title: RNAseq of Suaeda aralocaspica black dry seeds
design: Suaeda aralocaspica developing a unique combination of dispersal and germination strategies via producing dimorphic seeds is thought to be a bet-hedging strategy advantageous in harsh and unpredictable environments. With the advent of post-genomics technologies, large-scale gene expression profiling has been implemented at the RNA, protein and metabolite levels to unveil specific features of the complex germination process. Genome-wide expression studies in Arabidopsis have been previously applied to gain insight into temporal and spatial changes during Arabidopsis germination and provide important new information about mechanisms controlling germination. Nevertheless, a detailed knowledge of the temporal changes in gene expression in halophyte seed is far missing, but it is essential to understanding the control of the timing of germination as well as the underlying molecular processes contributed by the bet-hedging germination of desert annuals. Therefore, we have analyzed the Suaeda aralocaspica transcriptome by sampling 3 points along the germination time course. Our high throughput data set will establish meaningful connections linking genetic information to the physiological changes observed during halophyte germination.  Total RNA was extracted by using TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions, and RQ1 DNase (Promega, Madison, WI, USA) was used to remove contaminating genomic DNA. The quality and quantity of the purified RNA was monitored at the ratios of A260/A280 and A260/230 on SmartSpecPlus Spectrophotometer (BioRad, Philadelphia, PA, USA). RNA integrity was further verified by 1.5% agarose gel electrophoresis.  For RNA-seq, total RNA was extracted from each sample, 10 mg of total RNA was used for RNA sequencing (RNA-seq) library preparation. Polyadenylated mRNAs were purified and concentrated with Magnetic Beads Oligo (dT) (Invitrogen, Carlsbad, CA, USA) before used for directional RNA-seq library preparation. Purified mRNAs were iron fragmented followed by end repair and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified and PCR products were purified, quantified and applied to Illumina HiSeq 2000 system 101nt.