Fig. 4.

Multiplexed mRNA imaging in whole-mount chicken embryos with large unoptimized probe sets using in situ HCR v3.0. (A) Expression schematics for four target mRNAs in the head and neural crest: FoxD3, EphA4, Sox10 and Dmbx1. (B) Four-channel confocal micrograph. (C) Zoom of depicted region of B. (D) Four individual channels from C with signal-to-background ratio measurements (mean±s.e.m., n=3 embryos). Probe sets: 12-20 split-initiator probe pairs per target. Amplifiers: four orthogonal HCR amplifiers carrying spectrally distinct fluorophores. Embryo fixed at stage HH10. See Fig. S12 and Table S15 for additional data.