Fig 1: Visualizing Metadata and Gene Expression with CellTrails Maps(A) Cell origin metadata. Cells from lateral utricle preparations, which contained striolar cells (orange dots), distinctively accumulated along one of the two terminal branches of the CellTrails map (orange arrowhead; Fisher test p < 6 × 10-5). Cells from medial utricle preparations, which should not contain striolar cells, were more strongly associated with the other terminal branch (blue arrowhead; p < 3 × 10-3). Cells without collected metadata are not shown.(B) FM1–43 uptake metadata. Two hair cell branches with high FM1–43 uptake can be identified; cells labeled with medium FM1–43 intensity are found along the path leading to the bifurcation, and low FM1–43 cells are enriched at the remaining two major branches (purple arrowheads).(C) CellTrails maps project high expression of LOXHD1, TMC2, ATP2B2, and TNNC2 along the lateral-associated hair cell branch of the utricle. In situ hybridization on E15 chicken utricle cross-sections and whole-mount immunolabeling validated RNA or protein expression of these genes in striolar hair cells.(D) SKOR2 and SYN3 expression is associated with hair cells located along the medial-associated branch; in situ hybridization revealed corresponding transcripts in extrastriolar hair cells.(E) The spatiotemporal projection of high CALB2 gene expression at the bifurcation and the medial-associated branch was confirmed by in situ hybridization; CALB2 RNA was detected in extrastriolar and in scattered striolar cells.(F) Expression of supporting cell marker genes designates the progenitor cell pool located at the left side of the CellTrails maps. High TECTB expression was projected along the left branch within the progenitor population. Immunolabeling identified a subgroup of supporting cells located in the striola.(G) Transient peaks of ATOH1, KLHDC7A, and POU4F3 mark the nascent hair cell path between progenitors and the bifurcation toward maturing hair cells. POU4F3 mRNA was found in scattered extrastriolar and striolar cells.