As a scientist doing research on the Basal Ganglia, I’m looking for viral genetic tools that allow me to specifically target cell types in the striatum for an upcoming set of experiments.

I use the Genetic Tools Atlas from the Allen Institute to explore whether Allen scientists have publicly shared suitable tools.

‍

Step 1: I open the Genetic Tools Atlas and get a general overview by scrolling around.

I review the provided experiment metadata. I see that at a glance there are several enhancer-adeno-associated viruses (AAVs) targeting the striatum but also ones for many other brain regions.

‍

Step 2: I use filters to reduce the list to only experiments that target the striatum.

I open the filter panel and find the “Coarse Labeled ROI” filters. I scroll down and select the checkbox next to “Striatum“. I see that there are 372 results that match my query.

‍

Step 3: I filter further to a “finer labeled ROI” & cell type of interest.

I apply an additional filter to narrow the data to a fine labeled ROI of “Striatum“ and an observed labeled cell population of “Cholinergic“. I’ve narrowed down my search to 36 highly relevant experiments.

‍

Step 4: I review “Hall of Fame” entries and related image data

I notice that 2 results use AAVs that were designated as particularly notable, i.e. “Hall of Fame”. I review their EPI & STPT image data. I use Neuroglancer to see how these enhancers are expressed in my regions and cell populations of interest.

Useful Hot-Keys for Neuroglancer:

• “ctrl + scroll” zoom
• “R” and “E” rotate
• “Z” locks to the nearby “straight” orientation
• “scroll” move through volume for STPT images
• “Shift + scroll” fast move through volume for STPT images

See the dedicated Neuroglancer documentation for more details.

‍

Step 5: I consider the enhancer suitable for my purposes and order it on Addgene - Vector ID lookup

The expression pattern meets my expectations and I decide to use it in future experiments.

I go to http://addgene.org . I type in the Vector ID “AiP14496“ I received from Genetic Tools Atlas and hit the Search button.

The results return one relevant enhancer:

I click into the enhancer entry to access further details and ordering information.

‍

Step 6: I explore non “Hall of Fame” entries and their image data

I explore the other results and find AiP13038 and its related image data. I use Neuroglancer to see how these enhancers are expressed in my regions and cell populations of interest. I note that its Addgene ID is listed directly in the Genetic Tools Atlas.

‍

Step 7: I consider the enhancer suitable for my purposes and order it on Addgene - Addgene ID lookup

I go to addgene.org. I type in the enhancer ID “191720“ I received from Genetic Tools Atlas and hit the Search button.

The results return one relevant enhancer:

I click into the enhancer entry to access further details and ordering information.

‍