Fig. 3

The Gt(dmd-citrine)^ct90a trap line enables visualizing differential expression in homozygous and heterozygous embryos via in situ HCR.

(a, f, k) Schematic of in situ HCR experiment showing dmd and citrine HCR probe binding sites within dmd and dmd-citrine transcript. The dmd HCR probe should bind to both dmd and dmd-citrine transcripts, while citrine HCR probe binds only to dmd-citrine transcript. (b-e, g-j, l-o). in situ HCR analysis of dmd (blue) and dmd-citrine (green) transcript in wild type (b-e), heterozygous (g-j) and homozygous (l-o) Gt(dmd-citrine)^ct90a embryos. Tmp3 transcripts counter-stain muscles in red. Insets in (d),(i) and (n) show zoomed in view of transcription sites in the nuclei. Two dots are detected in homozygous embryos (k-n) whereas only one dot is detected in the nuclei of heterozygous ct90aGT embryos (f-i) while no citrine dots are detected in wild types embryos (a-d), consistent with the copy number of citrine inserted in the respective embryos. (e, j, o) Magnified images of the three types of embryos with nuclei stained in DAPI and the transcripts indicated by arrowheads. Scale bar (b-d, g-i, l-n)20µm (e,j,o)10µm.