RNA-seq profiles of tissues (upper lips, compound eyes and guts), whole body and instar stages of luminous and non-luminous ostracods

To understand the contributions of new and existing genes and their co-expression patterns to an evolutionarily novel bioluminescent upper lip, we conducted two major classes of analyses, with the sample sets summarized here. First, we performed Differential Expression (DE) analysis in two species - one luminous (Vargula tsujii) and one non-luminous (Skogsbergia sp.) - by sampling five biological replicates from each species across three tissue types: dissected upper lip, compound eye, and gut of adults, for a total of 30 RNA expression profiles. For DE, we used a previously published transcriptome for the luminous species but generated a de novo transcriptome from a single individual for the non-luminous Skogsbergia sp., which was lacking. For DE experiments and the de novo transcriptome, we extracted total RNA using Agencourt RNAClean magnetic beads (Beckman Coulter). Second, we quantified gene co-expression networks in the luminous species using data from RNA-seq samples, including all tissue types from the DE dataset (upper lip, compound eye, and gut), previously published upper lip samples, and additional RNA samples from whole bodies of juvenile instar stages and whole adult bodies, some of which were subjected to physical stimulation to produce bioluminescence. For the additional RNA samples, we extracted RNA using TRIzol (Invitrogen) and included 21 adult whole bodies and 18 juvenile V.tsujii samples comprising three to six biological replicates from each of the five juvenile instar stages (A-I male, A-I female, A-II, A-III, A-IV, A-V).