title: Calanus physiology microarray
status: Public on Mar 23 2012
contact.city: Groton
contact.first: Ebru
contact.last: Unal
contact.email: ebru.unal@uconn.edu
contact.state: CT
contact.address: 1080 Shennecossett Road
contact.department: Department of Marine Sciences
contact.country: USA
contact.institute: University of Connecticut
contact.phone: 860 4059066
organism: Calanus finmarchicus
manufacture_protocol: A normalized cDNA library for C. finmarchicus was previously created by David Towle (Mount Desert Island Biological Laboratory, Maine) and analyzed for ~10,000 ESTs from the library clones. The software program “Partigene” (http://xyala.cap.ed.ac.uk/bioinformatics/PartiGene/) was used to cluster the sequences into contigs, which were subsequently annotated by obtaining the ten best hits for each contig using the Tera-Blast P algorithm on a local Decypher processor (http://decypher.mdibl.org). Functional analysis was done to sort the ESTs by putative physiological function and to identify transcripts that encode proteins involved in the generation/regulation of population dynamics. A total of 995 ESTs that matched genes of known function were selected for inclusion in a custom “Calanus physiology microarray” printed with unique 50 base-pair oligonucleotide probes. Microarray slides were printed by using an arraying robot equipped with pin heads (OmniGrid Accent Arrayer) that prints the probes for EST contigs onto the Corning UltraGAPS slides by using Pronto Universal Spotting Solution (Corning). Each oligonucleotide probe was printed in duplicate. After printing, the slides were dried overnight in a vacuum desiccator and cross-linked in a UV Stratalinker (Stratagene) at a setting of 6000 x 100 μJ.