MIAME Minimum Information About a Microarray Experiment

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Presentation transcript:

MIAME Minimum Information About a Microarray Experiment

MIAME MIAME describes the Minimum Information About a Microarray Experiment that is needed to enable the interpretation of the results of the experiment unambiguously and potentially to reproduce the experiment.

MIAME – by wikipedia MIAME is a standard for reporting microarray experiments. It is intended to specify all the information necessary to interpret the results of the experiment unambiguously and to potentially to reproduce the experiment. While the standard defines the content required for compliant reports, it does not specify the format in which this data should be presented. There are a number of file formats for representing this data, and both public and subscription-based repositories for such expts. microarray

GEO & MIAME – by NCBI The MIAME guidelines outline the minimal information that should be included when describing a microarray experiment. Submitters and reviewers are encouraged to refer to the MIAME checklist and to use it as a guide to determine what information should be provided. MIAME checklist MIAME checklist GEO encourages submitters to supply MIAME compliant data. To assist with this, all GEO submission procedures are designed to closely follow the MIAME checklist.

hybridizationarray experiment datanormalization sample MIAME MIAME/Plant parameters & ontologies

experiment sample MIAME/Plant Pooling of experiments Experimental design parameters & ontologies Biosource properties - plant strain or line genotype, starting material, developmental stage, organism part (tissue) Biomaterial manipulations - growth conditions - substrate, environment - treatment type - biotic, abiotic, seed treatment, vernalization - separation technique Extraction methods MIAME

The MIAME Checklist for array based CGH experiments (draft December 2005) The purpose of this checklist is to guide authors, journal editors and referees in helping them to ensure that the data supporting published results based on array CGH experiments are made publicly available in a format that enables unambiguous interpretation of the data and potential verification of the conclusions. The purpose of this checklist is to guide authors, journal editors and referees in helping them to ensure that the data supporting published results based on array CGH experiments are made publicly available in a format that enables unambiguous interpretation of the data and potential verification of the conclusions.

The MIAME Checklist Experiment Design; Experiment Design; Samples used, extract preparation and labelling; Samples used, extract preparation and labelling; Hybridization procedures and parameters; Hybridization procedures and parameters; Measurement data and specifications; Measurement data and specifications; Array Design. Array Design.

Oligonucleotide arrayCGH description file example

BAC, PAC, fosmid, PCR amplicons, cDNA and/or cosmid arrayCGH description file example