Fig. 3. Characterization of glial subclasses. (A) Two
types of astrocytes (Astro1 and Astro2) identified by
common and distinct markers. (B) Immunohistochemistry
for glial fibrillary acidic protein (red, Astro1) and MFGE8
(green, Astro2). Scale bar, 50 mm. (C) Genes showing
expression restricted to microglia (Mgl), perivascular
macrophages (Pvm), and peritoneal macrophages (Pmac).
Error bars show standard deviations. (D) Cartoon illustrating
the morphology and localization of microglia and perivascular
macrophages. (E) Immunostaining for AIF1 (previously
known as Iba-1, blue) marking microglia, and for MRC1
(green) and LYVE1 (red) marking perivascular macrophages.
Asterisk, a microglia cell. Arrow, a perivascular macrophage
aligned to a vessel (not stained). Scale bar, 20 mm. (F) Heat
map showing progressive changes in gene expression along
oligodendrocyte differentiation, illustrated below. (G) Single-molecule RNA FISH for Itpr2 and Cnksr3 mark a strict
subset of oligodendrocytes (as identified by Plp1). Scale
bar, 11 mm.
MRC1 LYVE1 AIF1
GFAP GFAP/MFGE8 MFGE8 Pial surface
Oligo1 Oligo2 Oligo4 Oligo3Oligo5Oligo6
Fig. 4. Expression of regulatory genes across 47 subclasses. (A)
Transcription factors showing restricted expression across cell types.
Asterisks denote genes with additional expression in distinct subclasses: Sp8 in Int11, Msx1 in vascular cells and microglia. (B) Genes
specific to ependymal cells. Transcription factors Foxj1, Rfx2, and Rfx3 (with asterisk to indicate its wider expression) and their known targets are shown in red,
green, and blue, respectively. Arrows indicate known direct interactions between transcription factors. Only genes with known ciliary function are included.