Corresponding expression quantification files for the Trinity assembly files (https://doi.org/10.5281/zenodo.251828) generated with salmon v0.7.2 (https://github.com/COMBINE-lab/salmon). The Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP) data set contains cultured samples of pelagic and endosymbiotic marine eukaryotic species representing more than 40 phyla (Keeling et al. 2014). Methods for the de novo transcriptome assembly are described in the Eel pond khmer protocols (Brown et al. 2015). Scripts available on github: https://github.com/dib-lab/dib-MMETSP References: C. Titus Brown, Camille Scott, and Leigh Sheneman. 2015. The Eel Pond mRNAseq Protocol. https://khmer-protocols.readthedocs.io/en/ctb/mrnaseq/ Keeling et al. 2014. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing. http://dx.doi.org/10.1371/journal.pbio.100188