Cotton-reniform nematode transcriptome
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 cDNA library preparation, barcode tagging, and 100-bp, paired-end 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.