Limits...
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

Venn stave showing the proportions of the distinct tags mapped over the different reference data sets. Integrating data for Venn diagrams for sets larger than four or five can be a challenging task, so that, a linear projection of such a diagram is provided in the stave—showing the 20 topmost scoring comparisons from 752 different subsets, accounting for 62.26% (18,710 out of 30,053) of total mappings—for ten reference sequence sets: eight transcriptomes, the S. mediterranea ESTs from NCBI dbESTs [39-42], and the latest genome draft AUVC01 [43,44]. Color gradient scale is provided on the bottom bar and it is proportional to the number of unique tags mapped over each sequence subset. X-axis ticks present the number of tags and their relative percent; the numbers on the right Y-axis correspond to the total number of tags mapped into a given sequence sets comparison. It is easy to spot that 15% of the unique reads are mapping onto all the sequence sets.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Venn stave showing the proportions of the distinct tags mapped over the different reference data sets. Integrating data for Venn diagrams for sets larger than four or five can be a challenging task, so that, a linear projection of such a diagram is provided in the stave—showing the 20 topmost scoring comparisons from 752 different subsets, accounting for 62.26% (18,710 out of 30,053) of total mappings—for ten reference sequence sets: eight transcriptomes, the S. mediterranea ESTs from NCBI dbESTs [39-42], and the latest genome draft AUVC01 [43,44]. Color gradient scale is provided on the bottom bar and it is proportional to the number of unique tags mapped over each sequence subset. X-axis ticks present the number of tags and their relative percent; the numbers on the right Y-axis correspond to the total number of tags mapped into a given sequence sets comparison. It is easy to spot that 15% of the unique reads are mapping onto all the sequence sets.

Mentions: In an attempt to recover tags that did not map over the transcripts, tags were also mapped over the S. mediterranea genome assembly draft AUVC01 masked with the S. mediterranea repeats [23,43-45] (Table 1 and Figure 2). The overlap between transcriptomes was high. Although in most cases sets of reads mapping over a single transcriptome has a very low incidence, there were two cases where one could find a relatively small number of tags mapping to only one transcriptome: 327 tags (1.1%) for Labbé et al. 2012; 208 tags (0.7%) for Rohuana et al. 2012; 3,231 tags (10.7%) remarkably mapping only over the genome; and 26.1% of tags (10,617 out of 40,670) not mapping at all. For tags sequenced 10 times or more, the proportion of unmapped tags is similar: 20.5% (6,327 out of 30,806) (Additional file 2B). Even allowing up to two mismatches, 9.36% of the reads remain not mappable to the genome. This is still an important amount, considering that two mismatches is very permissive (it represents almost a 10% of nucleotide substitution in the read with respect to the reference sequence).Table 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)

Venn stave showing the proportions of the distinct tags mapped over the different reference data sets. Integrating data for Venn diagrams for sets larger than four or five can be a challenging task, so that, a linear projection of such a diagram is provided in the stave—showing the 20 topmost scoring comparisons from 752 different subsets, accounting for 62.26% (18,710 out of 30,053) of total mappings—for ten reference sequence sets: eight transcriptomes, the S. mediterranea ESTs from NCBI dbESTs [39-42], and the latest genome draft AUVC01 [43,44]. Color gradient scale is provided on the bottom bar and it is proportional to the number of unique tags mapped over each sequence subset. X-axis ticks present the number of tags and their relative percent; the numbers on the right Y-axis correspond to the total number of tags mapped into a given sequence sets comparison. It is easy to spot that 15% of the unique reads are mapping onto all the sequence sets.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Venn stave showing the proportions of the distinct tags mapped over the different reference data sets. Integrating data for Venn diagrams for sets larger than four or five can be a challenging task, so that, a linear projection of such a diagram is provided in the stave—showing the 20 topmost scoring comparisons from 752 different subsets, accounting for 62.26% (18,710 out of 30,053) of total mappings—for ten reference sequence sets: eight transcriptomes, the S. mediterranea ESTs from NCBI dbESTs [39-42], and the latest genome draft AUVC01 [43,44]. Color gradient scale is provided on the bottom bar and it is proportional to the number of unique tags mapped over each sequence subset. X-axis ticks present the number of tags and their relative percent; the numbers on the right Y-axis correspond to the total number of tags mapped into a given sequence sets comparison. It is easy to spot that 15% of the unique reads are mapping onto all the sequence sets.
Mentions: In an attempt to recover tags that did not map over the transcripts, tags were also mapped over the S. mediterranea genome assembly draft AUVC01 masked with the S. mediterranea repeats [23,43-45] (Table 1 and Figure 2). The overlap between transcriptomes was high. Although in most cases sets of reads mapping over a single transcriptome has a very low incidence, there were two cases where one could find a relatively small number of tags mapping to only one transcriptome: 327 tags (1.1%) for Labbé et al. 2012; 208 tags (0.7%) for Rohuana et al. 2012; 3,231 tags (10.7%) remarkably mapping only over the genome; and 26.1% of tags (10,617 out of 40,670) not mapping at all. For tags sequenced 10 times or more, the proportion of unmapped tags is similar: 20.5% (6,327 out of 30,806) (Additional file 2B). Even allowing up to two mismatches, 9.36% of the reads remain not mappable to the genome. This is still an important amount, considering that two mismatches is very permissive (it represents almost a 10% of nucleotide substitution in the read with respect to the reference sequence).Table 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