Mtrun_Shoot_TimeSeries_GEM

RNA was isolated from Medicago truncatula root and shoot samples using the E.Z.N.A.® Total RNA Kit (Omega Bio-tek, USA) according to the manufacturer’s protocols. RNA libraries were sequenced by Novogene Co.,<br>740 Ltd. (Beijing) from 100 to 1000 ng of total RNA prepared by a stranded kit (Illumina TruSeq Stranded<br>741 Total RNA Kit or NEB Next UltraTM II Directional RNA Library Prep Kit for Illumina). These libraries were included in a final dataset consisting of 60 libraries, including 30 libraries from this work (three replicates of five time points each for inoculated and uninoculated wild type (A17) shoot segments) and 30 libraries previously reported from inoculated and uninoculated wild type (A17) root segments. The PBS-GEM workflow (https://github.com/wpoehlm/PBS-GEM) was used to process RNA sequencing reads on Clemson University’s Palmetto Cluster. Poor quality reads and adapters were removed using Trimmomatic-0.38. Next, cleaned reads were mapped to the Mt4.0v1 reference genome using hisat2-2.1.0. Gene and transcript abundances were estimated using stringtie-1.3.4d. <br>