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

    Metadata Updated: November 10, 2020

    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.

    Access & Use Information

    Public: This dataset is intended for public access and use. License: Creative Commons CCZero

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    Dates

    Metadata Created Date November 10, 2020
    Metadata Updated Date November 10, 2020

    Metadata Source

    Harvested from USDA JSON

    Additional Metadata

    Resource Type Dataset
    Metadata Created Date November 10, 2020
    Metadata Updated Date November 10, 2020
    Publisher Agricultural Research Service
    Maintainer
    Identifier a0383cef-ac36-486d-9980-9e72530e5977
    Data Last Modified 2020-05-20
    Public Access Level public
    Bureau Code 005:18
    Metadata Context https://project-open-data.cio.gov/v1.1/schema/catalog.jsonld
    Schema Version https://project-open-data.cio.gov/v1.1/schema
    Catalog Describedby https://project-open-data.cio.gov/v1.1/schema/catalog.json
    Harvest Object Id 89a1a41f-d207-491c-9522-e2528946b879
    Harvest Source Id d3fafa34-0cb9-48f1-ab1d-5b5fdc783806
    Harvest Source Title USDA JSON
    License https://creativecommons.org/publicdomain/zero/1.0/
    Program Code 005:040
    Source Datajson Identifier True
    Source Hash b2442d5f37b097f34cce66d6aa4e1633a998a6ad
    Source Schema Version 1.1

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