@article {67274,
	title = {An open-source semi-automated robotics pipeline for embryo immunohistochemistry.},
	journal = {Scientific Reports},
	volume = {11},
	year = {2021},
	month = {2021 May 13},
	pages = {10314},
	abstract = {<p>A significant challenge for developmental systems biology is balancing throughput with controlled conditions that minimize experimental artifacts. Large-scale developmental screens such as unbiased mutagenesis surveys have been limited in their applicability to embryonic systems, as the technologies for quantifying precise expression patterns in whole animals has not kept pace with other sequencing-based technologies. Here, we outline an open-source semi-automated pipeline to chemically fixate, stain, and 3D-image Drosophila embryos. Central to this pipeline is a liquid handling robot, Flyspresso, which automates the steps of classical embryo fixation and staining. We provide the schematics and an overview of the technology for an engineer or someone equivalently trained to reproduce and further improve upon Flyspresso, and highlight the Drosophila embryo fixation and colorimetric or antibody staining protocols. Additionally, we provide a detailed overview and stepwise protocol for our adaptive-feedback pipeline for automated embryo imaging on confocal microscopes. We demonstrate the efficiency of this pipeline compared to classical techniques, and how it can be repurposed or scaled to other protocols and biological systems. We hope our pipeline will serve as a platform for future research, allowing a broader community of users to build, execute, and share similar experiments.</p>
},
	issn = {2045-2322},
	doi = {10.1038/s41598-021-89676-5},
	author = {Fuqua, Timothy and Jordan, Jeff and Halavatyi, Aliaksandr and Tischer, Christian and Richter, Kerstin and Crocker, Justin}
}
@article {65799,
	title = {Dense and pleiotropic regulatory information in a developmental enhancer.},
	journal = {Nature},
	volume = {587},
	year = {2020},
	month = {2020 Nov 01},
	pages = {235-39},
	abstract = {<p>Changes in gene regulation underlie much of phenotypic evolution. However, our understanding of the potential for regulatory evolution is biased, because most evidence comes from either natural variation or limited experimental perturbations. Using an automated robotics pipeline, we surveyed an unbiased mutation library for a developmental enhancer in Drosophila melanogaster. We found that almost all mutations altered gene expression and that parameters of gene expression-levels, location, and state-were convolved. The widespread pleiotropic effects of most mutations may constrain the evolvability of developmental enhancers. Consistent with these observations, comparisons of diverse Drosophila larvae revealed apparent biases in the phenotypes influenced by the enhancer. Developmental enhancers may encode a higher density of regulatory information than has been appreciated previously, imposing constraints on regulatory evolution.</p>
},
	issn = {1476-4687},
	doi = {10.1038/s41586-020-2816-5},
	author = {Fuqua, Timothy and Jordan, Jeff and van Breugel, Maria Elize and Halavatyi, Aliaksandr and Tischer, Christian and Polidoro, Peter and Abe, Namiko and Tsai, Albert and Mann, Richard S and Stern, David L and Crocker, Justin}
}
