Figure 1

Single-cell transcriptomic profile of zebrafish intestinal cells

(A) Experimental design of isolated zebrafish intestines for single-cell RNA-sequencing (scRNA-seq). Intestines of 5 dpf ret mutant tg(phox2bb:GFP) zebrafish were isolated and enzymatically dissociated, as previously described for wildtype tg(phox2bb:GFP).²⁴ FACS was used to sort live, single cells for scRNA-seq.

(B) Uniform manifold approximation and projection (UMAP) analysis of scRNA-seq shows 8 distinct intestinal cell types. UMAP atlas was separated between control (wildtype) and ret mutant zebrafish samples.

(C) Feature dot plot represents the expression level of the top 5 transcripts (ordered by average log₂ fold change) per cluster between wildtype and ret mutant zebrafish. Features were separated according to clusters.

(D) Expression pattern of ret in UMAP atlas of wildtype and ret mutant zebrafish samples. Navy-blue indicates lower expression levels, while yellow indicates higher expression levels. Gray shows cells with no ret expression.

(E) Cluster size comparison of each cell type between wildtype and ret mutant zebrafish cells. Significantly differentially distributed clusters are represented in orange. The significance of differences was determined by a threshold of the false discovery rate (FDR) < 0.05 and an absolute log₂ fold change >0.58. The dotted line indicates the threshold of log₂ fold change.

(F) Bar plot (left) and stacked bar plot (right) show the cell number contributing to each cluster for all cell types in control (wildtype, light-blue) and ret mutant (light-purple) zebrafish samples.