title: RNA-seq of Coffea arabica
design: All aboveground plant material was collected and flash-frozen in liquid nitrogen. The biological replicates were ground separately in liquid nitrogen with PVPP (polyvinyl polypyrrolidone) in a mortar and pestle. Approximately 5g of each biological replicate was pooled in a 1.5 ml flash-frozen polypropylene tube before vortexing and re-freezing. Total RNA was extracted using the standard protocol of the RNeasy Mini kit (Qiagen, Germany). In total, 20 samples were extracted with four technical replicates for each treatment: in planta arabica563-infected coffee plants; in axenic culture arabica563 ; in planta arabica908-infected coffee plants; in axenic culture arabica908 ; control (-inoculated with water) coffee plants. RNA quality assessment (Qubit and Fragment Analyzer), library preparation and Next Generation Sequencing (60M paired-end reads per sample) performed by Genewiz/ Azenta (Frankfurt, Germany). Fastq files were quality-trimmed using trimmomatic parameters "ILLUMINACLIP:$TRIMMOMATIC_DIR/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25".
library_name: H2O_planta_3