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Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation

Overview of attention for article published in Genome Biology (Online Edition), August 2018
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  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (84th percentile)

Mentioned by

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26 tweeters

Citations

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27 Dimensions

Readers on

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91 Mendeley
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Title
Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation
Published in
Genome Biology (Online Edition), August 2018
DOI 10.1186/s13059-018-1498-x
Pubmed ID
Authors

Lakshmipuram Seshadri Swapna, Alyssa M. Molinaro, Nicole Lindsay-Mosher, Bret J. Pearson, John Parkinson

Abstract

In the Lophotrochozoa/Spiralia superphylum, few organisms have as high a capacity for rapid testing of gene function and single-cell transcriptomics as the freshwater planaria. The species Schmidtea mediterranea in particular has become a powerful model to use in studying adult stem cell biology and mechanisms of regeneration. Despite this, systematic attempts to define gene complements and their annotations are lacking, restricting comparative analyses that detail the conservation of biochemical pathways and identify lineage-specific innovations. In this study we compare several transcriptomes and define a robust set of 35,232 transcripts. From this, we perform systematic functional annotations and undertake a genome-scale metabolic reconstruction for S. mediterranea. Cross-species comparisons of gene content identify conserved, lineage-specific, and expanded gene families, which may contribute to the regenerative properties of planarians. In particular, we find that the TRAF gene family has been greatly expanded in planarians. We further provide a single-cell RNA sequencing analysis of 2000 cells, revealing both known and novel cell types defined by unique signatures of gene expression. Among these are a novel mesenchymal cell population as well as a cell type involved in eye regeneration. Integration of our metabolic reconstruction further reveals the extent to which given cell types have adapted energy and nucleotide biosynthetic pathways to support their specialized roles. In general, S. mediterranea displays a high level of gene and pathway conservation compared with other model systems, rendering it a viable model to study the roles of these pathways in stem cell biology and regeneration.

Twitter Demographics

The data shown below were collected from the profiles of 26 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 91 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 91 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 25 27%
Student > Bachelor 11 12%
Researcher 11 12%
Student > Master 9 10%
Student > Doctoral Student 5 5%
Other 12 13%
Unknown 18 20%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 34 37%
Agricultural and Biological Sciences 24 26%
Computer Science 4 4%
Immunology and Microbiology 3 3%
Environmental Science 2 2%
Other 4 4%
Unknown 20 22%

Attention Score in Context

This research output has an Altmetric Attention Score of 13. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 06 January 2019.
All research outputs
#1,894,698
of 18,643,581 outputs
Outputs from Genome Biology (Online Edition)
#1,694
of 3,733 outputs
Outputs of similar age
#45,154
of 287,711 outputs
Outputs of similar age from Genome Biology (Online Edition)
#1
of 1 outputs
Altmetric has tracked 18,643,581 research outputs across all sources so far. Compared to these this one has done well and is in the 89th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 3,733 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 26.8. This one has gotten more attention than average, scoring higher than 54% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 287,711 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 84% of its contemporaries.
We're also able to compare this research output to 1 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them