RNA sequencing microglia depletion model

We developed an experimental model system in mice, in which microglia can be depleted selectively and temporarily from the prefrontal cortex (PFC) during a defined window of adolescence (6 weeks of age). This was achieved using a single, bilateral stereotaxic intra-PFC injection of clodronate disodium salt (CDS), which induces selective apoptosis of microglia. To ascertain the cellular selectivity of intra-PFC administration of CDS, we conducted next-generation RNA sequencing (RNAseq) of bulk medial PFC tissue from CDS- or phosphate buffered saline (PBS)-injected mice. PFC samples were extracted either during the peak of microglia depletion, that is, 5 days post injection (5 dpi) or in adulthood (12 weeks of age) after full microglia repopulation. Next-generation RNA sequencing of mouse medial prefrontal cortex samples a) in adolescence (6 weeks of age), 5 days after intra-PFC PBS or CDS injection and b) in adulthood (12 weeks of age), 6 weeks after intra-PFC PBS or CDS injection.