Extended Data Fig. 7: Defects in ciliogenesis block EndoMT.
From: Endocardial primary cilia and blood flow regulate EndoMT during endocardial cushion development
a) Integration of biological replicates for snRNAseq of the whole embryonic e9.5 heart (29,313 nuclei). b) Number of features and counts across biological replicates (Cilia WT nuclei=12,763, Cilia Het nuclei=12,030, Cilia Mut nuclei=11,503). Graphs of the percentage of cell types in the c) whole heart (29,313 nuclei) and d) endocardium (Cilia WT nuclei=1,340, Cilia Het nuclei=2,029, Cilia Mut nuclei=922) for each genotype (Replicates: Cilia WT n = 3, Cilia Het n = 2, Cilia Mut n = 2) (Late EndoMT Cilia WT vs Cilia KO p = 0.034). Statistically significant numbers are given in red. Dotplots for top DEGs for each cell type in the e) vEC/EndoMT cluster (1,496 nuclei), f) whole heart (29,313 nuclei) and i) endocardium (4,291 nuclei) from snRNA-seq data. Established marker genes for clusters found in the g) whole heart (29,313 nuclei) and h) endocardium (4,291 nuclei). Statistics: ns (p > 0.05), ** (p ≤ 0.01). Statistical test used was two-tailed t-test with Bonferroni correction. Statistical Data are represented as mean ± SEM. Unless otherwise stated, n is number of embryos. Box-plot stats for c): EC Cilia WT (min: 27.34, Q1: 28.12, median: 28.91, Q3: 30.73, max: 32.56, lower whisker: 27.34, upper whisker: 32.56), EC Cilia Het (min: 12.05, Q1: 19.53, median: 27.01, Q3: 34.48, max: 41.96, lower whisker: 12.05, upper whisker: 41.96), EC Cilia Mut (min: 25.57, Q1: 27.82, median: 30.07, Q3: 32.33, max: 34.58, lower whisker: 25.57, upper whisker: 34.58), EndoMT Cilia WT (min: 19.77, Q1: 20.94, median: 22.10, Q3: 27.60, max: 33.09, lower whisker: 19.77, upper whisker: 33.09), EndoMT Cilia Het (min: 15.14, Q1: 17.19, median: 19.23, Q3: 21.28, max: 23.33, lower whisker: 15.14, upper whisker: 23.33), EndoMT Cilia Mut (min: 30.51, Q1: 32.02, median: 33.54, Q3: 35.05, max: 36.57, lower whisker: 30.51, upper whisker: 36.57), HE Cilia WT (min: 3.11, Q1: 4.43, median: 5.76, Q3: 7.53, max: 9.30, lower whisker: 3.11, upper whisker: 9.30), HE Cilia Het (min: 1.38, Q1: 3.93, median: 6.47, Q3: 9.02, max: 11.57, lower whisker: 1.38, upper whisker: 11.57), HE Cilia Mut (min: 2.59, Q1: 4.71, median: 6.84, Q3: 8.96, max: 11.09, lower whisker: 2.59, upper whisker: 11.09), Late EndoMT Cilia WT (min: 6.95, Q1: 6.96, median: 6.98, Q3: 9.04, max: 11.11, lower whisker: 6.95, upper whisker: 11.11), Late EndoMT Cilia Het (min: 6.06, Q1: 6.26, median: 6.46, Q3: 6.66, max: 6.86, lower whisker: 6.06, upper whisker: 6.86), Late EndoMT Cilia Mut (min: 0.82, Q1: 1.34, median: 1.86, Q3: 2.39, max: 2.91, lower whisker: 0.82, upper whisker: 2.91), PIM Cilia WT (min: 5.26, Q1: 6.34, median: 7.43, Q3: 8.37, max: 9.30, lower whisker: 5.26, upper whisker: 9.30), PIM Cilia Het (min: 3.42, Q1: 3.45, median: 3.47, Q3: 3.50, max: 3.53, lower whisker: 3.42, upper whisker: 3.53), PIM Cilia Mut (min: 2.45, Q1: 3.38, median: 4.30, Q3: 5.23, max: 6.15, lower whisker: 2.45, upper whisker: 6.15), Prolif. EC 1 Cilia WT (min: 14.39, Q1: 17.66, median: 20.93, Q3: 23.19, max: 25.45, lower whisker: 14.39, upper whisker: 25.45), Prolif. EC 1 Cilia Het (min: 8.24, Q1: 14.21, median: 20.19, Q3: 26.16, max: 32.13, lower whisker: 8.24, upper whisker: 32.13), Prolif. EC 1 Cilia Mut (min: 2.77, Q1: 6.53, median: 10.29, Q3: 14.04, max: 17.80, lower whisker: 2.77, upper whisker: 17.80), Prolif. EC 2 Cilia WT (min: 0.00, Q1: 0.00, median: 0.00, Q3: 0.48, max: 0.96, lower whisker: 0.00, upper whisker: 0.96), Prolif. EC 2 Cilia Het (min: 0.00, Q1: 6.91, median: 13.82, Q3: 20.74, max: 27.65, lower whisker: 0.00, upper whisker: 27.65), Prolif. EC 2 Cilia Mut (min: 0.00, Q1: 0.08, median: 0.16, Q3: 0.24, max: 0.32, lower whisker: 0.00, upper whisker: 0.32), Valvular EC Cilia WT (min: 1.16, Q1: 2.13, median: 3.11, Q3: 4.08, max: 5.04, lower whisker: 1.16, upper whisker: 5.04), Valvular EC Cilia Het (min: 2.17, Q1: 2.75, median: 3.34, Q3: 3.92, max: 4.51, lower whisker: 2.17, upper whisker: 4.51), Valvular EC Cilia Mut (min: 8.09, Q1: 10.51, median: 12.94, Q3: 15.36, max: 17.78, lower whisker: 8.09, upper whisker: 17.78). Box-plot stats for d): Endocardium Cilia WT (min: 7.86, Q1: 10.50, median: 13.13, Q3: 14.79, max: 16.45, lower whisker: 7.86, upper whisker: 16.45), Endocardium Cilia Het (min: 13.05, Q1: 13.46, median: 13.87, Q3: 14.28, max: 14.69, lower whisker: 13.05, upper whisker: 14.69), Endocardium Cilia Mut (min: 15.07, Q1: 16.02, median: 16.96, Q3: 17.91, max: 18.85, lower whisker: 15.07, upper whisker: 18.85), Epicardium Cilia WT (min: 1.41, Q1: 1.76, median: 2.11, Q3: 2.33, max: 2.56, lower whisker: 1.41, upper whisker: 2.56), Epicardium Cilia Het (min: 1.32, Q1: 1.64, median: 1.96, Q3: 2.29, max: 2.61, lower whisker: 1.32, upper whisker: 2.61), Epicardium Cilia Mut (min: 1.22, Q1: 1.65, median: 2.08, Q3: 2.50, max: 2.93, lower whisker: 1.22, upper whisker: 2.93), Erythroid Cilia WT (min: 1.63, Q1: 2.14, median: 2.65, Q3: 4.74, max: 6.83, lower whisker: 1.63, upper whisker: 6.83), Erythroid Cilia Het (min: 1.31, Q1: 1.42, median: 1.52, Q3: 1.63, max: 1.74, lower whisker: 1.31, upper whisker: 1.74), Erythroid Cilia Mut (min: 0.89, Q1: 2.24, median: 3.58, Q3: 4.93, max: 6.28, lower whisker: 0.89, upper whisker: 6.28), Fibroblasts Cilia WT (min: 0.83, Q1: 1.05, median: 1.28, Q3: 1.63, max: 1.98, lower whisker: 0.83, upper whisker: 1.98), Fibroblasts Cilia Het (min: 0.87, Q1: 1.14, median: 1.41, Q3: 1.68, max: 1.95, lower whisker: 0.87, upper whisker: 1.95), Fibroblasts Cilia Mut (min: 0.61, Q1: 1.14, median: 1.68, Q3: 2.21, max: 2.75, lower whisker: 0.61, upper whisker: 2.75), Immune Cilia WT (min: 0.25, Q1: 0.26, median: 0.28, Q3: 0.83, max: 1.37, lower whisker: 0.25, upper whisker: 1.37), Immune Cilia Het (min: 0.31, Q1: 0.32, median: 0.32, Q3: 0.33, max: 0.34, lower whisker: 0.31, upper whisker: 0.34), Immune Cilia Mut (min: 0.64, Q1: 0.69, median: 0.74, Q3: 0.80, max: 0.85, lower whisker: 0.64, upper whisker: 0.85), Multipotent Progenitor Cilia WT (min: 1.28, Q1: 1.41, median: 1.54, Q3: 1.59, max: 1.65, lower whisker: 1.28, upper whisker: 1.65), Multipotent Progenitor Cilia Het (min: 0.51, Q1: 0.91, median: 1.31, Q3: 1.72, max: 2.12, lower whisker: 0.51, upper whisker: 2.12), Multipotent Progenitor Cilia Mut (min: 0.92, Q1: 2.58, median: 4.25, Q3: 5.91, max: 7.57, lower whisker: 0.92, upper whisker: 7.57), Myocardium 1 Cilia WT (min: 41.61, Q1: 42.25, median: 42.90, Q3: 49.70, max: 56.49, lower whisker: 41.61, upper whisker: 56.49), Myocardium 1 Cilia Het (min: 39.26, Q1: 42.10, median: 44.95, Q3: 47.79, max: 50.63, lower whisker: 39.26, upper whisker: 50.63), Myocardium 1 Cilia Mut (min: 21.86, Q1: 27.48, median: 33.11, Q3: 38.73, max: 44.36, lower whisker: 21.86, upper whisker: 44.36), Myocardium 2 Cilia WT (min: 26.14, Q1: 29.34, median: 32.55, Q3: 33.89, max: 35.23, lower whisker: 26.14, upper whisker: 35.23), Myocardium 2 Cilia Het (min: 27.64, Q1: 31.14, median: 34.64, Q3: 38.14, max: 41.64, lower whisker: 27.64, upper whisker: 41.64), Myocardium 2 Cilia Mut (min: 26.91, Q1: 32.26, median: 37.60, Q3: 42.95, max: 48.29, lower whisker: 26.91, upper whisker: 48.29). Abbreviations: A-Atrium, DEG-Differentially Expressed Gene, EC-Endocardial Cell, HE-Hematoendothelium, LV-Left Ventricle, PIM-Pro-inflammatory, vEC-Valvular Endocardial Cell, WT-Wildtype.
