Fig. 2: Cross-species multiome atlas comparison reveals conservation between species.
From: A multimodal cross-species comparison of pancreas development
a UMAPs of integrated human, pig, and mouse atlases of pancreas development. Cells were colored by cell type, with the same colors indicating the same cell types across species (Hs, Homo sapiens; Ss, Sus scrofa; Mm, Mus musculus). b Spearman correlation of mean normalized gene counts per cluster comparing pig-human and mouse-human pairs (based on human orthologs). Analysis is limited to the 851 genes shared in the intersection of all species’ 4000 highly variable genes. c Dot plot showing mean expression of cell-type-specific differentially expressed TFs in human (one-vs-rest analysis using edgeR; FDR-corrected p-value < 0.05; Supplementary Data 3). Top genes with the highest logfold change that are expressed in > 20% of cells of the cluster are shown across all clusters (square color = cell type color in a) for all three species. Genes are mapped to human orthologs. Dot size represents the fraction of expressing cells per cluster (logarithmic scale). d Coverage plots showing pig-human conserved NEUROG3 genomic regions. Link positions were converted from pig to human genome assembly with UCSC liftOver tool (http://genome.ucsc.edu)119. Pseudo-bulk accessibility tracks were used to visualize DNA accessibility in a region by averaging signals from all cells within a cluster. e Heatmap of top differentially active motifs across cell types computed with chromVAR121 using human 12wpc scATAC-seq (top) and pig multiome (bottom) datasets. f UMAP visualizations of the inferred TF network from human scGLUE48-integrated scRNA/ATAC-seq (left) and pig multiome (right) data. Nodes represent TFs, colored by their highly expressed clusters and sized by network centrality. Edges show TF-target interaction strengths (orange: activating; gray: inhibiting). a–c: scRNA-seq of pancreatic cells from wild-type and INS-eGFP pigs. d–f: Multiome analysis of pancreatic cells from PTF1A-codon-improved-Cre/ROSA-mTmG pigs. Detailed sample information is provided in Supplementary Data 1.
