FD-seq: Droplet-based RNA sequencing of fixed single cells

Current high-throughput single-cell RNA sequencing (scRNA-seq) methods are incompatible with paraformaldehyde (PFA) fixation, a common cell/tissue preservation and viral inactivation technique, which has prevented transcriptomic analysis of rare cells that require protein staining and enrichment. Here we present FD-seq, a method for high-throughput RNA sequencing of PFA-fixed, stained and FACS-sorted single cells. We used FD-seq to address two important questions in virology. First, by analyzing a rare population of cells supporting herpesvirus reactivation, we identified TMEM119 to mediate reactivation of Kaposi’s sarcoma-associated herpesvirus (KSHV), a tumor virus. Second, we studied the innate immune activation in cells infected with the coronavirus OC43, which causes the common cold and also serves as a safer model pathogen for SARS-CoV-2 studies. We found that pro-inflammatory cytokine induction, which is a major contributor to the severe pathogenicity in SARS-CoV-2-infected individuals, is primarily driven by uninfected or lowly infected bystander cells that are exposed to the virus but fail to express high level of viral genes. FD-seq is a simple method that is suitable for characterizing the transcriptome of rare cell populations of interest, and for studying high-containment biological samples such as SARS-CoV-2-infected cells after PFA inactivation. KSHV reactivation is chemically induced, and the mRNA from single reactivated and non-reactivated cells are sequenced. Bulk RNA-seq was performed to identify the mechanism of TMEM119-induced reactivation. OC43 infected and mock infected cells were sequenced to identify subpopulation of bystander cells. The performance of FD-seq was also compared to the standard Drop-seq method for methanol-fixed cells.