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De novo assembly of the Carcinus maenas transcriptome and characterization of innate immune system pathways

Overview of attention for article published in BMC Genomics, June 2015
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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 (88th percentile)

Mentioned by

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24 tweeters

Citations

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39 Dimensions

Readers on

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72 Mendeley
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Title
De novo assembly of the Carcinus maenas transcriptome and characterization of innate immune system pathways
Published in
BMC Genomics, June 2015
DOI 10.1186/s12864-015-1667-1
Pubmed ID
Authors

Bas Verbruggen, Lisa K. Bickley, Eduarda M. Santos, Charles R. Tyler, Grant D. Stentiford, Kelly S. Bateman, Ronny van Aerle

Abstract

The European shore crab, Carcinus maenas, is used widely in biomonitoring, ecotoxicology and for studies into host-pathogen interactions. It is also an important invasive species in numerous global locations. However, the genomic resources for this organism are still sparse, limiting research progress in these fields. To address this resource shortfall we produced a C. maenas transcriptome, enabled by the progress in next-generation sequencing technologies, and applied this to assemble information on the innate immune system in this species. We isolated and pooled RNA for twelve different tissues and organs from C. maenas individuals and sequenced the RNA using next generation sequencing on an Illumina HiSeq 2500 platform. After de novo assembly a transcriptome was generated encompassing 212,427 transcripts (153,699 loci). The transcripts were filtered, annotated and characterised using a variety of tools (including BLAST, MEGAN and RSEM) and databases (including NCBI, Gene Ontology and KEGG). There were differential patterns of expression for between 1,223 and 2,741 transcripts across tissues and organs with over-represented Gene Ontology terms relating to their specific function. Based on sequence homology to immune system components in other organisms, we show both the presence of transcripts for a series of known pathogen recognition receptors and response proteins that form part of the innate immune system, and transcripts representing the RNAi, Toll-like receptor signalling, IMD and JAK/STAT pathways. We have produced an assembled transcriptome for C. maenas that provides a significant molecular resource for wide ranging studies in this species. Analysis of the transcriptome has revealed the presence of a series of known targets and functional pathways that form part of their innate immune system and illustrate tissue specific differences in their expression patterns.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 72 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Norway 2 3%
Germany 1 1%
Slovakia 1 1%
Unknown 68 94%

Demographic breakdown

Readers by professional status Count As %
Researcher 21 29%
Student > Ph. D. Student 13 18%
Student > Master 12 17%
Student > Bachelor 6 8%
Student > Doctoral Student 3 4%
Other 10 14%
Unknown 7 10%
Readers by discipline Count As %
Agricultural and Biological Sciences 37 51%
Biochemistry, Genetics and Molecular Biology 9 13%
Environmental Science 5 7%
Computer Science 4 6%
Immunology and Microbiology 4 6%
Other 0 0%
Unknown 13 18%

Attention Score in Context

This research output has an Altmetric Attention Score of 14. 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 12 March 2016.
All research outputs
#1,756,866
of 18,552,435 outputs
Outputs from BMC Genomics
#571
of 9,601 outputs
Outputs of similar age
#22,260
of 199,457 outputs
Outputs of similar age from BMC Genomics
#1
of 1 outputs
Altmetric has tracked 18,552,435 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 90th percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 9,601 research outputs from this source. They receive a mean Attention Score of 4.5. This one has done particularly well, scoring higher than 94% of its peers.
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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