Spatially resolving the molecular expression of multiple probes in 3D can help us understand complex biological processes. For instance, our group has linked abnormal shear stress patterns caused by regurgitant blood flow with resultant congenital heart defects (CHDs). Abnormal shear stress mapped on images of molecular expression gives additional context to developmentally critical pathways such as epithelial-mesenchymal transition (EMT). However, highly multiplexed 3D imaging is needed to accurately identify regions of interest in the looping heart. In this study, we demonstrate a sequential imaging of a library of HCR FISH probes.
Due to its accessibility, hemodynamics can be imaged in early stage quail embryo hearts longitudinally. Our group has linked abnormal shear stress patterns caused by regurgitant blood flow with resultant congenital heart defects (CHDs). To understand the mechanisms behind the development of these CHDs, it is imperative to image molecular expression at the sites of abnormal shear stress. However, molecular probes for the quail model are not extensive and 3D imaging is needed to accurately identify regions of interest in the looping heart. In this study, we present HCR FISH probes that target the shear stress responsive genes
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