Single-cell in vivo imaging of cellular circadian oscillators in zebrafish
Fig 2
Characterization of nr1d1:VNP expressing cells.
(a) t-SNE visualization of brain cell clusters. The clusters were annotated by comparing to the adult zebrafish scRNA-seq data. (b) Violin plot demonstrated the clusters with enriched expression of nr1d1:VNP. Y axis denotes the normalized expression value. Note the highest levels in the pineal gland. (c) Fluorescence images show the co-expression of nr1d1:VNP (nuclear signal) and aanat2:mRFP (cytoplasmic signal) in the zebrafish pineal gland. The left graph illustrates the 3D location of the pineal gland in zebrafish larva. (d) Three-dimensional reconstruction of a common zebrafish pineal gland by aligning and averaging of six fish. The gray sphere represents the boundary of the pineal gland and the green color represents the density distribution of nr1d1:VNP-positive cells in the pineal gland. (e) Violin plot showed the expression of rod cell markers (rho, gnat1), cone markers (gnat2, gngt2a), and nr1d1:VNP in photoreceptor clusters. Y axis denotes the normalized expression value. (e) Fluorescence images showed the co-expression of nr1d1:VNP (nuclear signal) with the Tg(xops:nfsB-mCherry) fish line (cytoplasmic signal) and Tg(lws2:nfsB-mCherry) fish line (cytoplasmic signal) in the zebrafish pineal gland. The numerical values for panel b and e are in S1 Data. scRNA-seq, single-cell RNA-seq; t-SNE, t-distributed stochastic neighbor embedding; VNP, Venus-NLS-PEST.