Transgenic Characterization

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


Search the Transgenic Mouse project by entering a gene name, 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.

You can also browse through the data using the browse links on the search page; there are drop-down menus to view all of the #Driver Lines and #Reporter Lines used in this Database.

Driver Lines

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

Reporter Lines

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

Search Results

Clicking on Search will return a list of experiments based on your search criteria that outline 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

To compare multiple experiments, mark the checkboxes to the left of each row, then click the "Compare Selected Experiments" button. Any selections you make will remain selected until you click the "Clear Selections" button.

Experiment Detail Page

This page (see screenshot) includes all the experimental information.

The various sections of the experimental detail page are outlined 1-6 as follows:

  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
  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)
  5. * Transgenic Line Metadata:* Transgenic lines involved in this experiment including the Type, Name, Stock #, Source (link to Jackson Laboratories), and the Originating Lab.
  6. * Probe Information:* Probe ID, Type, NCBI Accession, GI, Orientation, Forward Primer, Reverse Primer and Sequence.

Image Viewer

All of the images in a series are displayed as a scrollable set of thumbnails. Clicking on one of the thumbnails will load the image into the large viewer above. To navigate the image use the toolbar buttons to the right of the viewer.

Using the Toolbar



Launch a High Resolution Image Viewer

Launch a contact sheet viewer

Pan left

Pan up

Pan down

Pan right

View fluorescent image (for fluorescent experiments only)

View ISH image (for ISH experiments only)

View #expression mask (for ISH experiments only)

View the nearest Nissl

Reset image defaults

Image Adjustment

Dark field images, such as fluorescent proteins (XFP), double fluorescent ISH (DFISH) & some immunohistochemistry (IHC) can be enhanced one color-channel at a time. To the right of each color slider control is the name of the probe expressed in that channel. The center position is neutral (image is neither enhanced nor diminished in that channel). Move the slider to the right to enhance the color, and to the left to diminish the color.

Bright-field images, such as colorimetric ISH and Nissl stained images have a single contrast slider control. Center is neutral, right is brighter, left is darker.

Experiment Metadata

Much of the background for each experiment is contained in the metadata panel. Where applicable, there are hyperlinks to the web site of the transgenic mouse distributor for further information on the mouse lines represented in the experiment. In most cases, there is also a link to the Allen Brain Atlas for the driver gene.

Clicking on the Related Data link will return a list of other Allen Institute projects using that particular gene.

Applicable probe details will be made visible by clicking on the "Show Probe Details" bar at the bottom of the metadata panel.

Expression Mask

The Expression mask image display highlights those cells that have the highest probability of gene expression using a heat map color scale (from low/blue to high/red).