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.
Gene expression profile analysis of Manila clam (Ruditapes philippinarum) hemocytes after a Vibrio alginolyticus challenge using an immune-enriched oligo-microarray
Gene expression profile of hemocytes from Manila clam (Venerupis philippinarum) after a Perkinsus olseni challenge using an immune-enriched oligo-microarray
Data table header descriptions
ID
Row
Feature location: row
Col
Feature location:column
SubTypeMask
Numeric code defining the subtype of any control feature
SubTypeName
Name of subtype of any control feature
ControlType
Feature control type (0: Control type none; 1: Positive control; -1: Negative control)
GB_ACC
GenBank accession.version
TSA_ACC
Transcriptome Shotgun Assembly (TSA) accession
SRA_ACC
Sequencing Read Archive (SRA) accession
ProbeName
Identifier for the probe synthesized on the microarray
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