Fig. 3
Quality control of the transcriptional impact of negative controls on LEC or BEC transcriptome. (a, b) Correlation of log2FC between differentially expressed (DE) genes in negative control A and B. Green dots: DE genes in common between negative control A and B; blue and orange dots: specific to either negative control A or B; red dots: opposite pattern (red). P-values were calculated using linear regression. (c-e) Top significantly (P-value < 0.05) enriched GO terms for biological processes of commonly DE genes between negative control A and B in LECs and BECs (c, d), and specific DE genes for negative control B (e), using g:ProfileR [19] (relative depth 1–5). GO terms were ordered according to -log(P-value) values. (f) Expression levels of FARS2, EXTL2, and COLEC12 in LECs and BECs after transfection with negative control A and B. Bars represent fold change (FC) values against untransfected cells. (g) Quantification of the 4-methylumbelliferyl heptanoate (MUH) proliferation assay over 72 h in neonatal LECs derived from the same donor after negative control A or B transfection. Dots represent FC of the fluorescence intensity against T0. In f and g, data are displayed as mean values + SD (n = 2 in f and n = 5 in g). In g, P-value: * < 0.05, *** < 0.001, **** < 0.0001, using two-way ANOVA with Dunnet’s multiple comparisons test against untransfected control. The in vitro assay was performed in neonatal LECs derived from the same donor