a dual platform approach to transcript discovery for the planarian schmidtea mediterranea to establish rnaseq for stem cell and regeneration biology双平台的方法记录发现的真涡虫schmidtea mediterranea建立rnaseq干细胞生物学和再生.pdfVIP

A Dual Platform Approach to Transcript Discovery for the Planarian Schmidtea Mediterranea to Establish RNAseq for Stem Cell and Regeneration Biology 1. 2. 1. 1. 1 2 Martin J. Blythe , Damian Kao , Sunir Malla , Joanna Rowsell , Ray Wilson , Deborah Evans , Jamie 2 2 2 2 1,2 Jowett , Amy Hall , Virginie Lemay , Sabrina Lam , A. Aziz Aboobaker * 1 Deep Seq, Faculty of Medicine and Health Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom, 2 Evolutionary Developmental Biology Laboratory, Centre for Genetics and Genomics, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom Abstract The use of planarians as a model system is expanding and the mechanisms that control planarian regeneration are being elucidated. The planarian Schmidtea mediterranea in particular has become a species of choice. Currently the planarian research community has access to this whole genome sequencing project and over 70,000 expressed sequence tags. However, the establishment of massively parallel sequencing technologies has provided the opportunity to define genetic content, and in particular transcriptomes, in unprecedented detail. Here we apply this approach to the planarian model system. We have sequenced, mapped and assembled 581,365 long and 507,719,814 short reads from RNA of intact and mixed stages of the first 7 days of planarian regeneration. We used an iterative mapping approach to identify and define de novo splice sites with short reads and increase confidence in our transcript predictions. We more than double the