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Alternative splicing in the obligate biotrophic oomycete pathogen, Pseudoperonospora cubensis

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  • We re-sequenced the Pseudoperonospora cubensis transcriptome to provide the first extensive transcriptome-wide survey of alternative splicing in an obligate biotrophic pathogen during host infection. The libraries from biological replicates of cucumber leaves infected with Ps. cubensis for 2, 3, 4, and 8 days post inoculation (dpi) were re-sequenced using 100-mer paired-end (PE) sequencing on four channels of an Illumina HiSeq. As a first step in the characterization of alternative splicing, we used the RNA-Seq reads to reannotate the Ps. cubensis genome, which is deposited as a gff file, along with a relational table that associates the most current annotation to the previous Ps. cubensis annotation.
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  • Burkhardt, Alyssa; Buchanan, Alex; Cumbie, Jason S.; Savory, Elizabeth, A.; Chang, Jeff H.; Day, Brad (2014): Alternative splicing in the obligate biotrophic oomycete pathogen, Pseudoperonospora cubensis. Oregon State University. Dataset. http://dx.doi.org/10.7267/N9TD9V7M
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  • See related paper: "Burkhardt, Alyssa, Alex Buchanan, Jason S Cumbie, Elizabeth A Savory, Jeff Chang, and Brad Day (2014) Alternative Splicing in the Obligate Biotrophic Oomycete Pathogen, Pseudoperonospora Cubensis. Molecular Plant-Microbe Interactions [issue forthcoming]
  • Article: Alternative Splicing in the Obligate Biotrophic Oomycete Pathogen Pseudoperonospora cubensis
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  • Work in the Day lab was supported by funds from Michigan State University Project GREEEN (GR13-007) and a grant from the United States Department of Agriculture Specialty Crops Research Initiative (2011-51181-30661). Work in the Chang lab was funded by National Institute of General Medical Sciences of the National Institutes of Health under Award Number R01GM104977.
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  • description.provenance : Approved for entry into archive by Amanda Whitmire(amanda.whitmire@oregonstate.edu) on 2014-06-05T17:48:46Z (GMT) No. of bitstreams: 2license_rdf: 1089 bytes, checksum: 0a703d871bf062c5fdc7850b1496693b (MD5)placeholder.txt: 224 bytes, checksum: bf2bb61d78831061bb1258faf048e778 (MD5)
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Thumbnail Title Date Uploaded Visibility Actions
file details PCU_annotation.gff 12/04/2017 Public
file details rename_map.csv 12/04/2017 Public
file details Updates_supplementalTable.csv 12/04/2017 Public