title: RNA-Seq of Solanum pennellii: leaf
design: Total RNA was extracted from leaves of control and VIGS plants of S. pennellii using the RNAqueous Total RNA Isolation kit (ThermoFischer), followed by treatment with the TURBO DNA-free kit (ThermoFischer) to remove genomic DNA. RNA-Seq libraries were prepared from poly(A)-selected RNA samples using the NEXTFLEX Poly(A) Beads 2.0 and Rapid Directional RNA-Seq kit 2.0 (PerkinElmer), and then sequenced on the Illumina NovaSeq 6000 SP v1.5 (2x150) platform at the Texas A&M Genomics and Bioinformatics service center. Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illuminas NCS 1.0.2 and RFV 1.0.2 software with default parameter settings. Sequencer .cbcl basecall files were demultiplexed and formatted into .fastq files using bcl2fastq 2 2.19.0 script configureBclToFastq.pl.