Genomics Technology Facility
The operation of the Facility centers on the Genetix Arraying Robot, a large flatbed robotic arm with video camera used to produce bacterial macro-array libraries and filters.  We currently maintain in -80°C freezers 27 different echinoderm libraries comprising a total of approximately three million arrayed clones.  In addition to providing these materials to academic research groups, we also offer the opportunity for outside groups from Caltech and elsewhere to array and spot their own libraries.  The existing genomic DNA and cDNA libraries that were so extensively employed for the annotation of the sea urchin genome are stably maintained in our freezers.  We print new filters for these as needed.  In addition, we have made and arrayed an Asterina miniata mixed-stage larval cDNA library in the pSport plasmid.  During the past year we have arrayed a total of 120,000 colonies and printed a total of 317 macroarray filters.  Research materials have been provided to research laboratories ranging from University of Washington to Stazione Zoologica Anton Dohrn (Italy).
Our collaboration with the Baylor College of Medicine, Human Genome Sequencing Center continues on several fronts.  We provided material for, and later computational analysis of a skim-sequencing project in two related species, Strongylocentrotus franciscanus and the deepwater species, Allocentrotus fragilis.  The 1X coverage provided only a glimpse into the genomic parameters between these and our reference species, Strongylocentrotus purpuratus.  Baylor has completed another round of 1X coverage for both related species and we expect to have it available for analysis in the next few weeks.  These sequences will be used to confirm our model that predicts a constraint for large insertions and deletions in cis-regulatory modules.