Figure 3. Integrating scRNA and snRNA-seq enables detection of outer and inner wall transcriptomes.

(A) snRNA-seq of C57BL/6 J limbal tissue identifies similar cell types as the sc RNA-seq but captures more endothelial cells (left panel). Expression of Egfl7 and Cdh5 in snRNA-seq endothelial cells (right panel). (B) Integration of sc and snRNA-seq endothelial cells followed by sub-clustering identifies BECs, LECs, IW SECs, OW SECs, and CC. Integration of sc- and sn- RNA sequencing shows distribution across clusters (bottom panel). (C) Heatmap of differentially expressed genes of the identified sub-clusters. (D) SECs and LEC sub-clusters identified in B, expressing Prox1. In the SEC cluster, IW cells express Npnt and OW cells Selp, CCs express Ackr1 and BECs robustly express Flt1. IW: Inner wall, OW: Outer wall, CC: Collector channels, BEC: Blood endothelial cell, LEC: Lymphatic endothelial cell, SEC: Schlemm’s canal endothelial cell.

Figure 3—figure supplement 1. EC and pericyte transcriptomes in scRNA-seq data guided by integrated multimodal data.

(A) Manually re-clustered UMAP showing BECs, pericytes, LECs, IW SECs, OW SECs, and CCs. (B, C) Differences in levels of gene expression among BEC, pericytes, LEC, IW SEC, OW SEC, and CC expressed in a heatmap (B) and a violin plot (C). OW: Outer wall, IW: Inner wall, CC: Collector channels, BEC: Blood endothelial cell, LEC: Lymphatic endothelial cell, SEC: Schlemm’s canal endothelial cell.