Extended Data Fig. 3: RNA-seq quality controls.
From: An atlas of rabbit development as a model for single-cell comparative genomics
a) Number of high-quality cells sampled from each of the 26 scRNA-seq samples. Annotations refer to the anatomical dissections performed for GD9 samples. b) Distribution of UMIs (c) genes detected and (d) percentage of mitochondrial reads recorded across cells sampled from each of the 26 scRNA-seq samples (N = 19 embryos), coloured by developmental stage. The lower and upper hinges of the boxplots relate to the first and third quartiles respectively. The center line denotes the median and the whiskers extend to the largest/smallest value no further than 1.5 times the inter-quartile range from the upper/lower hinge respectively. Outlier points are plotted if they exceed the ranges defined by the the upper and lower whiskers. The number of cells used to calculate each statistic are shown in A) and are provided in the source data. e) Cells from samples taken at each developmental stage and anatomical dissection are highlighted in the UMAP embedding. Following batch correction, the samples are well mixed within the UMAP visualization. A - anterior section, M - mid section; P - posterior section; YS -yolk-sac/extraembryonic tissues; EP - embryo proper. QC values for each cell are available in the source data.
