Hi @Denger,
Thanks for writing to the Forum. It’s exciting that you are working on COVID-19 research, as it relates to human brain. Looks like you have a few questions here:
- How to search for information on gene expression, across data sets?
- How do I know the brain health status for a specimen?
- How do I get more assistance with navigating the Allen Brain Map datasets?
Let’s start with 1: Search for genes across data sets.
It sounds like you are accustomed to accessing image data fro the Allen Human Brain Atlas (adult). If you navigate to that site, look for the ‘Search’ box in the upper right-hand section of the home page. Enter your gene of interest (Cldn5). You will see a Results page that includes information about this gene for most of our datasets, in the left-hand column. You can select what data you would like to limit based on those filters; for example, if you are not interested in mouse data, and just want to see gene expression for human, check the ‘Human’ box and re-filter. The results will cover a combination of datasets - in situ hybridization (ISH), microarray data, RNA-Seq data, etc. It will also cover a range of ages, conditions, all of which can be filtered. From the results shown, you can select what data you want to view.
2: How do I know the brain health status for a specimen?
For each dataset, the Technical Documentation is the first place to consult for more information. We recommend users familiarize themselves with the overall experimental design, the methods used, and consideration with analysis and presentation of the data. The Technical Documentation also has lists of references that complement or inform each dataset. Below are links to Technical Documentation for four different Human Brain datasets:
- Allen Human Brain Atlas - Adult: See Case Qualification and Donor Profiles (downloadable PDF)
- Allen Human Brain Atlas - Developing Brain. See Donor and Sample Metadata (downloadable PDF)
- Aging, Dementia and TBI: See ACT Cohort (downloadable PDF). A searchable summary table of donor information is available here.
- Allen Cell Types Database - Human Cell Types: See Case Qualification and Donors (downloadable PDF). A searchable summary table of donor information is available here.
3: How do I get assistance with learning how to navigate all this data?
There is a Forum topic on this question:
We wish you the best of luck with your research - consider sharing your insights here on the Forum, in our ‘Show and Tell’ section.