Extended Data Fig. 6: Whole embryo scATAC-seq and trophoblast annotation.
From: An atlas of rabbit development as a model for single-cell comparative genomics
a) An illustration of the 8 samples (N = 4 embryos) processed for single-cell ATAC-sequencing. b) Quality control of whole embryo scATAC-seq nuclei based on transcription start site (TSS) enrichment score, total number of fragments per cell, and fraction of reads in peaks (FRIP) across samples. 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. Number of nuclei per sample - BGRGP1:26250; BGRGP2 12246; BGRGP3 13008; BGRGP4 4887; BGRGP5 12192; BGRGP6 11982; BGRGP7 11313; BGRGP8 10368. c) The fragment size distribution plotted for each scATAC-seq sample. d) UMAP of 34,082 nuclei that passed quality control for scATAC-seq, colored by predicted cell type inferred from label transfer (see Methods). Inset shows the UMAP colored by developmental stage. e) Linear regression between mean RNA expression and mean ATAC gene scores across cell-types, for top 50 marker genes of annotated cell-types. Top left panel shows linear regression along with values across cell-types for SCT marker genes, other panels only show the linear model itself. Red dotted lines indicate a slope of 1 (see Methods). f) Gene Activity scores of marker genes for refined trophoblast to SCT cell-type annotation. g) Motif enrichment in marker peaks for refined trophoblast to SCT cell-type annotation. h) Genome browser views of the regions surrounding EOMES, CDH5, FOXA2, GATA1 & HDAC6, HBG1/2, PAX6, TBX6 for selected cell-types. N = 4 embryos in all panels. QC values, fragment size distributions, UMAP coordinates, predicted annotations, linear model parameters and heatmap values are all available in the source data.
