High-throughput analysis of morphogen gradients using a microfludic device. Yoosik Kim1, Kwanghun Chung2, Jitendra S. Kanodia1, Emily Gong2, Stanislav Y. Shvartsman1, Hang Lu2. 1) School of Chemical and Biological Engineering and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544 USA; 2) School of Chemical and Biomolecular Engineering and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA.

   Quantitative analysis of developmental systems requires information about the regulatory regions of genes comprising the network and the spatial distribution of patterning signals. The dorsoventral (DV) patterning system of Drosophila embryo is arguably one of the best understood systems with regard to its sequence-specific transcriptional regulation, but the information on the distribution of patterning signals is currently lacking, mainly due to the technical difficulties associated with imaging the spatial distribution of proteins and transcripts along the DV axis of the embryo. To enable high-throughput analysis of the DV patterning signals, we developed a Microfluidic Embryo Trap Array (META), a device in which hundreds of embryos can be oriented vertically in a matter of a few minutes. Here, we present the design and the physical principles behind this device and demonstrate how it can be used to quantify morphogen gradients in fixed embryos and monitor nuclear divisions in live embryos. This design allowed us to image a large number of embryos to statistically analyze the patterning signals in fixed embryos. Using META, we quantified the spatial extent of Dorsal morphogen gradients and demonstrated how this gradient and the distribution of its signaling and transcriptional targets can be quantitatively compared between wild type and mutant backgrounds.