Fig. 2

Multiplexed mRNA expression maps using in situ HCR. (A) Whole-mount fruit fly (Drosophila melanogaster) embryo: expression schematic and confocal micrographs for four target mRNAs on three planes. Embryo fixed: stage 4-6. (B) Mixed bacterial populations (Escherichia coli: WT, GFP+, RFP+): epifluorescence micrographs (single channels and merge) for three targets (gfp and rfp mRNAs and 16S rRNA). (C) Whole-mount sea urchin embryo (Strongylocentrotus purpuratus): expression schematic and three-dimensional reconstruction from confocal micrographs for three target mRNAs. Embryo fixed: 45 hpf. (D) Whole-mount zebrafish larva (Danio rerio): expression schematic and three-dimensional reconstruction from confocal micrographs for four target mRNAs within the brain. Larva fixed: 5 dpf. (E) Whole-mount nematode larva (Caenorhabditis elegans): expression schematic and confocal micrograph for three target mRNAs. Larva fixed: L3. (F) Whole-mount chicken embryo (Gallus gallus domesticus): expression schematic and confocal micrographs for three target mRNAs in the neural crest (merge and single-channel details). Embryo fixed: stage HH 11-12. (G) Whole-mount mouse embryo [Mus musculus: Tg(Wnt1-Cre; R26R-eGFP)]: expression schematic and three-dimensional reconstruction from confocal micrographs for three target mRNAs. Embryo fixed: E9.5. (H) FFPE human breast tissue section (Homo sapiens sapiens): expression schematic and epifluorescence micrographs for two target mRNAs and one rRNA (single channels and merges). Thickness: 4 µm. See Figs S2-S10 and Movies 1-5 for additional data.