Extended Data Fig. 6: Validation of the selected DE genes by qPCR and IF staining.
From: PICALM Alzheimer’s risk allele causes aberrant lipid droplets in microglia
(a) and (b) qPCR results for NEAT1, ATP6AP2, LDLR, HMGCS1, and DHCR7 in iMG (PICALM risk allele vs. non-risk). Expression was normalized to GAPDH. Each datapoint represents a single-well measurement from one experiment; for each gene and each condition (risk and non-risk), data are from 2 donor lines (CD04 and CD09; one clone per line), collected in one experiment with 2 wells of differentiations (n = 4). (c) IF staining and (d) quantification of the mean fluorescence intensity of selected DE genes in day-25 iMG (non-risk vs risk alleles). Scale bar, 50 µm. Each datapoint represents a single-well measurement from one experiment; for each gene and each condition (risk and non-risk), data are from 2 donor lines (CD04 and CD09; one clone per line), collected in one experiment with 2 wells of differentiations (n = 4). For all comparisons, LMM was used to test the fixed effect of genotype (risk vs. non-risk), with cell line identify (CD04 or CD09) as the random factor; two-sided test, nominal p-value; * P < 0.05, ** P < 0.01, ***, P < 0.001; mean ± s.e.m.
