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Data from: Deer keds and blacklegged ticks infesting ungulates in the United States: molecular detection of Bartonella spp., Rickettsia spp., Anaplasma spp., and Borrelia spp.

    Deer keds are blood-feeding flies from which several human and animal pathogens have been detected, including the causative agent of Lyme Disease (Borrelia burgdorferi). Cervids, which are the primary hosts of deer keds, are not natural reservoirs of B. burgdorferi, and it has been suggested that deer keds may acquire bacterial pathogens by co-feeding near ticks that are infected with the bacteria. We tested this hypothesis by using a molecular assay to screen for presence of Anaplasma spp., Bartonella spp., Borrelia spp., and Rickettsia spp. in specimens of European deer keds (n=306) and blacklegged ticks (n=315) collected from 38 individual white-tailed deer in Pennsylvania. There was limited similarity in the bacterial DNA detected between these ectoparasites per host, suggesting that co-feeding may not be a mechanism by which deer keds acquire these bacteria.

    Data from: Attraction, mobility, and preference by Lasioderma serricorne (F.) (Coleoptera: Ptinidae) to microbially-mediated volatile emissions by two species of fungi in stored grain

      Our goals were to 1) isolate, and culture two fungal morphotypes, 2) characterize the volatile emissions from grain inoculated by each fungal morphotype (Aspergillus flavus or Fusarium spp.) compared to uninoculated and sanitized grain, and 3) understand how MVOCs from each morphotype affects mobility, attraction, and preference by L. serricorne.

      Data from polishCLR: Example input genome assemblies

        In order to produce the best possible *de novo*, chromosome-scale genome assembly from error prone Pacific BioSciences continuous long reads (CLR) reads, we developed a publicly available, flexible and reproducible workflow that is containerized so it can be run on any conventional HPC, called polishCLR. This dataset provides example input primary contig assemblies to test and reproduce the demonstrated utility of our workflow.

        Data from: Estimation of pool construction and technical error

          Animals were incorporated into pools in different proportions to estimate error and evaluate factors influencing error. Animals were incorporated into 2 types of pools, sub-pools and super pools. Within phenotype, liver abscess or normal, 16 animals were combined into 4 sub-pools, 4 animals per sub-pool in parts of 1:2:3:4. Sub-pools were constructed based on crushed frozen liver tissue mass. Within phenotype, 4 sub-pools were incorporated into 2 super pools in parts of 1:2:3:4 for super pool 1 and 3:4:1:2 for super pool 2. Super pools were made based on DNA quantity. Errors in DNA quantification would create error in forming super pools from sub-pools and variation in cell content or DNA content of liver tissue would result in error in combining sub-pools from animals.

          Data from: Genomic regions associated with Mycoplasma ovipneumoniae presence in nasal secretions of domestic sheep

            Genotypes of significant SNPs in all breed and individual breed analysis with detected *Mycoplasma ovipneumoniae* DNA copy number and log10 *M. ovipneumoniae* DNA copy number. SNP is denoted in the column headers with its rs number and the first 7 SNP are from the all breed analysis, the following 9 SNP from the Rambouillet analysis, the following 3 from the Polypay analysis, and the final 9 from the Suffolk analysis.

            Evaluating accuracy of DNA pool construction based on white blood cell counts

              Pooling individual samples prior to DNA extraction can mitigate the cost of DNA extraction and genotyping; however, these methods need to accurately generate equal representation of individuals within pools. This data set was generated to determine accuracy of pool construction based on white blood cell counts compared to two common DNA quantification methods. The dataset includes: 1) pooling allele frequencies (PAF) for all pools and individual animals computed from normalized intensities for red (X) and green (Y); PAF = X/(X+Y). 2) Genotypes or number of copies of B(green) allele (0,1,2). 3) Definitions for each sample.

              Data from: Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

                We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly.