Culture shock: microglial heterogeneity, activation, and disrupted single-cell microglial networks in vitro

Table 1 Modules of co-regulated genes capturing diversity of microglia are robustly detected in in vitro cells

Gene Set	Description	Citation	Size	Number of Genes detected	Percent Detected
PROLIFERATION	Cell cycle genes marking actively proliferating microglia	Friedman et al., 2018	81	77	95.1%
MACROPHAGE	Unique markers of infiltrating and brain-boundary macrophages compared to microglia	Friedman et al., 2018 Hove et al., 2019	28	26	92.9%
LPS-RELATED	Genes upregulated in brain myeloid cells as a response to LPS injections and system inflammation	Friedman et al., 2018 Kang et al., 2018	86	75	87.2%
INTERFERON-RELATED	Genes upregulated in brain myeloid cells as a response to LCMV and Poly(I:C) injections	Friedman et al., 2018 Kang et al., 2018	52	52	91.2%
MONOCYTE	Unique markers of peripheral monocytes compared to other brain myeloid cell types	Friedman et al., 2018 Hove et al., 2019	82	64	78.0%
RESTING MICROGLIA	Unique markers of parenchymal microglia compared to other brain myeloid cell types	Friedman et al., 2018 Hove et al., 2019	50	49	98.0%
NEURODEGENERATION	Genes upregulated in the activation response of microglia seen in a variety of neurodegeneration models	Friedman et al., 2018	126	121	96.0%

GENE SET defines the name of each gene module. DESCRIPTION gives a short description to describe the genes contained. CITATION lists the sources which were used to create the gene set. SIZE gives the number of genes in the gene set. NUMBER OF GENES DETECTED lists how many genes in the gene set were detected in the cleaned myeloid in vitro cells (expressed in at least 10 cells). PERCENT DETECTED gives the number of detected genes as a percent of total gene set size. We see that with the exception of the Monocyte and LPS-related gene set—which had 78.0 and 87.2% respectively—more than 90% of genes from most gene sets were expressed

ISSN: 1750-1326