We have infected the model legume Medicago truncatula with Meloidogyne hapla and harvested tissue over a time course. Transcriptome sequencing was performed on each sample using the Illumina RNA-Seq method. [Longitudinal Experiment] RNA was isolated from M. hapla eggs and pre-penetration juveniles (J2) and also from a time course of M. truncatula infected with M. hapla J2 at five time points: 1, 2, 4, 5, and 7 days after inoculation (DAI). Roots (local) and shoots (global) tissues from infected and uninfected plants were sampled. Each sample was loaded on five lanes for sequencing. Collectively, 22 samples were generated in total from - M. hapla egg and J2 (two samples), - infected M. truncatula root 1-2-4-5-7 DAI (five samples), - infected M. truncatula shoot 1-2-4-5-7 DAI (five samples), - uninfected M. truncatula root 1-2-4-5-7 DAI (five samples), - and uninfected M. truncatula shoot 1-2-4-5-7 DAI (five samples). Thus, 110 fastq files (= 22 samples x 5 lanes). [Diunrnal Experiment] M. truncatula roots inoculated with M. hapla was sampled at 6 time-points: 22:30, 2:00, 5:00, 6:30, 14:00, and 21:00. Lighting was turned off at 22:00 and turned on at 06:00. Four biological replicates were taken for each time point, providing 24 samples in total. Thus, 24 fastq files (= 6 time points x 4 replicates).