title: Cotton-reniform nematode transcriptome
design: Approximately 500 mg (FW) of root tissue was harvested from both infected and the uninfected root systems of three replicate plants at 3, 6, 9, and 12 DAI, for a total of 21 samples (2 infection statuses X 3 dates X 3 biological replicates; three samples dropped because of poor library quality). Tissue was preserved in RNAlater (QIAGEN, Valencia, CA) and immediately shipped to the University of Arizona Genetics Core (Tucson, AZ) for 100-bp paired-end cDNA library preparation, barcode tagging, and sequencing on three lanes of the Illumina Hi-Seq platform (Illumina, San Diego, CA). Read quality was assessed with FastQC , followed by adaptor trimming with Trimmomatic and content-dependent quality trimming with ConDeTri. Cleaned and filtered reads are uploaded here.