28.7 Mb genome of Nannochloropsis oceanica CCMP1779 was assembled. RNA sequencing data from N-replete and N- depleted growth conditions support a total of 11,973 genes, which in addition to automatic annotation were manually inspected to predict the biochemical repertoire for this organism. In addition, a protocol for the transformation of the sequenced strain is provided. The availability of genomic and transcriptomic data for Nannochloropsis oceanica CCMP1779, along with efficient transformation protocol provides a blueprint for future detailed gene functional analysis and phylogenetic comparison of Nannochloropsis species by a growing academic community focused on this genus.