title: RNA-seq of Symbiotic Interactions:SUNN control shoot replicate1
design: RNA was extracted from three biological replicates per sample type and purified with RNeasy MiniElute Cleanup Kit (Qiagen) following the manufacturers instructions. Quality control was performed using a Bioanalyzer 2100 (Agilent). Library preparation was performed by GATC Biotech (Konstanz, Germany) using random primers and samples were sequenced with an Illumina HiSeq 2500 (50 bp single reads, 30 M reads per sample). RNA-seq datasets were mapped to a re-annotated version of the Medicago genome (de Bang et al., 2017b) to estimate raw counts and effective read lengths using Salmon (Patro et al., 2014). Raw counts were normalized by median normalization and differential expression genes (DEGs) were estimated using the DEseq2 module from the Bioconductor R package (Love et al., 2014).