RNA seq data: potato hairy roots inoculated with Spongospora / PMTV

Description

This data set contains gene expression matrices generated from an RNA-seq study conducted in potato hairy roots to assess gene expression post-infection by two pathogens. The two pathogens involved are Spongospora subterranea f.sp.subterranea (causal agent of the powdery scab disease) and the potato mop top virus (causal agent of the potato mop top disease). Hairy roots generated from three cultivars were used: Shepody ( susceptible to both pathogens), Russet Burbank (moderately susceptible to both), and Premier Russet (relatively resistant to both). Hairy roots of each cultivar were inoculated with either viruliferous or non-viruliferous Spongospora sporosori. Mock inoculation was done using Hoagland's solution, which was the solvent of the sporosori solutions. Root samples were collected 3,6, 12, 24, 48, and 72 hours post-inoculation. File "GEMmaker.GEM.raw.filtered.csv" contain the gene expression matrix generated using the RNAseq data from the samples. "RNA_seq_metadata.csv" file contains the metadata related to each sample ID used in gene expression data files. To remove the batch effect, data cleaning was done using the noisyR package in R. "GEM.raw.noisyR_corrected_sss_allcult.txt" file contains the resulting gene expression matrix for the comparison between mock-treated and non-viruliferous sporosori-treated samples. "GEM.raw.noisyR_corrected_SssvPMTV_allcult.txt" file contains the resulting gene expression matrix for the comparison between viruliferous and non-viruliferous sporosori-treated samples.

Institutions

• Washington State University

  Washington, Pullman

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