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.
In conclusion, we found that DGE is a valuable tool in our case 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.

• In-house scripts and source code developed for the DGE analysis are available as a repository.
• You can also access from this link to the DGE tags projected over the Smed454 transcriptome.
• Further details will be available at the following reference:
  “Digital Gene Expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea”
  Rodríguez-Esteban et al., BMC Genomics, 16:361, 2015 (AOP May 7th, 2015).  OPEN ACCESS

Data Tables

Transcriptomes relationship

Use the buttons below to access to the tables listing the correspondence between all the publicly available transcriptomes of S. mediterranea. Percentages refer to the minimum coverage cut-off:

Expression level

Follow the links on this section to access to the tables listing the expression levels corresponding to the transcripts of each dataset:

Publicly available transcriptomes:

S. mediterranea ESTs:

Genome assembly AUVC01 repeat masked:

Dotplot Overview of p-values