Application of a Modified Smart-seq2 Sample Preparation Protocol for Rare Cell Full-length Single-cell mRNA Sequencing to Mouse Oocytes

Endogenous retroviruses (ERV) are transposable retroelements that form similar to 10% of the murine genome and whose family members are differentially expressed throughout embryogenesis. However, precise regulation of ERV in germ cells remains unclear. To investigate ERV expression in oocytes, we adapted a single-cell mRNA-sequencing library preparation method to generate bulk sequencing libraries from growing oocytes in a time- and cost-efficient manner. Here, we present a modified Smart-seq2 protocol that yields full-length cDNA libraries from purified RNA obtained from low numbers of pooled immature or mature oocytes. Using this method, RNA-sequencing libraries can be generated from any rare or difficult-to-isolate populations for subsequent sequencing and retroelement expression analysis.