title: Aplysia Discovery (un-annotated) Array DAA
status: Public on Jan 05 2007
contact.city: St Augustine
contact.first: Andrea
contact.middle: B
contact.last: Kohn
contact.email: abkohn@msn.com
contact.state: FL
contact.address: 9505 Ocean Shore Blvd
contact.department: Whitney lab
contact.country: USA
contact.institute: University of Florida
contact.phone: 904 461-4007
organism: Aplysia californica
description: Microarray Probe Design and Aplysia Oligo-array Fabrication. We constructed two custom 44,000 oligonucleotide arrays in collaboration with Agilent TechnologiesTM. The 60-mer oligonucleotide sequences were designed from a set of 56,071 non-redundant Aplysia sequences from the current assembly, based on bioinformatics criteria such as melting temperature and secondary structure.  Based on the content of the arrays we distinguish between an annotated and discovery array. While the annotated array primarily contains probes originating from assembled sequences or full length clones with known identity, the majority of probes on the discovery array are unknown. Briefly, the first 44,000 features array called the Aplysia Annotated Array (AAA) had all annotated sequences consisting of: full length clones from the table 4S (labeled as f), 32 sequences which were truncated sequence from these same clones that were over 1.5 Kb in length (labeled as d); 67 NCBI Aplysia californica specific sequences (labeled as n); and 90 truncated sequences from NCBI (labeled as b). All these sequences have their ‘1st best’ selected probes spotted 3 times, 2nd best probe spotted once, and 3rd best probe spotted once giving (76+67+32+90)*5 = 1325 features which are also spotted on all 2 custom arrays. In addition, AAA represents Aplysia sequences from our EST assembly that have any of the following terms in their blast hit definition: “receptor”, “hormone”, “channel”, “transcription”, “factor”, “RNA”, “Hox”, “Homeobox”, “neuro*”, “synap*”, “calcium”, “cyclic”, “CREB”. These terms are matched as either complete word or part of the word in the transcriptome annotation and account for 6188 sequences. These sequences have their “1st best” probes spotted 3 times, and “2nd best probes” spotted once, occupying 6188*4 = 24,744 features (labeled as m). For all the remaining sequences with nr blastx e-value < 4e-6, their “1st best probes were spotted twice giving 7961 such sequences. They occupy 7961*2 = 15,922 features and are labeled as a. Thus, on AAA we have 1325 + 24,744 + 15,922 = 41,991 features.
  All the rest of the Aplysia sequences are regarded as un-annotated sequences and their best probe was spotted once on the 2nd Aplysia array that we named as DAA. There were 72,280 (including both plus and minus directions because direction is unknown) un-annotated Aplysia sequences and if they were contigs, they were spotted on DAA. There were 29,572 un-annotated contigs (labeled as c) leaving 42,708 un-annotated singlets (labeled as s). 11,137 un-annotated singlets were spotted on the 2nd DAA array and the remaining 31,571 un-annotated singlets were spotted on the 3rd array (we did not test this array in the current study). In summary the 2nd DAA array has 1325 + 29,572 + 11,137 = 42,034 features. Finally, each array has 2,000 random Agilent designed sequences that have been used in control tests.
manufacture_protocol: in situ synthesized array
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