metabolism | Ag Data Commons

Supporting Materials: Skeletal muscle transcriptome in myoglobin knockout mice

Excel file with RNASeq-derived results comparing wildtype vs. myoglobin knockout mice, gastrocnemius and soleus muscles. Male and female mice were fed a 45% of energy high fat diet for ~13 wk prior to tissue collection.

Supporting Materials: Brown adipose tissue transcriptome in myoglobin knockout mice

RNASeq-derived mRNA abundance patterns in the intrascapular brown adipose tissue (BAT) of female and male mice, comparing wildtype to homozygous myoglobin knockout animals.

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.

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Data from: Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations

The first complete global landscape of regulatory elements in cattle is presented and the dynamics of chromatin states in rumen epithelial cells induced by the rumen developmental regulator - butyrate- are explored.

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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.

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Data from: Responses of Aspergillus flavus to Oxidative Stress Are Related to Fungal Development Regulator, Antioxidant Enzyme, and Secondary Metabolite Biosynthetic Gene Expression

In order to better understand isolate-specific oxidative stress responses, the transcriptional responses of field isolates of *Aspergillus flavus* are examined with varying levels of aflatoxin production (NRRL3357, AF13, and Tox4) to H2O2-induced oxidative stress using an RNA sequencing approach.

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Data from: Exercise plasma metabolomics and xenometabolomics in obese, sedentary, insulin-resistant women: impact of a fitness and weight loss intervention

Plasma metabolite patterns were determined during exercise and recovery in overnight-fasted sedentary, obese, insulin resistant women under controlled conditions of diet and physical activity to test the hypothesisis that improved fitness and insulin sensitivity following a ~14 wk training and weight loss intervention would lead to fixed workload plasma metabolomics signatures reflective of metabolic health and muscle metabolism. Supporting Materials include graphs of blood patterns of metabolites in adult women during a sub-maximal exercise bout and recovery period, and primary data in spreadsheet format on model performance, exercise and recovery, and correlation statistics for metabolites.

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Data from: A Whole Genome Assembly of the Horn Fly, Haematobia irritans, and Prediction of Genes with Roles in Metabolism and Sex Determination

To provide a foundation for identification of genomic loci for insecticide resistance and for discovery of new control technology, we report the sequencing, assembly, and annotation of the horn fly genome.

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Data from: Metabolic Coevolution in the Bacterial Symbiosis of Whiteflies and Related Plant Sap-Feeding Insects

Genomic decay is a common feature of intracellular bacteria that have entered into symbiosis with plant sap-feeding insects. This study of the whitefly Bemisia tabaci and two bacteria (Portiera aleyrodidarum and Hamiltonella defensa) cohoused in each host cell investigated whether the decay of Portiera metabolism genes is complemented by host and Hamiltonella genes, and compared the metabolic traits of the whitefly symbiosis with other sap-feeding insects (aphids, psyllids, and mealybugs).

Data from: Condition‐dependent co‐regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum

The capability of the ascomycete *Neofusicoccum parvum* to colonize woody tissue, combined with the secretion of phytotoxic compounds, is thought to underlie its pathogenicity and virulence. The repertoire of virulence factors and their transcriptional dynamics as the fungus feeds on different substrates and colonizes the woody stem are described and a highly contiguous genome is assembled and annotated using single‐molecule real‐time DNA sequencing.

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