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X Demographics
Mendeley readers
Attention Score in Context
| 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. |
X Demographics
The data shown below were collected from the profiles of 24 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United Kingdom | 9 | 38% |
| United States | 2 | 8% |
| France | 1 | 4% |
| Norway | 1 | 4% |
| Guinea | 1 | 4% |
| Unknown | 10 | 42% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 13 | 54% |
| Members of the public | 10 | 42% |
| Practitioners (doctors, other healthcare professionals) | 1 | 4% |
Mendeley readers
The data shown below were compiled from readership statistics for 82 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Norway | 2 | 2% |
| Germany | 1 | 1% |
| Slovakia | 1 | 1% |
| Unknown | 78 | 95% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 21 | 26% |
| Student > Ph. D. Student | 13 | 16% |
| Student > Master | 13 | 16% |
| Student > Bachelor | 8 | 10% |
| Student > Doctoral Student | 3 | 4% |
| Other | 11 | 13% |
| Unknown | 13 | 16% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 39 | 48% |
| Biochemistry, Genetics and Molecular Biology | 11 | 13% |
| Environmental Science | 5 | 6% |
| Computer Science | 4 | 5% |
| Immunology and Microbiology | 4 | 5% |
| Other | 2 | 2% |
| Unknown | 17 | 21% |
Attention Score in Context
This research output has an Altmetric Attention Score of 15. 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
#2,391,555
of 25,161,628 outputs
Outputs from BMC Genomics
#635
of 11,174 outputs
Outputs of similar age
#26,680
of 245,033 outputs
Outputs of similar age from BMC Genomics
#21
of 245 outputs
Altmetric has tracked 25,161,628 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 11,174 research outputs from this source. They receive a mean Attention Score of 4.8. This one has done particularly well, scoring higher than 94% 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 245,033 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 89% of its contemporaries.
We're also able to compare this research output to 245 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 91% of its contemporaries.