title: Organ-specific transcriptome profiling of paprika
design: RNA-Seq paired end libraries were prepared using theIllumina TruSeq RNA Sample Preparation Kit v2 (catalog#RS-122-2001, Illumina, San Diego, ca.). Starting with totalRNA, mRNA was purifed using poly (A) selection or rRNAdepleted, then RNA chemically fragmented and convertedinto single-stranded cDNA using random hexamer priming.Next, the second strand was generated to create doublestranded cDNA. Library construction commenced with thegeneration of blunt-end cDNA fragments from ds-cDNA.Then A-base was added to the blunt-end in preparation forligation of sequencing adapters. After the ligates were sizeselected, the ligated cDNA fragments containing adaptersequences were enhanced via PCR using adapter specifcprimers. The library was quantifed with a KAPA libraryquantifcation kit (Kapa Biosystems KK4854) followingthe manufacturers instructions. Each library was loadedon an Illumina Hiseq4000 platform, and high-throughputsequencing was performed to ensure that each sample metthe desired average sequencing depth.