title: Agilent-036974 S. solea array (Feature Number version)
status: Public on Oct 07 2013
contact.city: Legnaro (PD)
contact.first: Serena
contact.last: Ferraresso
contact.email: serena.ferraresso@unipd.it
contact.state: Padova
contact.address: Viale dell'Università
contact.department: Dept of Comparative Biomedicine and Food Science
contact.country: Italy
contact.institute: University of Padova
contact.phone: +39 049 8272506
organism: Solea solea
description: GE 8x15k oligo microarray that covers 14,531 annotated transcripts (Isotigs and Singletons) of the common sole (Solea solea). Roche 454 sequence reads were produced from a normalized cDNA library constructed using a mixture of RNAs from whole larvae (1-4-6-11-13-18-20-33 days posth hatching) and adult tissues (liver and intestine). All 454 sequences were then assembled into Isotigs, representing putative transcripts, by using Newbler 2.6 software with default settings. All assembled Isotigs are stored in the public database Transcriptome Shotgun Assembly Sequence Database (TSA, http://www.ncbi.nlm.nih.gov/genbank/tsa) under accession number GAAQ00000000, while Singletons can be directly retrieved from the NCBI Sequence Read Archive (SRA) under accession number SRA058691. Microarray design has been carried out on the basis of 25,252 contigs (Isotigs) and 66,026 singletons (with a minimal length of 200 nt) obtained from the Roche 454 sequencing of a normalized cDNA library of sole larval stages (from 1 to 33 days post hatching) and adult tissues. Only annotated sequences were used for microarray design. One probe for annotated sequences with known orientation (14,357) was designed while, whenever possible, two probes with both orientations were designed for sequences with unknown/ambiguous orientation (174 indicated by Isotig/Singleton ID plus prefix S_ or AS_ ). A total of 14,701 oligonucleotide probes (60 nt) were in situ synthesized onto the array, using Agilent non-contact ink-jet technology (8 x 15K format, including default positive and negative controls).  Probe ID on the array corresponds to transcript name (either Isotig or Singleton).
manufacture_protocol: See SurePrint Technology at manufacturer's web site http://agilent.com/