transcription (genetics) | Ag Data Commons

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: 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: Gene expression during the early stages of host perception and attachment in adult female Rhipicephalus microplus ticks

This study produced a comprehensive transcriptome from newly molted adult ticks and will provide a useful resource for studies of tick feeding and host perception and also assist genome annotation refinements.

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Data from: Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean

Soybean aphid (*Aphis glycines*; SBA) and soybean cyst nematode (*Heterodera glycines*; SCN) are two major pests of soybean (*Glycine max*) in the United States of America. This study aims to characterize three-way interactions among soybean, SBA, and SCN using both demographic and genetic datasets. The data comprises of 47 libraries that are useful for further analyses of important genes, which are involved in interaction effects of SBA and SCN on soybean.

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Data from: Long-Distance Transportation Causes Temperature Stress in the Honey Bee, Apis mellifera (Hymenoptera: Apidae)

To test how temperature may contribute to bee (*Apis mellifera*) transportation stress, temperature sensors were placed in hives in different locations and orientations on the trailer during shipping. Colony size prior to shipping significantly contributed to loss of population immediately after shipping which contributed to colony failure with smaller colonies more likely to fail and fail faster. Colony size also affects thermoregulation and temperature stress.

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Data from: Sporobolus stapfianus: Insights into desiccation tolerance in the resurrection grasses from linking transcriptomics to metabolomics

Non-targeted metabolomics, combined with transcriptomics via a NimbleGen array platform, are used to study how gene expression and metabolite profiles can be linked to generate a more detailed mechanistic appreciation of the cellular response to both desiccation and rehydration in the C4 resurrection grass, *Sporobolus stapfianus* Gandoger, as a member of a group of important forage grasses.

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De novo transcriptome assembly and annotations for wheat curl mite (Aceria tosichella)

To study the impact of wheat streak mosaic virus on global gene expression in wheat curl mite, we generated a de novo transcriptome assembly using 50 x 50 paired end reads from the Illumina HiSeq 2500. Reads were assembled using Trinity (version 2.0.6) and contigs greater than 200 nt were retained. All assembled transcripts were annotated using the Trinotate pipeline using blastp searches against the Swiss-prot/Uni-Prot database, blastx searches against the Swiss-prot/Uni-Prot databases, HMM searches against the Pfam-A database, blastp searches against the non-redundant protein database, and signalP and tmHMM predictions. To reduce noise from low abundance transcripts not well supported by the data, we filtered the assembly to retain only those transcripts with TPM values >=0.5.

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Annotations of Unigenes Assembled from Schizaphis graminum and Sipha flava

Transcriptomes were assembled de novo from pools of adult aphids that were feeding on sorghum and switchgrass. Reads from all replicates were pooled, normalized in silico to 25X coverage, and assembled using Trinity. Only the most abundant isoform for each unigene was retained for annotation and unigenes with transcripts per million mapped reads (TPM) less than 0.5 were removed from the dataset. The remaining unigenes were annotated using Trinotate with BLASTP comparisons against the Swiss-Prot/UniProt database. In addition, Pfam-A assignments were computed using hmmer, signal peptide predictions were performed using SignalP, and transmembrane domain predictions were performed using tmHMM. Gene ontology (GO assignments) were retrieved from Trinotate using the highest scoring BLASTp matches as queries.

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Data from: Key molecular processes of the diapause to post‐diapause quiescence transition in the alfalfa leafcutting bee Megachile rotundata identified by comparative transcriptome analysis

Insect diapause (dormancy) synchronizes an insect's life cycle to seasonal changes in the abiotic and biotic resources required for development and reproduction. Transcription analysis of diapause to post‐diapause quiescent transition in the alfalfa leafcutting bee *Megachile rotundata* Fabricius identifies 643 post‐diapause up‐regulated gene transcripts and 242 post‐diapause down‐regulated transcripts. The log2 fold change in gene expression levels ranges from −5 to 7. Transcripts from several pivotal diapause‐related processes, including chromatin remodelling, cellular signalling pathways, microRNA processing, anaerobic glycolysis, cell cycle arrest and neuroendocrine control, are identified as being differentially expressed during the diapause to post‐diapause transition. In conjunction with studies from other insect species, the data indicate that there are several common mechanisms of diapause control and maintenance.

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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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