Extended Data Fig. 3: Quality Control for single cell and single embryo measurements of ribosome occupancy and RNA expression.
From: Single-cell quantification of ribosome occupancy in early mouse development
a, The number of reads (x-axis) is plotted against the number of detected genes (y-axis). Three representative replicates are shown for each stage of development used for single cell ribosome profiling experiments and from GSE162060 (Pro02_TCGTCAGTAC, Pro05_CCAATCCAGG and Dis01_TCGCTCTGCT). The three mouse cells highlighted from GSE162060 were selected to represent median coverage in that study. The total number of detected genes using all CDS mapping reads is indicated along with genes detected with 1.25k, 2.5k, 5k, 10k, 20k, 30k and 40k sub-sampled coding regions mapping UMIs. The inset plot shows the zoomed-in version of the same data in the x-axis from 0 to 5k. b, Ribosome footprints from n = 15 single cell Ribo-ITP samples from GV, MII and 1-cell stages were used to calculate the fraction of reads mapping to each reading frame (Methods). Error bars indicate the standard error of the mean of replicates. c, Metagene plots of translation start and stop sites from a representative RNA-Seq experiment. In contrast to the ribosome profiling data, there is no detectable peak observed at translation start or stop sites. d, Metagene plots of translation start and stop sites from a representative Ribo-ITP experiment using a 2-cell or a 4-cell stage mouse embryo. Start sites (light green, left) and stop sites (dark green, right) are at position 0 on the x-axis. Positions of the aligned reads are adjusted according to their A-site offsets. e, CDS-mapping read counts from each transcript were used to compute the Spearman correlation coefficient. Ribo-ITP (orange) and RNA-Seq (blue) experiments are ordered by developmental stage. The colors indicate the strength of the correlation.
