Table 2.

Single-cell profiles of specific microglia subsets at different developmental stages and pathological states. Ctsb, cathepsin B; Ctsd, cathepsin D; Lamp1, lysosomal associated membrane protein 1; Apoe, apolipoprotein E; Tmsb4x, thymosin beta 4 X-linked; Eef1a1, eukaryotic translation elongation factor 1 alpha 1; Rpl4, ribosomal protein L4; Cst3, cystatin 3; Tmem119, transmembrane protein 119; Selplg, selectin P ligand; Slc2a5, solute carrier family 2 member 5; Malat1, metastasis associated lung adenocarcinoma transcript 1; Lgals3, galectin-3; Cst7, cystatin F; Ccl4, C-C motif chemokine ligand 4; Ccl3, C-C motif chemokine ligand 3; Il1b, interleukin 1 beta; Id2, inhibitor of DNA binding 2; Atf3, activating transcription factor 3; Ifitm3, interferon induced transmembrane protein 3; Rtp4, receptor transporter protein 4; Oasl2, 2′–5′ oligoadenylate synthetase-like 2; Lpl, lipoprotein lipase; P2ry12, purinergic receptor P2Y12; Cx3cr1, C-X3-C motif chemokine receptor 1; GPNMB, glycoprotein nmb; HSP90AA1, heat shock protein 90 alpha family class A member 1; AD, Alzheimer’s disease; PD, Parkinson’s disease.

Species	Model	Microglia Subset	Gene	Protocol	Reference
CD-1 mice	In embryonic development	The subsets during CNS development and homeostasis in the adult brain	Ctsb, Ctsd, Lamp1, Apoe, Tmsb4x, Eef1a1, Rpl4, Cst3	SMART-seq2	[101]
	In postnatal development		Tmem119, Selplg, Slc2a5, Malat1
C57BL/6J mice	Aging brain (P540)	Aging clusters (OA) 2	Lgals3, Cst7, chemokines Ccl4, Ccl3, Il1b, Id2, Atf3	10 × Genomics	[102]
		Aging clusters (OA) 3	Ifitm3, Rtp4, Oasl2
Heterozygous 5XFAD transgenic mice	AD	Microglia type associated with neurodegenerative diseases (DAM)	Apoe, Lpl, Cst7 ↑ P2ry12, Cx3cr1, Tmem119 ↓	MARS-seq	[103]
Frozen human post-mortem midbrain tissue sections	Idiopathic PD	Microglia cluster involving inflammatory response	IL1B, GPNMB, HSP90AA1	10 × Genomics	[104]