title: Root of milk thistle
design:      This RNAseq experiment was designed to analyze the silybin synthetic pathway in milk thistle. Previous studies showed that silybin is mainly accumulated in the seed. So the expression of the pathway related genes was considerd to be tissue-dependent.      The libraries were constructed according to the Solexa TruSeq RNA sequencing protocol (Illumina). Total RNA from root, stem, leaf, flower, seedcoat, embryo and young seed was extracted separately (TruSeq Stranded Total RNA LT Sample Prep Kit, 48 Samples, Illumina). mRNA was purified and fragmented (TruSeq Stranded mRNA LT Sample Prep Kit, Illumina). rRNA was removed (Ribo-Zero rRNA Removal Kits, Epicentre). First and second strand cDNA was synthesized with SuperScript  II  Reverse  Transcriptase (100mM DTT and 5X First Strand Buffer, Invitrogen). The 3' ends were adenylated and adapters were ligated. the amplification was accomplished with High Sensitivity DNA Kit (Agilent). Qubit 2.0 fluorometer and Qubit dsDNA HS Assay Kit were used for the quantitative analysis of the library. Agilent2100 bioanalyzer was used for the distribution and purity analysis of the library. 