Extended Data Fig. 5: Multiplex smFISH and quantification.
From: Visualizing DNA folding and RNA in embryos at single-cell resolution
a, Sequentially acquired images from multiplex smFISH and intron-FISH for 18 cytosolic mRNAs and 11 nascent RNAs, respectively, in a laterally cryo-sectioned Drosophila embryo about 11 hpf. b, A dorsolateral cryosection of another embryo, about 11 hpf, showing the positions of all RNAs quantified. The zoomed-in view shows the segmented cells and a higher-resolution depiction of the RNA positions. Bright foci for each mRNA transcript (Fig. 2a) were identified using an automated counting algorithm with a manually defined threshold. The embryo images were segmented to identify cell boundaries and each RNA transcript identified is depicted as a single spot, colour-coded by RNA species. Note, Abd-B has two differentially expressed isoforms (known as m and r) which are transcribed from different promoters. Similar results to those shown were obtained for 15 embryos.
