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Designer

The BxDesignertm   is used in the experimental design process to create custom microarrays and to manage probe data. The descriptions of the different types of DNA and Protein microarrays is focused on presenting an architectural view for designing relational databases to handle each type.  The template database schemas are designed to hold the fundamental information about microarrays and they are linked to other tables that contain information about the manufactured or created microarrays. For example, the additional tables may contain the date of production, lot and part numbers, company, expiration date (if applicable), operator, chemical component sources and unique microarray IDs.

bulletOligo Microarrays
bulletOligo Database Schema
bulletcDNA Microarrays
bulletcDNA Database Schema
bulletProtein Microarrays
bulletProtein Microarrays Database Schema

Probes

DNA Probes are cDNA or Oligos that have a length of about 25 nucleotide bases. Other types of Probes are proteins, antibodies, ligands or other types of molecules that will bind probes. BxLibrariantm will manage each probe using a unique ID. For example, information about the source of the probe, its well location within the microtitre plate, its microtitre plate ID, its sequence and probe handling protocols will be linked to the probe's unique ID.

Slides/Chips

Slides and/or Chips have bound targets arranged in patterns. These patterns are determined by the type of experiments to be performed and by the type of comparative or differential analysis that is to be done. One type of strategy is to be able to have self validating and internal control targets. Self-validating means that duplicate targets are present and if one target is expressed than the other has to be expressed if the first is not to be considered a false expression. Internal control targets allow for normalizing the data in order to compare expressions from slide to slide. The database must have a mechanism for storing the pattern and relationships between targets within and across patterns and to know the different types of targets. It must also store the protocols for creating the slides or chips.  Therefore, each slide will have a unique ID and may also have lot or batch numbers.

NOTE: The Microsoft SQL Server 2000 database schemas that are presented should be viewed as a base schema upon which to build or extend. They may not be complete due to specifics of a particular microarray and the needs of the downstream instrument control and data mining applications. They also can be implemented on other client-server databases such as Oracle, Sybase and DB2.

Oligo Microarrays

The following figure depicts an architecture of a set of oligo microarrays.  Each microarray has a set number that ranges from 1 to the total number of arrays in the set. In addition each microarray has a length (ArrayLength), a width (ArrayWidth) and a number of rows (ArrayRows) and columns (ArrayCols). An array element is accessed by a row (ElRow) and column (ElCol) coordinate or an equivalent  index (ELIndex) that runs from 1 to the total number (ArrayRows*ArrayCols) of elements in the array.  The element index is calculated by  (ElRow-1)*ArrayCols + ElCol.   Each element is composed of a Subarray of oligo sequences where each is different from any other oligo in the array. The Subarray has a widh (SAWidth) and a length (SALength) and a number of columns (SACols) and rows (SARows). Each Oligo is accessed by a row (SARow) and column (SACol) coordinate or an equivalent index (SAIndex) that runs from 1 to the total number of oligos (SARows*SACols). 

  

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Oligo Database Schema

This database schema stores the information about the Oligo Microarray Set  described above and the term template is used to designate that many production microarrays will be manufactured based upon this information.  In addition to the physical attributes of the microarray set, dates, versions, descriptions of each array, species and reference information about each oligo is stored. The coordinates in the scanned image of the expressed values will be mapped to the coordinates in the template.

Additional database tables will be needed to store manufacturing information such as part numbers, lot numbers, date of manufacture and other related data. Each microarray will be assigned a unique ID for tracking back to the manufacturing process and forward through the experimental process and analysis.

  

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cDNA Microarrays

The following figure depicts three major components of a cDNA system. A set of arraying plates containing the cDNA, a linear set of Pens (not shown) that extract cDNA from the wells of the arraying plates and array the cDNA in a pattern onto the third component, which is a microarray with a prepared surface,  that binds the cDNA. Each arraying plate has a unique ID (PlateID) and each well has a row (WellRow) and a column (WellCol) coordinate. A linear pen array transfers the cDNA from the plates to the microarray with the distance (PenDelta) from one pen to another being the same as the distance from one well to another. There are a number of specified position values - an upper left corner of the array (XOffset, YOffset) and the distance between rows (RowDelta) and columns (ColDelta). The microarray has a length (ArrayLength), a width (ArrayWidth) and a number of rows (ArrayRows) and columns (ArrayCols).  Each Probe has a diameter that ranges from 50 to 300 microns and a row (ProbeRow) and column (ProbeCol) coordinate or an equivalent index (ProbeIndex) that runs from 1 to the total number of Probes (ArrayRows*ArrayRows) on the array. It is also linked back to the well in the source microtitre plate.  In addition,  complex patterns can be created that may consist of more than a single deposition of the cDNA and consist of controls.

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cDNA Database Schema

The first part of the database schema handles the data related to the microtitre arraying plates. The data contains information about the contents of each well which includes links to multiple databases and reference articles.  It also provides for user defined properties where the user can supply a name and a value for the property. The user defined properties are applied uniquely to each WellContentID and thus disparate information can be stored.

 

 

This part of the schema handles the pen layout data for the arrayed microarrays and shows the link to the first part that handles the microtitre arraying plates through the Well table. This information is directly related to the expressed values in the scanned images. In general these tables can be extended to utilize a dynamic arraying pattern model.

 

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Protein Microarrays

The following figure shows two different protein arrays where the affinity capture surfaces are arrayed in a standard microtitre plate arrangement. In this example an 8 x12 array; however, other standard microtitre plate sizes (e.g. 384, 1536) and non-standard sizes (10,000 locations) can be created. In addition,  the shape of the surface can be a circle or any polygon and the surface does not have to be homogeneous and all surfaces can be different from each other. The database schema stores the array pattern, shapes and properties of the affinity capture surface. The affinity capture surface can be antibodies, antigens, proteins and other specially prepared chemical surfaces that differentially bind molecules such as proteins.

 

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Protein Microarray Database Schema

The schema for Protein Probe Arrays supports the Protein Array figure above and is similar to the previous DNA microarrays.  The fields in the TemplateProtProbeRec table that pertain to the shape of the affinity capture surface allows for each site on the array to have a different shape. These fields could be moved to the TemplateProtArray table if all shapes on the array are the same. Each protein array will have its own instance of the set of Template Protein Tables. The detection system can be controlled by this information, especially the shape data,  as well as being linked to the results of the anlysis which can be a fluorescent image or a mass(m/z) vs. Intensity spectrum. The properties of the surfaces are important for helping in the identification of proteins that are captured; therefore, the ProtProbeProp table can be extended with more fields to contain more information about the surface.

 

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Last modified: December 22, 2014