Mus musculus strain:Mix of FVB/NJ, C57BL/6, and 129/Sv
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ABSTRACT:
PROVIDER: PRJNA246494 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1278760_1.fastq.gz | Fastqsanger.gz | |||
| SRR1278760_2.fastq.gz | Fastqsanger.gz | |||
| SRR1536771.fastq.gz | Fastqsanger.gz |
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Project description:BackgroundCommunicative behaviors play a vital role in mammals and are highly relevant to human neurodevelopmental conditions. Mice produce communicative vocalizations that occur in the ultrasonic range, which are commonly analyzed within the Avisoft recording system. Fully automated programs such as the Mouse Song Analyzer in MATLAB, have been developed to analyze USVs in a shorter time period, however, no study has compared the accuracy of MATLAB to Avisoft.New methodIn order to determine MATLAB's accuracy, we used data from four different mouse strains and assessed whether the total number of USVs detected was similar between systems.ResultsWe found that there was a high correlation between systems for the number of USVs emitted from C57BL/6 and NS-Pten mice however, Avisoft detected significantly more USVs than MATLAB for both strains. For Fmr1-FVB.129 and 129 mice, large correlations were observed between systems and no significant difference was present in the USVs detected. A partial correlation was run to control for the covariates: sex, age, strain, and treatment, and found that only strain substantially influences the relationship between the USVs detected in Avisoft and those detected in MATLAB.Comparison with existing methodThese findings demonstrate that there is a high degree of agreement between Avisoft and the Mouse Song Analyzer however, Avisoft does detect significantly more USVs depending on the strain assessed.ConclusionsTherefore, there are relative advantages and disadvantages with both systems that vocalization researchers should be aware of when interpreting USV results, and when using either system.
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Project description:Mus musculus strain:129/FVB/Black Swiss Raw sequence reads
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Project description:BackgroundThe FVB/NJ mouse strain has its origins in a colony of outbred Swiss mice established in 1935 at the National Institutes of Health. Mice derived from this source were selectively bred for sensitivity to histamine diphosphate and the B strain of Friend leukemia virus. This led to the establishment of the FVB/N inbred strain, which was subsequently imported to the Jackson Laboratory and designated FVB/NJ. The FVB/NJ mouse has several distinct characteristics, such as large pronuclear morphology, vigorous reproductive performance, and consistently large litters that make it highly desirable for transgenic strain production and general purpose use.ResultsUsing next-generation sequencing technology, we have sequenced the genome of FVB/NJ to approximately 50-fold coverage, and have generated a comprehensive catalog of single nucleotide polymorphisms, small insertion/deletion polymorphisms, and structural variants, relative to the reference C57BL/6J genome. We have examined a previously identified quantitative trait locus for atherosclerosis susceptibility on chromosome 10 and identify several previously unknown candidate causal variants.ConclusionThe sequencing of the FVB/NJ genome and generation of this catalog has increased the number of known variant sites in FVB/NJ by a factor of four, and will help accelerate the identification of the precise molecular variants that are responsible for phenotypes observed in this widely used strain.
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