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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

Online data sets and DGE data on Smed454 GBrowse2.A - To facilitate browsing of mapped tags over the transcripts we have worked with, we provide a dynamic table interface that paginates through the huge lists of records. This jQuery [112] interface allows the user to easily sort the output table by a given column—just by clicking on the column label—or to search for specific values on the cells—using either the form box just below the column labels or the advanced search available from the magnifying glass icon at the bottom of the table. Three tables, like the one in the background, contain the equivalences between contigs from different transcriptomes, as well as functional annotations, always focusing on the Smed454 data set. The other tables, like the one in the foreground, contain the tag mappings for each single transcriptomes considered to date. B - Previously published Smed454 database [10] has been ported to GBrowse2 in order to facilitate navigating through the transcripts annotations, such as predicted domains from Pfam, assembly reads mapping, etc. This panel shows the annotations on Smed-wi-3 homologous contig as an example. A customized track allows the integration of information about mapped DGE tags into single or combined tracks; tags are represented as boxes with height proportional to log of the normalized tag counts, the rank and the strand for the tag hit are shown in the label just below that box. Bottom left blue box zooms into one of those combined tracks to visualize the pop-up box that the user can recover when moving the mouse over a given tag feature. In addition, bottom right red box displays the details page one can get when clicking on a tag feature.
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Fig4: Online data sets and DGE data on Smed454 GBrowse2.A - To facilitate browsing of mapped tags over the transcripts we have worked with, we provide a dynamic table interface that paginates through the huge lists of records. This jQuery [112] interface allows the user to easily sort the output table by a given column—just by clicking on the column label—or to search for specific values on the cells—using either the form box just below the column labels or the advanced search available from the magnifying glass icon at the bottom of the table. Three tables, like the one in the background, contain the equivalences between contigs from different transcriptomes, as well as functional annotations, always focusing on the Smed454 data set. The other tables, like the one in the foreground, contain the tag mappings for each single transcriptomes considered to date. B - Previously published Smed454 database [10] has been ported to GBrowse2 in order to facilitate navigating through the transcripts annotations, such as predicted domains from Pfam, assembly reads mapping, etc. This panel shows the annotations on Smed-wi-3 homologous contig as an example. A customized track allows the integration of information about mapped DGE tags into single or combined tracks; tags are represented as boxes with height proportional to log of the normalized tag counts, the rank and the strand for the tag hit are shown in the label just below that box. Bottom left blue box zooms into one of those combined tracks to visualize the pop-up box that the user can recover when moving the mouse over a given tag feature. In addition, bottom right red box displays the details page one can get when clicking on a tag feature.

Mentions: Predicted functional domains for several of the selected transcript candidates. Functional domains annotation based on Pfam hidden Markov models. Legend box shows a classification of the domain hits based on its match to complete domain model; the boxes height is proportional to the E-value score provided for each match. Significant matches were considered for HMMER [117] E-value < 0.001; however, low-significance matches are also shown, as well as hits to Pfam-B models produced by automated alignment protocols. Further annotation over Smed454 transcripts is already available at the GBrowse2 URL planarian.bio.ub.edu/gbrowse/smed454_transcriptome; an example can also be found on Figure 4.


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)

Online data sets and DGE data on Smed454 GBrowse2.A - To facilitate browsing of mapped tags over the transcripts we have worked with, we provide a dynamic table interface that paginates through the huge lists of records. This jQuery [112] interface allows the user to easily sort the output table by a given column—just by clicking on the column label—or to search for specific values on the cells—using either the form box just below the column labels or the advanced search available from the magnifying glass icon at the bottom of the table. Three tables, like the one in the background, contain the equivalences between contigs from different transcriptomes, as well as functional annotations, always focusing on the Smed454 data set. The other tables, like the one in the foreground, contain the tag mappings for each single transcriptomes considered to date. B - Previously published Smed454 database [10] has been ported to GBrowse2 in order to facilitate navigating through the transcripts annotations, such as predicted domains from Pfam, assembly reads mapping, etc. This panel shows the annotations on Smed-wi-3 homologous contig as an example. A customized track allows the integration of information about mapped DGE tags into single or combined tracks; tags are represented as boxes with height proportional to log of the normalized tag counts, the rank and the strand for the tag hit are shown in the label just below that box. Bottom left blue box zooms into one of those combined tracks to visualize the pop-up box that the user can recover when moving the mouse over a given tag feature. In addition, bottom right red box displays the details page one can get when clicking on a tag feature.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Online data sets and DGE data on Smed454 GBrowse2.A - To facilitate browsing of mapped tags over the transcripts we have worked with, we provide a dynamic table interface that paginates through the huge lists of records. This jQuery [112] interface allows the user to easily sort the output table by a given column—just by clicking on the column label—or to search for specific values on the cells—using either the form box just below the column labels or the advanced search available from the magnifying glass icon at the bottom of the table. Three tables, like the one in the background, contain the equivalences between contigs from different transcriptomes, as well as functional annotations, always focusing on the Smed454 data set. The other tables, like the one in the foreground, contain the tag mappings for each single transcriptomes considered to date. B - Previously published Smed454 database [10] has been ported to GBrowse2 in order to facilitate navigating through the transcripts annotations, such as predicted domains from Pfam, assembly reads mapping, etc. This panel shows the annotations on Smed-wi-3 homologous contig as an example. A customized track allows the integration of information about mapped DGE tags into single or combined tracks; tags are represented as boxes with height proportional to log of the normalized tag counts, the rank and the strand for the tag hit are shown in the label just below that box. Bottom left blue box zooms into one of those combined tracks to visualize the pop-up box that the user can recover when moving the mouse over a given tag feature. In addition, bottom right red box displays the details page one can get when clicking on a tag feature.
Mentions: Predicted functional domains for several of the selected transcript candidates. Functional domains annotation based on Pfam hidden Markov models. Legend box shows a classification of the domain hits based on its match to complete domain model; the boxes height is proportional to the E-value score provided for each match. Significant matches were considered for HMMER [117] E-value < 0.001; however, low-significance matches are also shown, as well as hits to Pfam-B models produced by automated alignment protocols. Further annotation over Smed454 transcripts is already available at the GBrowse2 URL planarian.bio.ub.edu/gbrowse/smed454_transcriptome; an example can also be found on Figure 4.

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