# Tutorial: Finding AAVs for targeting Cholinergic cell populations in the striatum **URL:** https://community.brain-map.org/t/tutorial-finding-aavs-for-targeting-cholinergic-cell-populations-in-the-striatum/3673 **Category:** Genetic Tools Atlas **Created:** [September 16, 2024, 4:12pm UTC](https://community.brain-map.org/t/tutorial-finding-aavs-for-targeting-cholinergic-cell-populations-in-the-striatum/3673 "2024-09-16T16:12:05Z") **Posts on this page:** 1 **Page:** 1
### Author: ![SvenOtto](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/svenotto/32/893_2.png) [@SvenOtto](https://community.brain-map.org/u/SvenOtto) #### Post date: [September 16, 2024, 4:12pm UTC](https://community.brain-map.org/t/tutorial-finding-aavs-for-targeting-cholinergic-cell-populations-in-the-striatum/3673/1 "2024-09-16T16:12:05Z")
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**](https://knowledge.brain-map.org/data/7CVKSF7QGAKIQ8LM5LC/specimens) **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. ![image](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/2X/f/f668f470006e08953c8a30f2132071806311426b.png) **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. ![image](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/2X/c/c1342a5d7f14097a0676210a73514baaddc069b4.png) **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. ![image](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/2X/c/c847a2bfa21a71e839012628a7e3edd036747fc2.png) ![image](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/2X/b/b33450763b98bcc4c886d1f593cc0e4068f843c9.png) **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. ![image](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/2X/0/0a65ee2d7e998fd5eab478bd31ffaa6919b486bf.png) **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](https://community.brain-map.org/t/using-neuroglancer-to-explore-images/) for more details. ![AiP14496_EPI](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/2X/8/8cc3efa242b19e77cafc637bf2633db120309071.jpeg) ![AiP14496_STPT](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/2X/4/49492f1c6ef685a8b28505612e11f019cff36b90.jpeg) **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](http://addgene.org/) . I type in the Vector ID “AiP14496“ I received from Genetic Tools Atlas and hit the Search button. ![AiP_step1](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/2X/3/362176838d2615b77d6e4c1e1e0f3785c0e18ca8.jpeg) The results return one relevant enhancer: ![AiP_step2](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/2X/0/040205a2fc7c87355c820f10b8d16b443dcfc185.jpeg) I click into the enhancer entry to access further details and ordering information. ![AiP_step3](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/2X/f/f98981c32ee4c7480af6e88fd8777d53c739588f.jpeg) **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. ![GTA_addgeneID](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/2X/8/8ceb21c7e137aeb2e8c188e33087bea9d3cc166b.jpeg) ![AiP13038_EPI](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/2X/c/cdb744ae825f3bb050547cc8a6708c7cf08cbe6a.jpeg) ![AiP13038_STPT](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/2X/4/467e492d9378ece2fe19cb10104bc00f55b9e518.jpeg) **Step 7: I consider the enhancer suitable for my purposes and order it on Addgene - Addgene ID lookup** I go to [addgene.org](http://addgene.org/). I type in the enhancer ID “191720“ I received from Genetic Tools Atlas and hit the Search button. ![addgeneID_step1](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/2X/c/c72e03a6e62317fcbaac23a61edbe0e5e0f6d20a.jpeg) The results return one relevant enhancer: ![addgeneID_step2](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/2X/8/8c59274e6be3f42a202182d4acbb55636839803b.jpeg) I click into the enhancer entry to access further details and ordering information. ![addgeneID_step3](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/2X/c/c99c3ee12b6c14b3345a396c3bf222c4935fcf33.jpeg)