Fig. 5
Quality control and PCA of the RNA-seq data. (a) Mean base quality scores across read positions, shown as Phred scores for all libraries. (b) Distribution of mean quality scores across all reads in each sample. (c) Percentage of undetermined bases (N) at each position along the reads, with individual samples represented by green lines. Shaded regions indicate quality thresholds: green for high quality, yellow for moderate quality, and red for low quality. (d) Gene-body coverage profiles showing normalized read coverage from the 5′ to 3′ end across transcripts, indicating uniform coverage and minimal positional bias. (e) Sequencing-depth saturation curves showing the number of genes detected (≥10 counts) as a function of the number of reads retained, demonstrating adequate sensitivity at the achieved read depth. (f) Principal Component Analysis (PCA) showing variance in RNA expression profiles across the differentiation time course, with separation by day and clustering of biological replicates.
