title: RNA-seq of stage 17 silique: pPLAIIgamma:RNAi
design: Total RNA was extracted from stage 17 siliques of Col-0 and pPLAIIgamma:RNAi plants. After a cDNA library was constructed using TruSeq RNA Sample Preparation Kits, libraries were sequenced using Illumina Hi-Seq, creating 151 bp paired-end sequencing reads. Raw reads were subjected to quality checks and trimming with SolexaQA using a Phred quality score of 20 and a read length of 25 bp as cut-off values. Clean reads were mapped to the Arabidopsis reference genome using HISAT2 software software. Only uniquely mapped reads were used to obtain read counts for each gene. The number of mapped clean reads for each transcript was counted using HTSeq (v.0.11.0) and then normalized with the DESeq package.