Fig 1.
The Q cell lineage migration and differentiation.
(A) Schematic representation of the migration and cell divisions of Q neuroblasts and their descendants. (B) The Q cell lineage. (C) UMAP plot of the Q cell lineage during development with each cell type identified. Cell stage boundaries (e.g., separation between QR.a and QR.ap) were inferred from transcriptional differences and may be slightly offset from the actual timing of cell division. (D-E) Violin plots showing the variation in number of UMIs (D) or genes expressed (E) across the different Q cell types. (F-M) UMAP plots showing the expression pattern of marker genes used to identify the different Q cell types.
Fig 2.
Trajectory inference and gene expression dynamics.
(A) UMAP plot of the Q cell lineage showing the inferred trajectory (green line) across pseudotime. (B) Functional annotation of module groups obtained using WormCat. Categories in bold and marked with an * were observed only in that module group. Enrichment was determined using WormCat’s standard settings (Fisher’s exact test with Bonferroni correction; P < 0.01), and the categories shown correspond to the broadest functional level (Category 1) provided by WormCat. (C) Clustered heatmap showing modules of co-regulated genes expression across different Q cell types. Module groups were established based on module clustering.
Fig 3.
Analysis of Q neuroblast initial migration.
(A) UMAP plot clustering the early and late Q cells apart. (B) Volcano plot showing genes differentially expressed between early and late Q cells. (C) Expression of genes associated with initial Q cell polarization and migration plotted in pseudotime. The arrowhead indicates the point in pseudotime in which the first cell division occurs. (D) Micrographs of worms during the first few hours of postembryonic development showing the expression of an apical junction marker (ajm-1) by Q cells during their initial migration. (E) Dot plot showing the average expression of transcription factors differentially expressed in early Q cells. Results were filtered to display genes expressed in at least 5% of cells in any cluster.
Fig 4.
Differential expression analysis of genes with L-R asymmetry.
(A) UMAP segregating cells from the left- (red) or right-side (blue) lineages. Grey cells represent clusters in which we could not differentiate left from right. (B-F) Volcano plots showing genes asymmetrically expressed in the parent Q cells (B), the first (C) and second descendant (E) of the anterior lineage, and the first (D) and second descendant (F) of the posterior lineage.
Fig 5.
Analysis of genes differentially expressed between lineages and cell types regardless of L-R asymmetry.
(A) UMAP plot showing Q cell types clustering without L-R segregation. (B) Heatmap showing the top 10 markers differentially expressed in each cluster. (C) Volcano plot showing genes differentially expressed between the first descendants of the anterior and posterior lineages.
Fig 6.
Expression analysis of Wnt-related genes.
(A) Dot plot showing the average expression of Wnt-related genes in different Q cell types. Results were filtered to display genes expressed in at least 10% of cells in any cluster. (B-G) UMAP plots showing the expression pattern of selected Wnt-related genes.