Exploring the cellular and molecular basis of murine cardiac development through spatiotemporal transcriptome sequencing

Figure 1:. Spatial and temporal atlas of mouse heart development. (A) Mouse heart sampling and Stereo-seq protocol. (B) Uniform manifold approximation and projection (UMAP) of Stereo-seq clustering and annotation of 22 spatial mouse chips. (C) Heatmap of the expression of the top 3 marker genes for each cell type. (D) Spatial and temporal distribution of mouse heart cells. (E) Proportional changes of different cell types at 4 time points.

Figure 2:. Cell–cell interactions of different cell types. (A) Cell interaction strength and interaction count at 4 time points. (B) Cell interaction strength among cells at E20. The direction of the arrow indicates the direction of the signal, and the thickness of the line segment indicates the signal strength. (C) Ingoing interaction strength of different cell types at 4 time points. (D) Outgoing interaction strength of different cell types at 4 time points. (E) Signal pathway strength of different cell types at 4 time points. The shade represents the relative strength of the interaction between the 2 cell types.

Figure 3:. Classification of cell subtypes. (A–C) Subtype clustering of vCMs, aCMs, and FBs. (D–F) Expression of the top 5 marker genes in vCMs, aCMs, and FBs. (G–I) Enrichment of the top 5 GO functions in vCMs, aCMs, and FBs.

Figure 4:. Trajectory analysis and transcription factor analysis. (A) Trajectory analysis of 3 cell types (aCMs, vCMs, FBs). The distribution of pseudo-time, cell types, time points, and cell states along the trajectory from left to right. (B) Heatmap of gene expression changes in 3 cell states at branch node 1 and GO enrichment results of different clustered genes. The left cluster tree divides genes into 3 groups according to the trend of gene expression. (C) Transcription factor activity changes among 3 cell types (aCMs, vCMs, FBs) at 4 time points. (D) Changes in the activity of transcription factors targeting the gene Igf2 in 3 different cell types over time. (E) Correlation between Plagl1 transcription factor activity and gene expression. The red dots represent the target genes of Plagl1. (F) Relative quantification of Plagl1 at 4 time points using quantitative PCR. (G) Relative quantification of Igf2 at 4 time points using quantitative PCR.

Figure 5:. Identification of left and right atria. (A–D) The spatial representation of HE sections, the actual regions of the left and right atria, and the clustering results of mouse hearts at 4 time points. (E) Accuracy of clustering results of the left and right atria relative to the actual distribution. (F) Differential expression of genes comparing the left atrium to the right atrium at 4 time points. (G) Intersection of highly variable genes in the left atrium at 4 time points. (H) Intersection of highly variable genes in the right atrium at 4 time points.