As disease-associated microglia (DAM) states have been described in rodent models of neurodegenerative disease and ageing [46], we investigated the expression of selected immune genes across all microglia clusters (Fig. 3E), and found that the microglial cluster Mglia Daisy expressed low levels of CX3CR1, P2RY12, TMEM119 and high levels of the immune related genes TYROBP, CTSB, APOE, TREM2, AXL, CTSL, LPL, ITGAX, TIMP2. Here, CTSB is linked to neurodegenerative disease.