Microarray target preparation

Gold D et al. A comparative analysis of data generated using two different target preparation methods for hybridization to high-density oligonucleotide microarrays. BMC Genomics 2004 5 2. 

Spike-ins are usually RNA transcripts used to calibrate measurements in a DNA microarray experiment. Each spike-in is designed to hybridize with a specific control probe on the target array. Manufacturers of commercially available microarrays typically offer companion RNA spike-ins kits . Known amounts of RNA spike-ins are mixed with the experiment sample during preparation. Subsequently the measured degree of hybridization between the spike-ins and the control probes is used to normalize the hybridization measurements of the sample RNA. 

In this method, peptides or small molecules are prepared by the split-mix synthesis method and cleaved from the resin to form an encoded solution-phase library such that each library compound is tethered to a PNA code via a hydrophilic linker (11). The library then is mixed with the target protein and later exposed to planar oligonucleotide microarrays of predetermined sequences. Alternatively, the encoded soluble library can be hybridized to the oligonucleotide microarrays before incubation with the target protein. 

In some respects, this comparative approach to hunting for changes that result from a given treatment is analogous to the common approach adopted for microarrays described above. However, one notable difference is that a change evident on an array can immediately be linked to one specific gene because the identity of each element on an array is predefined. With proteomics, unless a comprehensive cell or tissue protein map has already been prepared, the identity of most spots will not be known and characterization of the target proteins is still required. 

A successful sample preparation ensures robust microarray analysis, which requires high quality surfaces for the reaction between target and probe. Of the many different types of... 

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