An integrated toolkit for human microglia functional genomics

Table 1 iMG differentiation and characterization benchmarks (MS: mass spectrometry, ATAC-Seq: assay for transposase-accessible chromatin with sequencing, sc: single cell, hSNS: human synaptosome, mNeuron: mouse neuron, hAstro: human astrocytes

iMG characterization	New protocol	Muffat et al., [12]	Abud et al., [11]	Douvaras et al., [17]	Haenseler et al., [18]	Pandya et al., [13]	Takara et al., [20]	McQuade et al., [19]	Andreone et al., [14]	Drager et al., [22]
Days required for Differentiation	20	74	38	65	70	29	46	38	23	8
Step-by-step protocol reported	Yes	No	No	No	No	No	No	No	No	No
Multi-omic web-resource	Yes	No	No	No	No	No	No	No	No	No
Sequential harvesting of iMG	Yes	No	No	No	No	No	No	No	Yes	No
Proteomics profiling of iMG	MS-global Proteomics	No	No	No	No	No	No	No	No	No
Chromatin accessibility profiling of iMG	Yes, ATAC-Seq	No	No	No	No	No	No	No	No	No
Transcriptional profiling of iMG	scRNA-seq	RNA-seq	RNA-seq	RNA-seq	None	Microarray	None	RNA-seq	RNA-seq	RNA-seq
Cytokine expression profiling	LASER-bead 71plex	Cytokine Array Kit	V-PLEX 30-plex	Cytokine Array Kit	Luminex100 Bio-Plex	TNF-α	Magnetic Luminex	None	mRNA expression	36-cytokine proteome
No. of plasmids used for iMG differentiation	0	0	0	0	0	0	0	0	0	2
Phagocytosis Assays	Aβ, hSNS, myelin	Latex beads	E coli, hSNS	Latex beads	Zymosan	E coli	Beads, AMRA- Aβ	Aβ, S.aureus, zymosan	mNeuron/myelin	Rat-SNS, beads
Assessment of iMG calcium signaling	Calcimycin, ATP-response	None	ADP-response	ADP-response	None	None	None	None	None	None
iMG culture system	Mono-culture	Mono-culture	Mono-culture	Mono-culture	Mono-culture	hAstro/iMG co-culture	Neuron/iMGco-culture	Mono-culture	hAstro/iMGco-culture	Mono-culture
Antibiotics required for iMG differentiation	None	None	None	None	None	None	None	None	None	Doxycycline
Homeostatic culturing conditions reported	Yes	Yes	No	No	No	No	No	No	Yes	No

ISSN: 1757-6512