FIGURE SUMMARY
Title

Mapping a multiplexed zoo of mRNA expression

Authors
Choi, H.M., Calvert, C.R., Husain, N., Huss, D., Barsi, J.C., Deverman, B.E., Hunter, R.C., Kato, M., Lee, S.M., Abelin, A.C., Rosenthal, A.Z., Akbari, O.S., Li, Y., Hay, B.A., Sternberg, P.W., Patterson, P.H., Davidson, E.H., Mazmanian, S.K., Prober, D.A., van de Rijn, M., Leadbetter, J.R., Newman, D.K., Readhead, C., Bronner, M.E., Wold, B., Lansford, R., Sauka-Spengler, T., Fraser, S.E., Pierce, N.A.
Source
Full text @ Development
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.

EXPRESSION / LABELING:
Genes:
Fish:
Anatomical Term:
Stage: Day 5
Fig. S6

Multiplexed in situ HCR in whole-mount zebrafish larvae (D. rerio). (a) Individual channels from 4-channel confocal images. For each of three replicate larvae, a representative optical section was selected for each channel based on the expression depth of the corresponding target mRNA. (b) Pixel intensity histograms for Signal + Background (pixels within solid boundary) and Background (pixels within dashed boundary). For each image, the total number of pixels within solid and dashed boundaries is the same. Larvae fixed: 5 dpf. Scale bar: 25 μm.
Acknowledgments
This image is the copyrighted work of the attributed author or publisher, and ZFIN has permission only to display this image to its users. Additional permissions should be obtained from the applicable author or publisher of the image. Full text @ Development
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