title: Agilent-035923 UniversityPadova_Ruditapes philippinarum_8x15K_v2.0
status: Public on Jul 01 2014
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: From the total of 1,438,665 R. philippinarum reads obtained through 454 sequencing (SRA020646 and SRA046855), the Newbler software package (GS De Novo Assembler v2.6, Roche) was able to assemble 88.24% of the raw sequences, with 11.76% of them (169,223) remaining as singletons. The assembly resulted in 26,708 isotigs grouped into 15,175 isogroups and 156 contigs. The longest isotig of each isogroup, the contigs, the singletons with more than 200 bp of continuous sequence with a Phred Q>20 (18,545) and the NCBI EST sequences (2,050) were then considered for the annotation. Putative identities of assembled sequences and singletons were obtained by running Blastx and Blastn similarity searches on several protein and nucleotide reference databases. Alignments with an E-value of at most 1 E-3 and 1 E-5 were considered significant for the protein and nucleotide databases, respectively. A total of 12,156 successfully annotated transcripts were considered for the R. philippinarum DNA microrrray design. All Isotigs are stored in the public Transcriptome Shotgun Assembly Sequence Database (TSA, http://www.ncbi.nlm.nih.gov/genbank/tsa/) under accession number GAEH00000000 (note: publicly available after paper publication). All singletons considered for the microarray design are stored in the public database Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra/) under accession numbers SRA020646 and SRA04685. As most sequence reads were obtained from a non-directional cDNA library, sense strand orientation was inferred putatively from that of homologous 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. A total of 13, 671 probes representing 12,108 unique transcripts were designed using the Agilent eArray interface (https://earray.chem.agilent.com/earray/), which applies proprietary prediction algorithms to design 60-mer oligoprobes.
manufacture_protocol: See SurePrint Technology at the manufacturer's web site (http://www.agilent.com).