Fig. 5
From: Impact of microglia isolation and culture methodology on transcriptional profile and function
Transcriptomic profile of untreated microglia compared to developmental states. A Scatter dot plots showing the normalized gene counts for NMF metagenes identified in the external dataset, across our untreated conditions (Protocol 1, Protocol 2, Protocol 3), and corresponding to specific microglial developmental stages (Yolk sac, Early Microglia, Pre Microglia, Adult Microglia). B PCA plot illustrating the overlap between our bulk sequencing dataset for untreated conditions and external dataset. C Heatmap of Pearson correlation R2 values comparing five conditions, untreated, from our dataset (Protocol_1A, Protocol_1B, Protocol_1C, Protocol_2, Protocol_3) with those in the external dataset (Early_microglia, Pre_microglia, Adult_microglia); white corresponds to R2 = 0.3 and red to R2 = 0.8. D Log2 fold-change plot displaying DEGs comparing Protocol 1 vs Protocol 3 and Early Microglia vs Adult Microglia; green dots represent DEGs significant only in the early vs adult comparison (p < 0.05), blue dots are significant only in Prot 1 vs Prot 3 comparison(p < 0.05), and red dots are significant in both. E Bar graph depicting the number of significant DEGs unique to each comparison and those common to both; colors correspond to those in panel D. F Summary chart of Gene Ontology (GO) analysis conducted on genes with log2 fold-change > 2, and p < 0.01, in both our dataset comparing Protocol 1 with Protocol 3, and in the external dataset, comparing Early Microglia with Adult Microglia; analysis utilized EnrichR to identify GO Biological Process 2023 terms