However, the GeneChip with 25-mer oligos has an advantage over microarrays with cDNAs or longer oligos.
In contrast, the distribution of cDNA versus oligo microarray correlations had more of a beta shape, indicating that data generated from many pairs of corresponding probes in the two array systems strongly correlated, but some pairs yielded results that correlated poorly, which decreased the mean correlation coefficient.
Large EST databases are publicly available and a 24 K oligo microarray has been developed and used to examine the transcriptome profile of B. rapa [ 8].
In this pilot microarray, oligos were designed both in forward and reverse sequence orientation.
49, 70, 71 Oligo microarrays have shorter fragments of cDNA spotted on the chip, so they are less ideal for cross-species work, since few numbers of polymorphism may affect hybridization greatly.
As listed below, three whole-genome oligo microarray platforms have been developed for rice based on early rice gene predictions (called pseudomolecules) from The Institute for Genomic Research TIGRR) and/or rice full-length cDNAs available from the Knowledge-based Oryza Molecular biological Encyclopedia (KOME, http://cdna01.dna.affrc.go.jp/cDNA/) [23].
Whilst the design and validation of a custom oligo DNA microarray has become a straightforward procedure, a proper functional classification for the collection of unique transcripts that are represented onto the DNA microarray is certainly more difficult to achieve in non-model species, particularly in teleost fish.
A low-density oligo-DNA microarray (5k) has been tested also for the Atlantic salmon [ 26].
However, the Oligo DNA microarray may have limits in terms of specificity, as the AAD14 gene, which has one mismatch with the AAD4 gene, was recognized as the induced gene.
In addition, the sequence information generated in the project, jointly with previous information on sequences from both F. xananassa and F. vesca, has allowed designing an oligo-based microarray that has been used to compare the transcriptome of the ripe receptacle of the diploid and octoploid species.
