
The assay section contains a description of the assay performed and key parameters. Because
the effect of RNAi can be measured at various stages, e.g. transcriptome and proteome, this
section is technology independent.
• Assay description
• Assay reagents
o Assay reagent name
o Assay reagent catalog number
o Assay reagent manufacturer
• Control definition
• Assay protocol
• Instrument
o Instrument name
o Instrument manufacturer
o Instrument catalogue number
o Type of readout
o Instrument settings
Data Analysis
The ‘data analysis’ section requires a definition of the transformation, normalisation and scoring
procedures applied to the data produced as described in the assay section.
• Details of filtering of data
• Transformation details
• Reference to analysis script
• Analysis software
o Analysis software name and version
o Analysis software manufacturer
• Normalisation method
o Normalization parameters
o Controls used to normalize data
• Scoring method
• Quality controls steps
Data
The ‘data’ section describes the required quantitative and or qualitative data.
• Quantitative data
o Description of quantified data
o Unprocessed quantified data
o Normalised quantified data
o Scored data
• Qualitative data
o Description of qualitative data
o Qualitative data
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