Fig. 4: Single-cell RNA sequencing in BVSC(+/−) cells during WT cell differentiation in high and low oxygen concentrations. | Communications Biology

Fig. 4: Single-cell RNA sequencing in BVSC(+/−) cells during WT cell differentiation in high and low oxygen concentrations.

From: Oxygen tension modulates the mitochondrial genetic bottleneck and influences the segregation of a heteroplasmic mtDNA variant in vitro

Fig. 4

a Volcano plots showing the differentially expressed genes for each day between positive cells differentiating with the conventional (20% oxygen) and the modified (3% oxygen) protocol. Coloured dots represent significantly up-regulated (purple) and down-regulated (green) genes with multiple-testing corrected p-value < 0.05, as identified by Wilcoxon rank-sum tests (20% O2: D4: 47 cells, D5: 40 cells, D6: 45 cells, D7: 48 cells, n = 3; 3% O2: D4: 40 cells, D5: 48 cells, D6: 48 cells, D7: 48 cells, n = 3). b Scatter plots with marginal distributions showing the metabolism-related gene expressions in PGCLC at D5 and D6 (data combined together) when differentiated at low (blue) and high (red) oxygen concentration. Each dot represents a single cell. Its (x,y) coordinates are calculated by the number of genes expressed related to glycolytic (y axis) and OXPHOS (x axis) metabolism. Data consider the expression of 85 glycolytic genes and 96 OXPHOS genes (Supplementary Data 2). OXPHOS activity p-value = 4 × 10−3, glycolytic activity p-value = 2 × 10−7, Wilcoxon rank-sum tests were applied with significance threshold of 0.05 for DEG discovery, and Benjamini-Hochberg procedure was used to obtain multiple-testing corrected p-values (3% O2: 96 cells; 20% O2: 85 cells; n = 3). c Line plot showing the number of mtDNA-replication-related genes expressed per cell (mtDNA replication score, x axis) during PGCLC differentiation using the conventional protocol (red, 180 cells, n = 3) and modified protocol (blue, 184 cells, n = 3). The mtDNA replication score is calculated based on the expression of 18 genes (Supplementary Data 2), p-value = 0.0004, Wilcoxon rank-sum tests were applied with significance threshold of 0.05 for DEG discovery, and Benjamini-Hochberg procedure was used to obtain multiple-testing corrected p-values. d, e Mgme1 and Mthfd2 gene expressions during PGCLC differentiation at 20% (d) and 3% (e) oxygen concentration. Data represent the median of read counts ± SD. Wilcoxon rank-sum tests were applied with significance threshold of 0.05 for Differentially Expressed Gene (DEG) discovery and Benjamini-Hochberg procedure was used to obtain multiple-testing corrected p-values.

Back to article page