biological interpretation of the right of call microarray experimental data for the relevant explanations. MIAME guidelines that are widely accepted give, organism-independent standard generic for minimum information about microarray experiments. In the overall structure, MIAME very common and specification covers most of the aspects of technical, while the specific relevant organisms useful for understanding the underlying experiment is mostly gone. If the plant biologists want to use the results of microarray experiments published, they need detailed information about the biological aspects, such as the growing conditions, time of harvest, or harvest the organ (s). Here, we propose MIAME / Plants, standard describes the biological details that will be taken to describe microarray experiments involving plants.
We hope that a more detailed explanation and a more systematic microarray experiments will greatly increase the use of transcriptome data sets for the scientific community. The strength and value of systematic explanation convincing microarray data indicated by the data warehouse as Genevestigator (R) or NASCArrays and better experimental explanation will make this application even more powerful. The technology reduces the cost of high-throughput functional genomics is creating a flood of high-volume, complex data, puts a strain on resources and the development of bioinformatics tools.
The Bacterial Microarray Group at St George (BμG @ S) has been at the forefront of design microarray bacteria and analysis for more than a decade and while serving as the hub of a global network of research groups of microbes have developed BμG @ Sbase, microbial genes expression and databases comparative genomics. BμG @ Sbase is a web-browsable, expertly curated, MIAME-compliant database that stores a comprehensive explanation of experimental and some raw and analyzed data format. consistent explanation is activated through a series of structured web form, which guides the user through the process follows a set of best practices and controlled vocabulary.
The database currently contains 86 expert curated set of data available to the public (with over 124 yet published) and get a full explanation for the 59 bacterial microarray design. The data can be accessed and queried using the explorer-like interface; integrates an intuitive tree diagram for an experimental compound is present clear and concise details. Furthermore, the modular design of the database will provide a strong platform to integrate other data types beyond the microarray to be more future analysis system based on.
MIAME/Plant – adding value to plant microarrray experiments.
THEME: web tool for the analysis of microarray design loop data.
A number of recent studies have shown that loop-design that is more efficient than the reference control design. Data analysis for loop-designed microarray experiments is generally performed using a linear model and statistical tests.
This technique requires specialized knowledge in statistical programming. However, limited-loop web-based design tool available. We have developed THEME (Tsing Hua Engineering from microarray experiments) that exploits all the necessary data analysis tools for microarray study-design loop. TEMA allows users to build linear models and to apply some user-defined statistical test to detect DEG hypothesis (which is expressed differently genes).
Description: Interleukin-7 Human Recombinant produced in yeast is a single, glycosylated polypeptide chain containing 152 amino acids and having a molecular mass of 17.4 kDa. The IL-7 is purified by proprietary chromatographic techniques.
BMP-7 Bone Morphogenetic Protein-7 Human Recombinant Protein
Description: Bone Morphogenetic Protein-7 Human Recombinant produced in E.Coli is a monomeric, non-glycosylated, polypeptide chain containing 139 amino acids and having a molecular mass of 15679.97 Dalton. ;The BMP-7 is purified by proprietary chromatographic techniques.
Description: Lung tissue lysate (7 Days Old) was prepared by homogenization in modified RIPA buffer (150 mM sodium chloride, 50 mM Tris-HCl, pH 7.4, 1 mM ethylenediaminetetraacetic acid, 1 mM phenylmethylsulfonyl fluoride, 1% Triton X-100, 1% sodium deoxycholic acid, 0.1% sodium dodecylsulfate, 5 μg/ml of aprotinin, 5 μg/ml of leupeptin. Tissue and cell debris was removed by centrifugation. Protein concentration was determined with Bio-Rad protein assay. The product was boiled for 5 min in 1 x SDS sample buffer (50 mM Tris-HCl pH 6.8, 12.5% glycerol, 1% sodium dodecylsulfate, 0.01% bromophenol blue) containing 50 mM DTT.
Description: Brain tissue lysate (7 Days Old) was prepared by homogenization in modified RIPA buffer (150 mM sodium chloride, 50 mM Tris-HCl, pH 7.4, 1 mM ethylenediaminetetraacetic acid, 1 mM phenylmethylsulfonyl fluoride, 1% Triton X-100, 1% sodium deoxycholic acid, 0.1% sodium dodecylsulfate, 5 μg/ml of aprotinin, 5 μg/ml of leupeptin. Tissue and cell debris was removed by centrifugation. Protein concentration was determined with Bio-Rad protein assay. The product was boiled for 5 min in 1 x SDS sample buffer (50 mM Tris-HCl pH 6.8, 12.5% glycerol, 1% sodium dodecylsulfate, 0.01% bromophenol blue) containing 50 mM DTT.
Description: Liver tissue lysate (7 Days Old) was prepared by homogenization in modified RIPA buffer (150 mM sodium chloride, 50 mM Tris-HCl, pH 7.4, 1 mM ethylenediaminetetraacetic acid, 1 mM phenylmethylsulfonyl fluoride, 1% Triton X-100, 1% sodium deoxycholic acid, 0.1% sodium dodecylsulfate, 5 μg/ml of aprotinin, 5 μg/ml of leupeptin. Tissue and cell debris was removed by centrifugation. Protein concentration was determined with Bio-Rad protein assay. The product was boiled for 5 min in 1 x SDS sample buffer (50 mM Tris-HCl pH 6.8, 12.5% glycerol, 1% sodium dodecylsulfate, 0.01% bromophenol blue) containing 50 mM DTT.
Description: Kidney tissue lysate (7 Days Old) was prepared by homogenization in modified RIPA buffer (150 mM sodium chloride, 50 mM Tris-HCl, pH 7.4, 1 mM ethylenediaminetetraacetic acid, 1 mM phenylmethylsulfonyl fluoride, 1% Triton X-100, 1% sodium deoxycholic acid, 0.1% sodium dodecylsulfate, 5 μg/ml of aprotinin, 5 μg/ml of leupeptin. Tissue and cell debris was removed by centrifugation. Protein concentration was determined with Bio-Rad protein assay. The product was boiled for 5 min in 1 x SDS sample buffer (50 mM Tris-HCl pH 6.8, 12.5% glycerol, 1% sodium dodecylsulfate, 0.01% bromophenol blue) containing 50 mM DTT.
Description: Spleen tissue lysate (7 Days Old) was prepared by homogenization in modified RIPA buffer (150 mM sodium chloride, 50 mM Tris-HCl, pH 7.4, 1 mM ethylenediaminetetraacetic acid, 1 mM phenylmethylsulfonyl fluoride, 1% Triton X-100, 1% sodium deoxycholic acid, 0.1% sodium dodecylsulfate, 5 μg/ml of aprotinin, 5 μg/ml of leupeptin. Tissue and cell debris was removed by centrifugation. Protein concentration was determined with Bio-Rad protein assay. The product was boiled for 5 min in 1 x SDS sample buffer (50 mM Tris-HCl pH 6.8, 12.5% glycerol, 1% sodium dodecylsulfate, 0.01% bromophenol blue) containing 50 mM DTT.
Description: Thymus tissue lysate (7 Days Old) was prepared by homogenization in modified RIPA buffer (150 mM sodium chloride, 50 mM Tris-HCl, pH 7.4, 1 mM ethylenediaminetetraacetic acid, 1 mM phenylmethylsulfonyl fluoride, 1% Triton X-100, 1% sodium deoxycholic acid, 0.1% sodium dodecylsulfate, 5 μg/ml of aprotinin, 5 μg/ml of leupeptin. Tissue and cell debris was removed by centrifugation. Protein concentration was determined with Bio-Rad protein assay. The product was boiled for 5 min in 1 x SDS sample buffer (50 mM Tris-HCl pH 6.8, 12.5% glycerol, 1% sodium dodecylsulfate, 0.01% bromophenol blue) containing 50 mM DTT.
Description: Stomach tissue lysate (7 Day Old) was prepared by homogenization in modified RIPA buffer (150 mM sodium chloride, 50 mM Tris-HCl, pH 7.4, 1 mM ethylenediaminetetraacetic acid, 1 mM phenylmethylsulfonyl fluoride, 1% Triton X-100, 1% sodium deoxycholic acid, 0.1% sodium dodecylsulfate, 5 μg/ml of aprotinin, 5 μg/ml of leupeptin. Tissue and cell debris was removed by centrifugation. Protein concentration was determined with Bio-Rad protein assay. The product was boiled for 5 min in 1 x SDS sample buffer (50 mM Tris-HCl pH 6.8, 12.5% glycerol, 1% sodium dodecylsulfate, 0.01% bromophenol blue) containing 50 mM DTT.
Description: Skin tissue lysate (7 Days Old) was prepared by homogenization in modified RIPA buffer (150 mM sodium chloride, 50 mM Tris-HCl, pH 7.4, 1 mM ethylenediaminetetraacetic acid, 1 mM phenylmethylsulfonyl fluoride, 1% Triton X-100, 1% sodium deoxycholic acid, 0.1% sodium dodecylsulfate, 5 μg/ml of aprotinin, 5 μg/ml of leupeptin. Tissue and cell debris was removed by centrifugation. Protein concentration was determined with Bio-Rad protein assay. The product was boiled for 5 min in 1 x SDS sample buffer (50 mM Tris-HCl pH 6.8, 12.5% glycerol, 1% sodium dodecylsulfate, 0.01% bromophenol blue) containing 50 mM DTT.
Description: Eye tissue lysate (7 Days Old) was prepared by homogenization in modified RIPA buffer (150 mM sodium chloride, 50 mM Tris-HCl, pH 7.4, 1 mM ethylenediaminetetraacetic acid, 1 mM phenylmethylsulfonyl fluoride, 1% Triton X-100, 1% sodium deoxycholic acid, 0.1% sodium dodecylsulfate, 5 μg/ml of aprotinin, 5 μg/ml of leupeptin. Tissue and cell debris was removed by centrifugation. Protein concentration was determined with Bio-Rad protein assay. The product was boiled for 5 min in 1 x SDS sample buffer (50 mM Tris-HCl pH 6.8, 12.5% glycerol, 1% sodium dodecylsulfate, 0.01% bromophenol blue) containing 50 mM DTT.
Users can modify the entries of the matrix design for experimental design and contrasting matrix for statistical hypothesis testing. Output of some user-defined statistical test hypotheses, register DEG, can be cross-validated. Web platform provides an assessment of data and visualization tools that significantly help users when evaluating the performance of microarray experimental procedure. TEMA also MIAME (Minimum Information About Microarray Experiment) compliant system, which allows users to export files formatted for GEO (Gene Expression Omnibus) filing.
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