RNA sequencing for Salpingoeca rosetta Hippo, Warts, and Yorkie mutated strains

This study aims to compare the transcriptome profiles of S. rosetta wild-type strains with those of mutant strains of the Hippo signaling pathway: Hippo (PTSG_10780), Warts (PTSG_04961), and Yorkie (PTSG_06057).Mutant strains were generated by CRISPR/Cas9 using two strategies: insertion of a pac cassette containing stop codons and a puromycin resistance gene (insertion), or deletion of the target gene, replaced with the pac cassette (deletion).Two RNA sequencing experiments were performed. The first included at least triplicate samples for the following conditions: wild-type (WT), cells expressing an episomal pac cassette (with and without puromycin) and two clones each of warts, yorkie, and hippo insertion mutants, all cultured either as slow swimmers/chains (with E. pacifica only) or as rosettes (after addition of Algoriphagus machipongonensis). The second experiment included triplicates of WT and of two independent clones of each warts and yorkie deletion strains, all in slow swimmer form.