Fig 1. Gene-expression patterns of early, pre- and mature WT and Psen1^KI/KI microglia.

RNA sequencing performed in microglia progenitors from yolk sac and brain rudiment at embryonic day 9.5, pre-microglia at postnatal day 1.5 and adult microglia at 3 months. (A) Schematic diagram showing the strategy used to profile microglia-enriched transcripts during key periods of development. (B) Gene Set Enrichment Analysis (for details see Methods) was used to identify GO Biological Processes differentially regulated in Psen1^KI/KI microglia (C) Multidimensional scaling of all genes of microglia progenitors in yolk sac, brain rudiment and pre-adult and adult microglia. Significance of difference between WT and Psen1^KI/KI microglia between developmental stages are assessed by permutation test (for details see Methods). (D) Principal component analysis restricted to microglia identity genes expressed in WT or Psen1^KI/KI early, pre- and adult microglia (YS = Yolk Sac, BR = Brain Rudiment, N = Neonate, A = Adult). For microglia progenitors, N = 3–4 biologically independent measures from 6–12 pooled yolk sacs or brain rudiment. For neonate and adult microglia, N = 4 animals per group.