Oligonucleotide array design algorithms are often unable to design oligos specific for all transcripts in a genome, especially for each alternatively spliced transcript.
For example, the oligonucleotide array design utilized by Affymetrix, the leading manufacturer of expression arrays, has significantly changed over the last decade, resulting in many datasets with a variant probe set content and addressing variable numbers of genes.
The HpaII tiny fragment Enrichment by Ligation-mediated PCR (HELP) assay was performed as described in the original report employing a published rat-specific Nimblegen oligonucleotide array design.
By hybridizing genomic DNA to a custom oligonucleotide array designed for maximum gene coverage, we were able to identify polymorphisms using two approaches for pair-wise comparisons, as well as a highly parallel method that compared all 52 genotypes simultaneously.
Development of a target secondary structure criterion for oligonucleotide array design is expected to impose restrictions on the probe selection beyond the sequence similarity and melting temperature criteria that are currently used, especially in cases where short probe length restricts the annealing temperature used in the hybridization protocol to 22 37°.
Labeled mRNA solutions were prepared and hybridized to oligonucleotide arrays designed to monitor ∼1300 murine, full-length genes.
Microarrays utilised custom designed oligonucleotide arrays designed by Compugen and synthesised by Sigma-Genosys [ 77].
Our analysis demonstrated that the use of multiple probes per target sequence is not essential for in-situ synthesized 60mer oligonucleotide arrays designed against bacteria.
Our sensitivity analyses showed that hybridization of genomic DNA to long-oligonucleotide arrays designed mainly from transcript sequences can potentially detect sequence divergence at the level of roughly 2 or more mismatches per 60 nt probe length (or above 3% divergence).
The HITChip oligonucleotide array was designed at Wageningen University, the Netherlands [23].
Here we present the first study utilizing a 35,000 feature 70-mer oligonucleotide array, originally designed for expression analysis, for detailed genomic characterization of nine prostate cancer cell lines.
