title: University Padova Chamelea gallina 8x15K
status: Public on Jan 08 2016
contact.city: Legnaro
contact.first: Massimo
contact.last: Milan
contact.email: massimo.milan@unipd.it
contact.state: PD
contact.address: Viale dell'Università 16
contact.department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene
contact.country: Italy
contact.institute: University of Padova
contact.phone: +39 0498272941
organism: Chamelea gallina
description: To design  the first C. gallina-specific oligo-array, the transcriptome obtained by Coppe and colleagues (2012) representing 36,422 contigs of high quality has been considered.  These contigs have been re-annotated  through blastx similarity searches conducted against SwissProt database and few protein databases available on Ensembl Genome Browser: Crassostrea gigas, Strongylocentrus purpuratus, Homo sapiens, Danio rerio, and Drosophila melanogaster. Alignments with an E-value of at most 1 E-5 were considered significant and only the best hit per contig was taken into account.   Probe design started with the selection of target sequences to be represented onto the C. gallina microarray. All annotated entries (9,939) were included. In addition, to fill the DNA microarray platform, a total of   2,167 non annotated transcripts with highest sequence quality have been considered. As most sequence reads were obtained from a non-directional cDNA library, sense strand orientation was inferred putatively from that of homologuous protein sequences of other species. One probe for annotated transcripts with known orientation was designed, while two probes with both orientations were designed for non annotated contigs and for contigs with ambiguous orientation. Probe design was carried out using the Agilent eArray interface [https://earray.chem.agilent.com/earray/], which applies proprietary prediction algorithms to design 60 mer oligoprobes. A total of 14,719, representing 12,064 C: gallina transcripts were successfully obtained. Of these, 300 probes designed on known-orientation transcripts, were synthesized in duplicate on the array in order to test for “reproducibility-within-array”. New microarrays were synthesized in situ using the Agilent ink-jet technology with a 8 × 15 K format. Each array included default positive and negative controls.
manufacture_protocol: See SurePrint Technology at manufacturer's web site http://agilent.com/