Array Design

Array Design generates species-specific interspecies tiling arrays and probe sets using maskless array synthesis to enable high-resolution comparative analysis of orthologous DNA sequences across species.

Key Features:

• Interspecies Tiling Array Strategy: Creates interspecies tiling arrays that allow direct comparison of orthologous genomic regions across different species in a single experiment.
• Species-Specific Probe Sets: Generates high-resolution probe sets tailored to each species via an adapted maskless array synthesis strategy, with probe design tolerant of repetitive elements.
• High-Resolution Comparative Analysis: Supports competitive hybridizations to distinguish subtle sequence differences among highly similar DNA sequences.
• Complementary Techniques Integration: Integrates with DNA isolation and analysis methods including Chromatin Immunoprecipitation (ChIP), nuclease sensitivity assays, and nuclear matrix association assays.

Scientific Applications:

• Gene Expression Studies: Applied to analyze human protamine domains in a transgenic mouse model, reproducing human testis expression levels without disrupting endogenous mouse protamine expression.
• Comparative Genomics: Enables direct comparison of orthologous sequences for evolutionary and functional genomics studies, informing on conserved elements and species-specific adaptations.
• Pre-Sequencing Analysis: Serves as a rapid genomic interrogation method prior to deep sequencing to identify regions of interest or confirm sequence integrity.

Methodology:

Identification of target genomic regions followed by strategic design of species-specific probe sets and synthesis of probes using a maskless array strategy to maximize coverage and minimize cross-hybridization.