@article {45418,
	title = {Atlas-builder software and the eNeuro atlas: resources for developmental biology and neuroscience.},
	journal = {Development},
	volume = {141},
	year = {2014},
	month = {2014 Jun},
	pages = {2524-32},
	abstract = {<p>A major limitation in understanding embryonic development is the lack of cell type-specific markers. Existing gene expression and marker atlases provide valuable tools, but they typically have one or more limitations: a lack of single-cell resolution; an inability to register multiple expression patterns to determine their precise relationship; an inability to be upgraded by users; an inability to compare novel patterns with the database patterns; and a lack of three-dimensional images. Here, we develop new {\textquoteright}atlas-builder{\textquoteright} software that overcomes each of these limitations. A newly generated atlas is three-dimensional, allows the precise registration of an infinite number of cell type-specific markers, is searchable and is open-ended. Our software can be used to create an atlas of any tissue in any organism that contains stereotyped cell positions. We used the software to generate an {\textquoteright}eNeuro{\textquoteright} atlas of the Drosophila embryonic CNS containing eight transcription factors that mark the major CNS cell types (motor neurons, glia, neurosecretory cells and interneurons). We found neuronal, but not glial, nuclei occupied stereotyped locations. We added 75 new Gal4 markers to the atlas to identify over 50\% of all interneurons in the ventral CNS, and these lines allowed functional access to those interneurons for the first time. We expect the atlas-builder software to benefit a large proportion of the developmental biology community, and the eNeuro atlas to serve as a publicly accessible hub for integrating neuronal attributes - cell lineage, gene expression patterns, axon/dendrite projections, neurotransmitters--and linking them to individual neurons.</p>
},
	keywords = {Animals, Axons, Cell Lineage, Central Nervous System, Computational Biology, Databases, Genetic, Dendrites, Drosophila melanogaster, Drosophila Proteins, Gene Expression Profiling, Gene Expression Regulation, Developmental, Genetic Markers, Interneurons, Mice, Neurons, Neurotransmitter Agents, Rats, Software},
	issn = {1477-9129},
	doi = {10.1242/dev.108720},
	author = {Heckscher, Ellie S and Long, Fuhui and Layden, Michael J and Chuang, Chein-Hui and Manning, Laurina and Richart, Jourdain and Pearson, Joseph C and Crews, Stephen T and Peng, Hanchuan and Myers, Eugene and Doe, Chris Q}
}
@article {6515,
	title = {A resource for manipulating gene expression and analyzing cis-regulatory modules in the Drosophila CNS.},
	journal = {Cell Reports},
	volume = {2},
	year = {2012},
	month = {2012 Oct 25},
	pages = {1002-13},
	abstract = {<p>Here, we describe the embryonic central nervous system expression of 5,000 GAL4 lines made using molecularly defined cis-regulatory DNA inserted into a single attP genomic location. We document and annotate the patterns in early embryos when neurogenesis is at its peak, and in older embryos where there is maximal neuronal diversity and the first neural circuits are established. We note expression in other tissues, such as the lateral body wall (muscle, sensory neurons, and trachea) and viscera. Companion papers report on the adult brain and larval imaginal discs, and the integrated data sets\&nbsp;are available online (http://www.janelia.org/gal4-gen1). This collection of embryonically expressed GAL4 lines will be valuable for determining neuronal morphology and function. The 1,862 lines expressed in small subsets of neurons (\&lt;20/segment) will be especially valuable for characterizing\&nbsp;interneuronal diversity and function, because although interneurons comprise the majority of all central nervous system neurons, their gene expression profile and function remain virtually unexplored.</p>
},
	keywords = {Animals, Central Nervous System, Databases, Drosophila, Drosophila Proteins, Embryo, Factual, Female, Gene Expression, Genes, Genetically Modified, Internet, Male, Nonmammalian, Regulatory Elements, Reporter, Transcription Factors, Transcriptional},
	issn = {2211-1247},
	doi = {10.1016/j.celrep.2012.09.009},
	author = {Manning, Laurina and Heckscher, Ellie S and Purice, Maria D and Roberts, Jourdain and Bennett, Alysha L and Kroll, Jason R and Pollard, Jill L and Strader, Marie E and Lupton, Josh R and Dyukareva, Anna V and Doan, Phuong Nam and Bauer, David M and Wilbur, Allison N and Tanner, Stephanie and Kelly, Jimmy J and Lai, Sen-Lin and Tran, Khoa D and Kohwi, Minoree and Laverty, Todd R and Pearson, Joseph C and Crews, Stephen T and Rubin, Gerald M and Doe, Chris Q}
}
