Abstract: The deep sea is the most common habitat of the biosphere, as most Earth’s surface is covered by water with an average depth around 3000 meters. Photobacterium profundum, viable both at high (28 MPa) and atmospheric (0.1 MPa) pressure, is the model organism for high pressure adaptation. Its transmembrane transcription factor ToxR is a pressure sensing transductor. To better understand the role of ToxR on the expression profile of P. profundum, a microarray-based analysis was performed both on wild-type and ToxR defective strains. For this purpouse a new generation of custom oligonucleotide DNA microarrays, developed by CombiMatrix®, was implemented. The aims of my project were: 1. The setting up of procedures and data analysis workflow for CombiMatrix® custom microarrays; 2. The obtaining of a provisional expression profile of P. profundum wild type and of a ToxR defective mutant; 3. The obtaining of a list of putative ToxR regulated transcripts in order to discover putative regulatory motifs; CombiMatrix® microarrays were found to be cost effective, sensitive and flexible tools for expression profiling, and new tools were developed to better manage the experimental workflow. The new platform allowed the discovery of 257 new transcripts and the presence of 12 small regulatory RNA. Provisional results onfirmed the expression pattern for the wild type strain, that was extended finding several cold shock and ribosomal proteins overexpressed at atmospheric pressure.