Questions about how to search cross-ABA data: ISH images and gene expression

[Denger]

My boss gave me a task to find some gene markers in ALLEN BRAIN ATLAS . And he gave me an example about “ACE2” which is related to Corona Virus. He hopes that I can find gene expression about ACE2.
I don’t know how to start my work at the beginning; then my boss told me that I can try to find a known gene marker “Cldn5” in ABA. Cldn5 appears in his nature article.

What I don’t understand is how I find the Cldn5 in TBI in HUMAN BRAIN ATLAS.
I just know how to find it in the ISH for HUMAN BRAIN ATLAS. I don’t know if it is in a healthy person, or a TBI patient sample. Who can help me? And thank you very much.

[brain]

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:

1. How to search for information on gene expression, across data sets?
2. How do I know the brain health status for a specimen?
3. 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:

About tutorials & training for the Allen Brain Atlas resources: something for everyone!

Our original Allen Mouse Brain Atlas started with “simple” options for exploration: search for a gene by its name, or by anatomical structure that it might be expressed in; or, search for a brain structure to see its spatial location in a reference map. Over the past 15+ years, we’ve expanded beyond genes, brain anatomy and mouse: our projects and data have grown in quantity, diversity and complexity. Sometimes it can be hard to grasp what all the data is that’s available, and how (or if!) …

We wish you the best of luck with your research - consider sharing your insights here on the Forum, in our ‘Show and Tell’ section.

[amyb]

Hi @Denger,
If you are interested in searching data just in the Aging, Dementia and TBI dataset, the format of that datasets is different from the Human Brain Atlas, and does not have comprehensive ISH image sets and microarray data. There are selected assays done, and RNA-Seq data covering genome-wide expression, from selected brain areas and samples that cover a range of pathological states.
Review the experimental overview in the Technical Documentation, and search for expression of your gene of interest in the ‘Search’ field in the upper right corner of the RNA-Seq data page. Use the ‘Select Donors’ dropdown menu on that same page to sub-select what sample profile you want (e.g., select Dementia cases if those cases are what you want to limit your analysis to). If you still have questions, try reading the Help section for more information on how to use the dataset.