Profiling of alternative transcription start sites and alternative polyadenylation sites in Xenopus tropicalis

We have developed both WTSS-seq (whole transcriptome start site sequencing) and WTTS-seq (whole transcriptome termini site sequencing) methods to capture either 5'- or 3'-ends of transcripts. HATT-seq (head and tail tag sequencing) is still under development, which can be used to capture both 5'- and 3' ends of each transcript simultaneously. Iso-seq was used to produce full-length transcripts, which can be used to validate both alternative transcription start sites and alternative polyadenylation sites. CAGE-seq was used to confirm alternative transcription start sites only. Overall design: A total of 14 WTSS-seq libraries were constructed using six individual adult males, six individual adult females and an RNA pool with three adult females (repeated twice). One CAGE-seq library was prepared with the three adult female pool using service provided by DNAFORM Precision Gene Technologies, Yokohama, Japan. The same three-female pool was used to develop one HATT-seq library. The same six individual males and six individual females were also used to profile 3'-ends of transcripts using WTTS-seq for a total of 12 libraries. One embryo pool was formed using total RNA collected from two families at stage 6, 8, 11, 15 and 28. As well, an adult pool was prepared from three male and three female adults. The embryo and adult pools were used to construct a total of one Iso-seq libraries. In brief, this submission involved 30 libraries in total.