This database contains 309,278 raw DNA trace files of Chlamydomonas reinhardtii Expressed Sequence Tags (ESTs). The relevant cDNA libraries were constructed using oligo-dT primers, and represent various sampling strategies with regard to different strains, genders, growth conditions and/or environmental stressors. All the traces have been reprocessed using our novel bioinformatics pipeline, WebTraceMiner, which focuses on detecting in-silico verified cDNA termini/ends. 57% of all ESTs had cDNA termini(us) that matched the expected structures according to their cDNA library construction, with a high quality and clean region of >=75 nt. When compared with our final sequences, lots of EST counterparts in GenBank dbEST and/or used for community EST assemblies and gene annotation contain under trimmed terminus parts, exerting deleterious impacts to many downstream EST applications. Meanwhile, many public ESTs are over trimmed in terms of their terminal structures, representing a loss of directional, positional and structural information of cDNA termini and therefore mRNA 3'/5' ends. Using GMAP, individual ESTs with in-silico authenticated termini have been mapped to the draft genome (JGI release 3.1). In particular, we annotated mRNA transcript 3'/5' end positions in the genome. Clearly, our EST terminus data provides the research community a unique resource to determine gene structure, improve gene annotation and explore transcriptome and mRNA metabolism in C. reinhardtii. Two publications in GENETICS: Liang, C., Y. Liu, L. Liu, A. C. Davis, Y. Shen and Q. Q. Li (2008) ESTs with cDNA termini - previously overlooked resources for gene annotation and transcriptome exploration in Chlamydomonas reinhardtii. doi:10.1534/genetics.107.085605 (In Press). Shen, Y., Y. Liu, L. Liu, Liang, C. and Q. Q. Li (2008) Unique features of nuclear mRNA poly(A) signals and alternative polyadenylation in Chlamydomonas reinhardtii. doi:10.1534/genetics.108.088971 (In Press). |
