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Brain-wide cellular resolution imaging of Cre transgenic zebrafish lines for functional circuit-mapping.

Kathryn M Tabor | Gregory D Marquart | Christopher Hurt | Trevor S Smith | Alexandra K Geoca | Ashwin A Bhandiwad | Abhignya Subedi | Jennifer L Sinclair | Hannah M Rose | Nicholas F Polys | Harold A Burgess
eLife | 2019

Decoding the functional connectivity of the nervous system is facilitated by transgenic methods that express a genetically encoded reporter or effector in specific neurons; however, most transgenic lines show broad spatiotemporal and cell-type expression. Increased specificity can be achieved using intersectional genetic methods which restrict reporter expression to cells that co-express multiple drivers, such as Gal4 and Cre. To facilitate intersectional targeting in zebrafish, we have generated more than 50 new Cre lines, and co-registered brain expression images with the Zebrafish Brain Browser, a cellular resolution atlas of 264 transgenic lines. Lines labeling neurons of interest can be identified using a web-browser to perform a 3D spatial search (zbbrowser.com). This resource facilitates the design of intersectional genetic experiments and will advance a wide range of precision circuit-mapping studies.

Pubmed ID: 30735129

Research resources used in this publication

None found

Antibodies used in this publication

None found

Associated grants

  • Agency: Eunice Kennedy Shriver National Institute of Child Health and Human Development, International
    Id: 1ZIAHD008884-04
  • Agency: Virginia Tech, International
    Id: Advanced Research Computing
  • Agency: Virginia Tech Advanced Research Computing, International
    Id: NA

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This is a list of tools and resources that we have found mentioned in this publication.


MATLAB (tool)

RRID:SCR_001622

Multi paradigm numerical computing environment and fourth generation programming language developed by MathWorks. Allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, Java, Fortran and Python. Used to explore and visualize ideas and collaborate across disciplines including signal and image processing, communications, control systems, and computational finance.

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GitHub (tool)

RRID:SCR_002630

A web-based hosting service for software development projects that use the Git revision control system offering powerful collaboration, code review, and code management. It offers both paid plans for private repositories, and free accounts for open source projects. Large or small, every repository comes with the same powerful tools. These tools are open to the community for public projects and secure for private projects. Features include: * Integrated issue tracking * Collaborative code review * Easily manage teams within organizations * Text entry with understated power * A growing list of programming languages and data formats * On the desktop and in your pocket - Android app and mobile web views let you keep track of your projects on the go.

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Zebrafish International Resource Center (tool)

RRID:SCR_005065

Center that supplies access to wild-type, mutant, and transgenic zebrafish lines, EST's/cDNAs, antibodies and fish health services. ZIRC Health Services include diagnostic pathology testing for zebrafish and other small laboratory fish species.

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