Computational protocol: Apoplastic Venom Allergen-like Proteins of Cyst Nematodes Modulate the Activation of Basal Plant Innate Immunity by Cell Surface Receptors

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Protocol publication

[…] Two-weeks-old transgenic Arabidopsis plants, grown under the same conditions as for the infection with H. schachtii, were collected, flash-frozen in liquid nitrogen and total RNA was extracted with the Maxwell® 16 LEV simplyRNA purification kit (Promega). cDNA synthesis, library preparation (200-bp inserts), and Illumina sequencing (90-bp paired-end reads) was performed at BGI (Hong-Kong). Reads were mapped to the Arabidopsis genome (tair10) using TopHat and transformed into a count per gene per sample by using the BEDTools suite (function coverageBed). The edgeR method was used to analyze differentially expressed genes (DEGs) between groups. DEGs were mapped to Gene Ontology (GO) terms in the database (http://www.geneontology.org/), and gene numbers were calculated for every term using an ultra-geometric test to find significantly enriched GO terms in DEGs. Calculated p-value went through a Bonferroni Correction, taking corrected p-value ≤0.05 as a threshold. KEGG pathway enrichment analysis was used to identify significantly enriched metabolic pathways or signal transduction pathways in DEGs comparing with the whole genome background. Subcellular localization was determined for all DEGs using the SUBcellular localization database for Arabidopsis proteins . […]

Pipeline specifications

Software tools TopHat, BEDTools, edgeR
Databases TAIR KEGG PATHWAY
Application RNA-seq analysis
Organisms Arabidopsis thaliana, Caenorhabditis elegans, Solanum tuberosum, Beta vulgaris, Meloidogyne javanica, Meloidogyne incognita
Diseases Infection, Nematode Infections, Parasitic Diseases