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Splicing landscape of the eight collaborative cross founder strains

Overview of attention for article published in BMC Genomics, February 2015
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Title
Splicing landscape of the eight collaborative cross founder strains
Published in
BMC Genomics, February 2015
DOI 10.1186/s12864-015-1267-0
Pubmed ID
Authors

Christina L Zheng, Beth Wilmot, Nicole AR Walter, Denesa Oberbeck, Sunita Kawane, Robert P Searles, Shannon K McWeeney, Robert Hitzemann

Abstract

BackgroundThe Collaborative Cross (CC) is a large panel of genetically diverse recombinant inbred mouse strains specifically designed to provide a systems genetics resource for the study of complex traits. In part, the utility of the CC stems from the extensive genome-wide annotations of founder strain sequence and structural variation. Still missing, however, are transcriptome-specific annotations of the CC founder strains that could further enhance the utility of this resource.ResultsWe provide a comprehensive survey of the splicing landscape of the 8 CC founder strains by leveraging the high level of alternative splicing within the brain. Using deep transcriptome sequencing, we found that a majority of the splicing landscape is conserved among the 8 strains, with ~65% of junctions being shared by at least 2 strains. We, however, found a large number of potential strain-specific splicing events as well, with an average of ~3000 and ~500 with ¿3 and ¿10 sequence read coverage, respectively, within each strain. To better understand strain-specific splicing within the CC founder strains, we defined criteria for and identified high-confidence strain-specific splicing events. These splicing events were defined as exon-exon junctions 1) found within only one strain, 2) with a read coverage ¿10, and 3) defined by a canonical splice site. With these criteria, a total of 1509 high-confidence strain-specific splicing events were identified, with the majority found within two of the wild-derived strains, CAST and PWK. Strikingly, the overwhelming majority, 94%, of these strain-specific splicing events are not yet annotated. Strain-specific splicing was also located within genomic regions recently reported to be over- and under-represented within CC populations.ConclusionsPhenotypic characterization of CC populations is increasing; thus these results will not only aid in further elucidating the transcriptomic architecture of the individual CC founder strains, but they will also help in guiding the utilization of the CC populations in the study of complex traits. This report is also the first to establish guidelines in defining and identifying strain-specific splicing across different mouse strains.

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Geographical breakdown

Country Count As %
United Kingdom 1 4%
United States 1 4%
Unknown 21 91%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 7 30%
Researcher 4 17%
Student > Master 3 13%
Student > Doctoral Student 2 9%
Student > Bachelor 1 4%
Other 2 9%
Unknown 4 17%
Readers by discipline Count As %
Agricultural and Biological Sciences 7 30%
Biochemistry, Genetics and Molecular Biology 6 26%
Social Sciences 2 9%
Nursing and Health Professions 1 4%
Engineering 1 4%
Other 0 0%
Unknown 6 26%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. 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 07 February 2015.
All research outputs
#15,321,186
of 22,787,797 outputs
Outputs from BMC Genomics
#6,689
of 10,647 outputs
Outputs of similar age
#209,648
of 352,181 outputs
Outputs of similar age from BMC Genomics
#158
of 248 outputs
Altmetric has tracked 22,787,797 research outputs across all sources so far. This one is in the 22nd percentile – i.e., 22% of other outputs scored the same or lower than it.
So far Altmetric has tracked 10,647 research outputs from this source. They receive a mean Attention Score of 4.7. This one is in the 29th percentile – i.e., 29% of its peers scored the same or lower than it.
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