title: Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea.
abstract: BACKGROUND
  The freshwater planarian Schmidtea mediterranea is recognised as a valuable model for research into adult stem cells and regeneration. With the advent of the high-throughput sequencing technologies, it has become feasible to undertake detailed transcriptional analysis of its unique stem cell population, the neoblasts. Nonetheless, a reliable reference for this type of studies is still lacking.
  
  
  RESULTS
  Taking advantage of digital gene expression (DGE) sequencing technology we compare all the available transcriptomes for S. mediterranea and improve their annotation. These results are accessible via web for the community of researchers. Using the quantitative nature of DGE, we describe the transcriptional profile of neoblasts and present 42 new neoblast genes, including several cancer-related genes and transcription factors. Furthermore, we describe in detail the Smed-meis-like gene and the three Nuclear Factor Y subunits Smed-nf-YA, Smed-nf-YB-2 and Smed-nf-YC.
  
  
  CONCLUSIONS
  DGE is a valuable tool for gene discovery, quantification and annotation. The application of DGE in S. mediterranea confirms the planarian stem cells or neoblasts as a complex population of pluripotent and multipotent cells regulated by a mixture of transcription factors and cancer-related genes.
authors.affiliation: Departament de Genètica, Facultat de Biologia, Universitat de Barcelona (UB), and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Av. Diagonal 643, Barcelona, 08028, Catalonia, Spain. gresteban@scientist.com.
authors.forename: Gustavo
authors.initials: G
authors.lastname: Rodríguez-Esteban
authors.affiliation: Departament de Genètica, Facultat de Biologia, Universitat de Barcelona (UB), and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Av. Diagonal 643, Barcelona, 08028, Catalonia, Spain. gonzalezsastre@gmail.com.
authors.forename: Alejandro
authors.initials: A
authors.lastname: González-Sastre
authors.affiliation: Departament de Genètica, Facultat de Biologia, Universitat de Barcelona (UB), and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Av. Diagonal 643, Barcelona, 08028, Catalonia, Spain. joserojolaguna@gmail.com.
authors.forename: José Ignacio
authors.initials: JI
authors.lastname: Rojo-Laguna
authors.affiliation: Departament de Genètica, Facultat de Biologia, Universitat de Barcelona (UB), and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Av. Diagonal 643, Barcelona, 08028, Catalonia, Spain. esalo@ub.edu.
authors.forename: Emili
authors.initials: E
authors.lastname: Saló
authors.affiliation: Departament de Genètica, Facultat de Biologia, Universitat de Barcelona (UB), and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Av. Diagonal 643, Barcelona, 08028, Catalonia, Spain. jabril@ub.edu.
authors.forename: Josep F
authors.initials: JF
authors.lastname: Abril
mesh_terms: D000818:Animals; D023081:CCAAT-Binding Factor / Q000235:genetics; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D017238:Genes, Helminth; D018398:Homeodomain Proteins / Q000235:genetics; D023421:Models, Animal; D008969:Molecular Sequence Data; D010932:Planarians / Q000166:cytology / Q000235:genetics*; D018510:RNA, Helminth / Q000032:analysis*; D017423:Sequence Analysis, RNA / Q000379:methods*; D013234:Stem Cells / Q000166:cytology* / Q000378:metabolism
chemical_list: D023081:CCAAT-Binding Factor; D018398:Homeodomain Proteins; D018510:RNA, Helminth; C402244:nuclear factor Y