design, validation and annotation of transcriptome-wide oligonucleotide probes for the oligochaete annelid eisenia fetida设计、验证和注释transcriptome-wide寡核苷酸探针的寡毛纲动物环节动物eisenia fetida.pdfVIP

Design, Validation and Annotation of Transcriptome- Wide Oligonucleotide Probes for the Oligochaete Annelid Eisenia fetida 1 2 1 3 Ping Gong *, Mehdi Pirooznia , Xin Guan , Edward J. Perkins 1 Environmental Services, SpecPro Inc., Vicksburg, Mississippi, United States of America, 2 Department of Psychiatry, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America, 3 Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, Mississippi, United States of America Abstract High density oligonucleotide probe arrays have increasingly become an important tool in genomics studies. In organisms with incomplete genome sequence, one strategy for oligo probe design is to reduce the number of unique probes that target every non-redundant transcript through bioinformatic analysis and experimental testing. Here we adopted this strategy in making oligo probes for the earthworm Eisenia fetida, a species for which we have sequenced transcriptome- scale expressed sequence tags (ESTs). Our objectives were to identify unique transcripts as targets, to select an optimal and non-redundant oligo probe for each of these target ESTs, and to annotate the selected target sequences. We developed a streamlined and easy-to-follow approach to the design, validation and annotation of species-specific array probes. Four 244K-formatted oligo arrays were designed using eArray and were hybridized to a pooled E. fetida cRNA sample. We identified 63,541 probes with unsaturated signal intensities consistently above the background level. Target transcripts of these probes were annotated using several sequence alignment algorithms. Significant hits were obtained for 37,439 (59%) probed targets. We validated a