Jones, Allan R., and Overly, Caroline C. "Mapping the Mind" (Scientific American)
Allen Institute for Brain Science. "Most comprehensive wiring diagram of the mammalian brain to date" (ScienceDaily)
Oh et al., A mesoscale connectome of the mouse brain, Nature (2014): BrainAtlasNaturePaper.pdf
This is the original paper describing the mouse brain connectivity data.
In this virtual lab, you will learn how to use the freely-accessible Allen Brain Atlas. You will learn how to use this resource to find where in a mouse brain a specific gene is expressed. You will then identify a brain region that expresses your gene of interest and figure out which other brain regions are connected to it. You can access the atlas at www.brain-map.org and you will see that it is composed of various sections. We will be focusing on the Mouse Brain and Mouse Connectivity datasets. If you need some help in navigating this resource, the site provides some pretty good tutorials. It is also assumed that you have familiarized yourself with some basic anatomical orientation terms (such as coronal, sagittal, anterior, posterior, etc.) as well as the fundamentals of mammalian brain anatomy as we reviewed in this lesson. The readings for this lesson will introduce you to the brain atlas both for the gene expression and connectivity studies.
The videos below provide an example of how to do the exercise, but other than that I’m not going to provide more examples. However, you are encouraged to work together. Please use Piazza to work collaboratively. Ask your own questions and answer your classmates' inquiries. If you are wondering how to figure out what a specific gene does, entering the gene's name into Google. Use the internet to pull up information from a bunch of different regions, likewise for figuring out brain regions. The rest you should be able to figure out using the Allen brain atlas. Do your best and let’s see what you come up with!
This video tells you how to find the expression pattern of your gene of interest:
This second tutorial explains how to find the projection patterns of your gene of interest:
There are a number of ways to submit this assignment. Choose the option below that best suits your needs. Ideally, we would like all of your work submitted as one assignment as either a .doc, .docx, or .pdf.
1. Download the following worksheet: AllenVLab.doc
2. Save the worksheet on your computer and rename it: LastName.FirstName.AllenVLab.doc
3. Keep the worksheet open and toggle back and forth between the virtual lab and worksheet, making sure to answer each question based on the simulator. Remember to save regularly.
Note: To add images (.jpg, .png, .tiff, etc.) to a Word document, click 'Insert' and choose photo. For more detailed instructions from Microsoft, click here.
4. Click 'Submit Assignment' and upload your completed worksheet on this assignment page.
1. Open 'Google Docs'. (You must have a google account first. To set up a Google account, click here.)
2. Create a new 'Document'.
3. Click here and then cut and paste the assignment questions into your new Google doc. and enter your answers.
Note: To add images (.jpg, .png, .tiff) to a Google document, click 'Insert' and choose photo. For more detailed instructions from Google, click here.
4. When you are finished with your work, use the 'File' menu to rename the document as LastName.FirstName.AllenVLab and download it as a .pdf.
5. Click 'Submit Assignment' and upload your completed worksheet on this assignment page as .pdf.