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studies/TranscriptomeDataSets/protocols/DataSetResources.md

+## Transcriptome data sets
+
+A total of 315 transcriptome datasets of tomato (Zouari et al., 2014; Du et al., 2015; Barad et al., 2017; Sarkar et al., 2017; Sugimura and Saito, 2017; Xue et al., 2017; Yang et al., 2017; Zheng et al., 2017;
+Chen et al., 2018; Shukla et al., 2018; Fawke et al., 2019; Pesti et al., 2019; Wang et al., 2019b) and potato (Goyer et al., 2015; Zuluaga et al., 2015; Dees et al., 2016; Gao and Bradeen, 2016; Kochetov et al., 2017; Levy et al., 2017; Li et al., 2017; Lysøe et al., 2017; Hao et al., 2018; Kumar et al., 2018) were obtained from the Sequence Read Archive (Figure S1). These studies included treatments with potentially beneficial organisms (arbuscular mycorrhizal fungi (AMF) and biocontrol agents) as well as detrimental organisms (pathogenic bacteria, nematodes, fungi, viruses, viroids, insects and oomycetes). Only studies with at least one mock treatment were included. The collected tissues included roots, stems, leaves, fruits and tubers. The time points of sampling after infection range from 0 days post-infection (dpi) up to 42 dpi or until the end of the host’s life cycle (Figure S1). Approximately 20% of all tomato and potato cultivars were denoted as resistant to the applied pathogens.
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