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Ag Data Commons migration begins October 18, 2023

The Ag Data Commons is migrating to a new platform – an institutional portal on Figshare. Starting October 18 the current system will be available for search and download only. Submissions will resume after the launch of our portal on Figshare in November. Stay tuned for details!

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.

    Data from: Data of epigenomic profiling of histone marks and CTCF binding sites in bovine rumen epithelial primary cells before and after butyrate treatment

      To explore the bovine functional genomic elements and the vital roles of butyrate on the epigenetic modifications of bovine genomic activities, we generated and deposited the genome-wide datasets of transcript factor binding sites of CTCF (CCCTC-binding factor, insulator binding protein), histone methylation (H3H27me3, H3K4me1, H3K4me3) and histone acetylation (H3K27ac) from bovine rumen epithelial primary cells (REPC) before and after butyrate treatment (https://doi.org/10.1186/s12915-019-0687-8). This dataset provides detailed information on experiment design, data generation, data quality assessment and guideline for data re-use.

      Data from: Profile of the Spleen Transcriptome in Beef Steers with Variation in Gain and Feed Intake

        This study examines the spleen in beef steers, a major lymphatic organ near the digestive tract, to determine whether it was also influencing individual feed efficiency status through immune responses. A total of 1216 genes were identified as differentially expressed. Data suggests the splenic contribution to some of the underlying variation among gain and intake may be a result of immune function and stress response. In addition, some of the differences in immune response functions may be related to gene copy number.

        National Animal Nutrition Program (NANP) Modeling: Animal Performance Information

          This page allows you to download data from the National Animal Nutrition Program animal performance data repository directly into an Excel file. Component data sets: [NRC Dairy Report](https://animalnutrition.org/node/12); [Lofgreen Garrett](https://animalnutrition.org/node/13); [Environmental Stress](https://animalnutrition.org/node/27): [to follow]; [Beef Digestiblity](https://animalnutrition.org/beef-digestibility): [to follow]; [USDA Beltsville Agricultural Research Center](https://animalnutrition.org/usda-barc).

          Data from: Pyrosequencing-Based Analysis of the Microbiome Associated with the Horn Fly, Haematobia irritans

            The bacterial 16S tag-encoded FLX-titanium amplicon pyrosequencing (bTEFAP) method was used to carry out the classification analysis of bacterial flora in adult female and male horn flies and horn fly eggs. The bTEFAP method identified 16S rDNA sequences in our samples which allowed the identification of various prokaryotic taxa associated with the life stage examined. This is the first comprehensive report of bacterial flora associated with the horn fly using a culture-independent method. Several rumen, environmental, symbiotic and pathogenic bacteria associated with the horn fly were identified and quantified. This is the first report of the presence of Wolbachia in horn flies of USA origin and is the first report of the presence of Rikenella in an obligatory blood feeding insect.