Extended Data Fig. 1: Temporal and transcriptional analysis of multiomics data set.
a) WNN embedding of cells (1b) colored based on time point origin. b) Proportion of the number of cells within each identified WNN cluster relative to total number of cells from 0 dpi or 2 dpi across the full embedding (top). Relative proportion of number of cells within each identified WNN cluster from either 0 dpi or 2 dpi relative to total number of cells from both timepoints within each cluster (bottom). c) UMAP plot visualizing intestinal cell types generated using unsupervised clustering of single nuclei RNA-Seq data at 0 and 2 dpi. Clusters identified at higher resolutions (colour coded) were collapsed into groups corresponding to the indicated major lineages. d) Clusterwise median of the weighting of ATAC (red bar) and RNA (blue bar) data on the nuclei embedding for each of the indicated WNN clusters (x axis) identified in Fig. 1b. e) Relative proportion of nuclei (legend) from each WNN cluster (x axis) that mapped to the indicated ATAC cluster is shown as a heatmap. f) Proportion of the number of cells within each identified ATAC cluster relative to total number of cells from 0 dpi (blue) or 2 dpi (red) across the full embedding (top). Relative proportion of number of cells within each identified ATAC cluster from either 0 dpi (blue) or 2 dpi (red) relative to total number of cells from both timepoints within each cluster (bottom). g) Dot plot of the average ChromVAR Z-scores of each cell type for the indicated motifs. Size of the dot corresponds to the percentage of nuclei from any given cell type that that has >0 or <0 ChromVAR z-scores depending on if the average is positive or negative, respectively. Multiomics source data available at GEO: GSE230766.
