Protocols: Among three repeat experiments over two time points (5 and 10 days post infection) roots were collected. Total RNA was isolated from 200 mg of ground root tissues using TRIzol. From which, 1 Âµg was prepared using Illumina TruSeq small RNA library preperation protocol. Small RNA-seq libraries were pooled for multiplexed sequencing using Illumina HiSeq 2500. The NEBnext mRNA library prep master mix was used to generate mRNA-seq libraries from 250 ng of isolated mRNA which were extracted from 20 mg of ground root tissue using magnetic mRNA isolation kit. Genomic DNA was extracted using DNEasy Plant Mini Kit from 100 mg root tissues in order to prepare methylC-seq libraries sequenced using Illumina HiSeq.These efforts were undertaken in order to elucidate the dynamic interplay of DNA methylation patterns, small RNA abundance, and gene expression levels in Arabidopsis roots in response to infection by the cyst nematode Heterodera schachtii.