RNA-seq in roots of ancestrally nematode-infected and non-infected rice plants
2 ug of total RNA was used for library preparation using QuantSeq 3 mRNA-Seq Library Prep Kit (Lexogen) as following. An oligodT primer containing an Illumina-compatible linker sequence at its 5 end was hybridized to the RNA and reverse transcription was performed. After first strand synthesis, the RNA was removed and second strand synthesis was initiated by random priming and a DNA polymerase. The random primer also contained an Illumina-compatible linker sequence at its 5 end. The second strand synthesis was followed by a magnetic bead-based purification step. Amplification of libraries was performed, including addition of external barcodes during the PCR amplification step. In the final step, the double-stranded libraries were purified by magnetic beads to remove all reaction components.