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From this tab you can browse and select from reporter lines and driver lines used in the creation of the Allen Mouse Brain Connectivity Atlas.

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Searching

Search the Transgenic Mouse dataset by entering a gene symbol or mouse line name into the search box. You will be prompted with suggestions once you have started typing. Click "Search" or hit the Enter key.

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Each driver line is represented by its name, a representative image (which is magnified when clicked) and a description of expression. Clicking on the line name will return results from all characterization experiments for that particular line.

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Reporter Lines

This drop-down menu lists all the characterized reporter lines with a description of their expression patterns.

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Search Results

Clicking on Search will return a list of experiments based on your search criteria with information on the Experiment ID, Line Name, Driver, Reporter, Probes, Age, Sex, Treatments and Image Count. Click on the Experiment ID to be taken to the #Experiment Detail Page

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To compare multiple experiments, mark the checkboxes to the left of each row, then click the "Compare Selected Experiments" button. Note: the selection list may contain experiments from the "Projection" or "BDA/AAV" studies but these will not appear when you 'View Selections' for the Transgenic Characterization data. Your choices are stored in a browser 'cookie' on your computer and will remain in effect until you click the "Clear Selections" button, or clear your Web browser cookie cache.

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Experiment Detail Page

Clicking on the experiment summary link returns a summary of the experimental details (see screenshot).

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  1. Experimental Metadata: Experiment ID, Transgenic Mouse, Driver, Reporter, Related Gene (click for Adult Mouse data), Probes, Plane of Section, Treatments, Induction; Specimen Data: Specimen ID, Organism, Strain, Age, Sex. Related Institute Data: provides links to related data in other Allen Brain Atlas resources
  2. Image Viewer: Zoom and Pan Viewer
  3. 3-D Thumbnail Viewer: Rotate using the slider bar under the image
  4. Histogram: Relative gene expression in large structures of the brain (for stages older than P28). Hovering your mouse over the histogram will sync the image in the single image viewer with the section corresponding to that structure and expression.
  5. Transgenic Line Metadata: Transgenic lines involved in this experiment including the Type, Name, Stock #, Source (link to provider), and the Originating Lab.
  6. Probe Information: Probe ID, Type, NCBI Accession, GI, Orientation, Forward Primer, Reverse Primer and Sequence.

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Using the Zoom And Pan (ZAP)

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Image Viewer

The Zoom and Pan (ZAP) Image Viewer is a powerful tool to navigate and view the images in an experiment. The main part of the viewer is an interactive window where an image can be repositioned by dragging with a mouse. Use the scroll wheel, on-screen navigation buttons or the keyboard commands to zoom in or out.

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Key

Function

F

Advance to the next image in the series

D

Go back to the previous image in the series

R

Advance to the last image in the series

E

Go back to the first image in the series

A

Zoom in

Z

Zoom out

S

Sync all viewers on the page to the zoom level and location of the active viewer

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Zoom in. Please note that some keyboards may require the [Shift] key be held down while pressing the [+] key

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Zoom out

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