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DGE Analysis on Schmidtea mediterranea

 
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.

  • Processed DGE data can be accessed from this page.
  • Raw libraries and source sequencing files can be downloaded at the NCBI GEO repository(external link).
  • In-house scripts and source code developed for the DGE analysis are available as a repository(external link).
  • 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(external link) (AOP May 7th, 2015). Open Access

 

Transcriptome Sequencing by 454

 
A detailed description of the planarian transcriptome is essential for future investigation into regenerative processes using planarians as a model system. In order to obtain the most representative set of planarian genes expressed under different physiological conditions, total RNA was isolated from a mixture of non-irradiated and irradiated intact and regenerating planarians of species Schmidtea mediterranea. We have performed sequence analyses on the assemblies of reads obtained by 454-sequencing from that pool of transcripts. Among those analyses, functional annotation was useful in order to identify putative homologues of several gene families that may play a key role during regeneration, such as neurotransmitter and hormone receptors, homeobox-containing genes, and genes related to eye function.

  • Further details are available at the following reference:
    "Smed454 dataset: unravelling the transcriptome
    of Schmidtea mediterranea"
    Abril, Cebrià et al., BMC Genomics, 2010, 11:731(external link). Open Access
  • Data is available on this Smed454 web site, which includes:
    • a contig assembly browser (click on VIEWER button),
    • BLAST searches (see BLAST button),
    • as well as the sequence files ready for download as compressed tarballs (follow the DATA button).

 

Proteomic Analyses on Planarian Neoblasts

 
The genome sequencing of S. mediterranea and some EST projects generated interesting data to delineate neoblast cells features. There are some molecular aspects not reflected at both, genomic and transcriptomic levels, because little information at protein dynamics level exists. This work attempted to open a new unexplored area in the planarian research field. We developed a proteomics strategy in order to identify and characterize neoblast specific proteins. In this paper we describe the method and discuss the results in comparison with genomic analysis carried out in planaria, as well as with proteomic studies using other stem cell model systems.

  • Further details are available at the following reference:
        A proteomics approach to decipher the molecular nature of planarian stem cells
        Fernández-Taboada, et al, BMC Genomics, 2011, 12:133(external link). Open Access
  • Planarian Proteomics page contains both raw and processed data from the proteomics experiments and the posterior computational analyses. This page was provided as additional material on the paper above.

Page last modified on Thursday 07 of May, 2015 17:22:43 CEST

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