E-learning in analysis of genomic and proteomic data 2. Data analysis 2.2. Analysis of high-density genomic data 2.2.1. DNA microarrays Microarray production

Microarray slides are produced either commercially or as a custom products in individual laboratories.
The advantage of commercial microarrays is that they are of high quality. Most companies offer microarrays designed for the most commonly studied organisms as human, mouse, rat, and yeast. Many of them have also specialized arrays available for more focused investigations (colon cancer arrays, breast cancer arrays, …). On the other hand, the custom production of micorarrays has an advantage of a flexibility on the genes that are to be covered and microrarays can be produced in small batches. However, this requires a laboratory to have a microarray printer or spotter facility to produce the array.
There are two major techniques that are used for microarray production (or placing the probes onto spots at the solid surface), spotting and in-situ synthesis.

     The probes (oligonucleotides, cDNA clones) are synthesized prior to deposition on the array surface and are then placed (spotted) onto microarray surface. This procedure is performed by a robotic arm with fine pins (needles). During the printing process the pins are dipped into wells containing the probes, depositing than each probe at designated location on the array surface. Because the probes and printing locations can be easily adjusted, this technique is used worldwide for the custom production of microarrays by research groups in their own laboratories.

    Following video shows a spotting microarray robot in action:

A special approach uses microscopic beads instead of the large solid support. The probes are placed onto microscopic beads, which are than randomly placed onto microarray surface into small wells. This approach is used in Illumina arrays.


In situ synthesis
     The short probe sequences are synthetised directly onto a slide. This techniques is usually applied with short probe sequences (oligonucleotides). The method used for in-situ synthesis is based on photolitographic synthesis. Here the light and light-sensitive masking agents are used to "build" a sequence one nucleotide at a time across the entire array.(Pease et al.,1994) Each probe that is to be prolonged is selectively "unmasked" using the light and mask frame. Than the array is washed with a solution containing a single nucleotide of interest. The nucleotides binds onto unmasked probes. Consequently, the a masking reaction takes place and the next set of probes are unmasked in preparation for a different nucleotide exposure. This process is repeated until all probesets are constructed into their full length.

     A nice demonstration of the process can be seen in this video: