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Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea.

Rodríguez-Esteban G, González-Sastre A, Rojo-Laguna JI, Saló E, Abril JF - BMC Genomics (2015)

Bottom Line: These results are accessible via web for the community of researchers.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.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.


Related in: MedlinePlus

Saturation plot for the distinct tags mapped over each reference data set. Tag sequences were randomly taken to build, by steps of 200,000 tags, increasing-size libraries that were then mapped against the reference data sets. Saturation is reached for libraries around two million tags.
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Fig1: Saturation plot for the distinct tags mapped over each reference data set. Tag sequences were randomly taken to build, by steps of 200,000 tags, increasing-size libraries that were then mapped against the reference data sets. Saturation is reached for libraries around two million tags.

Mentions: Three DGE libraries were obtained from FACS-isolated cell populations X1 (proliferating stem cells, S/G2/M), X2 (a mix of stem cell progeny and proliferating, G0/G1), and Xin (differentiated cells, G0/G1) [30] (Additional file 1). 8,298,210 total reads were sequenced (X1: 3,641,099; X2: 3,488,712; Xin: 1,168,399), representing 98,156 distinct tags (X1: 70,849; X2: 24,621; Xin: 25,221), with an average of 84.5 reads per tag (X1: 51.4; X2: 141.7; Xin: 46.3). The distribution of the tags in each cell population can be observed in Additional file 2A. DGE is reported to achieve near saturation in genes detected after 6-8 million tags [22]. Furthermore, for moderately to very highly expressed genes (>2 cpm) it occurs with three or even just two million tags [22,34]. Figure 1 shows that saturation was reached at around two million tags for most of the data sets which the distinct tags were mapped to, although the slope for the total number of distinct tags decreases without saturating. It is worth noting that all the reference transcriptome sets performed similarly, achieving a maximum near 20,000 mapped tags. However, when looking at how many distinct tags map to any of those transcriptomes, about 5,000 tags appear not to be shared among all of them (see the “All mapped” and the “All distinct” data series on Figure 1, and further details on mapping below).Figure 1


Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea.

Rodríguez-Esteban G, González-Sastre A, Rojo-Laguna JI, Saló E, Abril JF - BMC Genomics (2015)

Saturation plot for the distinct tags mapped over each reference data set. Tag sequences were randomly taken to build, by steps of 200,000 tags, increasing-size libraries that were then mapped against the reference data sets. Saturation is reached for libraries around two million tags.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4494696&req=5

Fig1: Saturation plot for the distinct tags mapped over each reference data set. Tag sequences were randomly taken to build, by steps of 200,000 tags, increasing-size libraries that were then mapped against the reference data sets. Saturation is reached for libraries around two million tags.
Mentions: Three DGE libraries were obtained from FACS-isolated cell populations X1 (proliferating stem cells, S/G2/M), X2 (a mix of stem cell progeny and proliferating, G0/G1), and Xin (differentiated cells, G0/G1) [30] (Additional file 1). 8,298,210 total reads were sequenced (X1: 3,641,099; X2: 3,488,712; Xin: 1,168,399), representing 98,156 distinct tags (X1: 70,849; X2: 24,621; Xin: 25,221), with an average of 84.5 reads per tag (X1: 51.4; X2: 141.7; Xin: 46.3). The distribution of the tags in each cell population can be observed in Additional file 2A. DGE is reported to achieve near saturation in genes detected after 6-8 million tags [22]. Furthermore, for moderately to very highly expressed genes (>2 cpm) it occurs with three or even just two million tags [22,34]. Figure 1 shows that saturation was reached at around two million tags for most of the data sets which the distinct tags were mapped to, although the slope for the total number of distinct tags decreases without saturating. It is worth noting that all the reference transcriptome sets performed similarly, achieving a maximum near 20,000 mapped tags. However, when looking at how many distinct tags map to any of those transcriptomes, about 5,000 tags appear not to be shared among all of them (see the “All mapped” and the “All distinct” data series on Figure 1, and further details on mapping below).Figure 1

Bottom Line: These results are accessible via web for the community of researchers.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.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.


Related in: MedlinePlus