*7.2.1 Transcriptomics*

High-throughput analysis of protein-encoding mRNA (transcriptomic approaches) has explored the differential expression of genes at different stages of the Chlamydial infectious cycle, allowing the identification of previously unrecognized early Chlamydial gene expression and complex host cell responses [102–104]. However, such bulk-cell approaches can potentially miss cell-cell variability or cells that contribute to overlapping phenotypic characteristics, potentially masking critical biological heterogeneity as irrelevant signals from non-participating cells that can skew the average [105].

Single-cell RNA sequencing (scRNA-seq) is an alternative to bulk cell populations as it can analyze RNA molecules in individual cells with high resolution and on a genomic scale [105]. The construction of a pilot dataset, applying scRNA-Seq to *C. trachomatis* infected and mock-infected epithelial cells (HEp-2) has allowed the differential expression of genes involved with cell cycle regulation, innate immune responses, cytoskeletal components, lipid biosynthesis, and cellular stress at early times of infection [105].
