GSE201835
Total and Nascent Transcriptome of Xenopus laevis Embryos at 5-9 hpf (stage 7-9)
To characterize the nascent transcriptome during zygotic genome activation (ZGA) of Xenopus laevis embryos, we microinjected 5-ethynyl uridine (EU) into 1-cell stage embryos and isolated total RNAs from whole embryos at 5, 6, 7, 8 and 9 hours post-fertilization (hpf) at room temperature, respectively, covering the stages of pre-ZGA to widespread ZGA (stage 7-9). To purify nascent transcripts, total RNAs were biotinylated using disulfide biotin azide via click reaction and biotinylated nascent transcripts were purified using streptavidin beads. Libraries were constructed from using the total RNA ('All'), nascent transcripts ('Bead') and the flowthrough after purification of nascent transcripts ('FL'), respectively. To categorize maternal-zygotic (MZ) genes and zygotic-only (Z) genes, total RNAs from eggs were isolated for constructing libraries. All libraries were sequenced on illumina NextSeq 500. Overall design: Two experiments were conducted. In the first experiment, two clutches of embryos at 5-9 hpf (two biological replicates) were used for sequecing 'All' (total RNA), 'Bead' (nascent transcripts) and FL (flowthrough RNAs), repsecitvely. In the second experiment, two clutches of embryos at 5-9 hpf (two biological replicates) were used for sequecing 'Bead' (nascent transcripts) and FL (flowthrough RNAs), repsecitvely, two clutches of unfertilized eggs (teo biilogical replicates) were used for sequencing 'All' (total RNA), and two clutches of embryos at 5 hpf (two biological replicates) were used for sequecing 'All' (total RNA).