title: Agilent-038779 UniversityPadova_Ruditapes philippinarum_8x15K_v4
status: Public on Sep 22 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: Ruditapes philippinarum
description: In situ long-oligonucleotide microarray
  GE 8x15k oligo microarray that covers 14,805  transcripts of the Manila clam (Ruditapes philippinarum).  Illumina libraries public available produced by Passamonti et al. (2012), 454 sequences produced by Milan et al. (2011; SRX022422), and 454 sequences produced by Moreira et al. (2012; SRX100159) were assembled by using CLC Genomic Workbench 5 (default parameters). A total of 283.752 assembled contigs produced by CLC bio assembly have been annotated  through blastx similarity searches conducted against UniProtKB/SwissProt database and few protein databases available on Ensembl Genome Browser: Homo sapiens, Danio rerio, and Drosophila melanogaster. Alignments with an E-value of at most 1 E-4 were considered significant and only the best hit per contig was taken into account. In order to recover probes employed and validated in the previous versions of R. philippinarum microarray (Milan et al. 2011; Milan et al. 2014) blastn has been performed versus the “new” annotated contigs generated. In addition, probes representing transcripts  correlated to pollutants concentrations in previous study (Milan et al. 2013) have been also considered. A total of 866 probes were already employed on a previous versions of the microarray (GPL10900 and GPL15723) and maintained the same Probe ID (contig ID plus suffix _1, _2, _AS or _S). For the others transcipts probe design started with selection of 15,098 non-redundant annotated contigs to be represented onto the R. philippinarum microarray. 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 to construct a high-density oligo-DNA microarray, while two probes with both orientations were designed 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 14,171 probes have been successfully obtained and considered for the microarray design. A total of 15,037 probes (14,171 “new” probes, and 866 probes represented in previous R. philippinarum microarray platform) representing 14,805 transcripts were successfully represented in the new DNA microarray platform. Both independent probes designed for the same transcript are named with an univocal ID; the sense probes are distinguished by suffix_S while the anti-sense probes are distinguished by suffix _AS. Oligonucleotides, 60-mer plus a “linker”, are synthesized directly on glass slide using the Agilent’s SurePrint Tecnology.
  
  Please note that the contig are not available in any public database yet. A "txt file" with new contigs considered will be provide as supplementary file with the associated publication. In addition, we are uploading a Ruditapes philippinarum database containing all contigs obtained to date: http://compgen.bio.unipd.it/ruphibase/. However this database has not yet been updated.
manufacture_protocol: See SurePrint Technology at manufacturer's web site http://agilent.com/