Whole transcriptome target sequencing: profiling gene expression and alternative polyadenylation with one pipeline.

We have developed a deep sequencing method called Whole Transcriptome Target Sequencing (WTTS), which sequences the 3’ ends of polyA+ RNA. This method can simultaneously profile gene expression and alternative polyadenylation. A pooled total RNA sample derived from three male and three female adult frogs was used in seven trials to develop the WTTS assay. The same sample was sequenced using RNA-seq as control. Technical replicates of the same female adult frog were analyzed using the finalized WTTS library preparation method. Biological replicates, which included 10 embryo pools collected from two families at stages 6, 8, 11, 15 and 28 were subsequently analyzed to validate the finalized WTTS method. Six embryo samples collected at stages of 6, 8 and 11 were also sequenced using RNA-seq. Therefore, this submission involved a total of 26 libraries.