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New Open Science Database Published to Study Microglia
Microglia—the immune cells of the brain—have been an important area of study over the last decade, especially with respect to their impact on brain disorders. In a recently published paper, DMCBH member Dr. Annie Ciernia and her team used an open science platform to help researchers understand how certain genes are regulated in microglia.
“There has been a large amount of data generated in the last 10 years looking at microglia in terms of how their genes are regulated in different disease states, but the data comes from many different labs and is spread out across multiple papers and websites,” says Dr. Ciernia. “This makes it hard to draw any real conclusions across studies unless you find the genes you’re looking for and manually compare them, which is very laborious and time consuming.”
To make it easier for researchers to study microglia, Dr. Ciernia’s undergraduate student Justin Jao built a database comprised of over 160 previously published microglia and brain disorder-relevant gene lists. This way, anyone interested can upload their genes of interest into the database to better understand how specific microglial genes might be impacted in different disorders and at various stages of development.
“What we wanted to do was put all this information into one simple and easy to use place so that users can access it without writing any computer code,” says Dr. Ciernia.
Dr. Ciernia’s lab is interested in microglia because many neurodevelopmental disorders show hallmark changes in microglia, suggesting these cells might play an important role. However, this microglia dataset provides a launching pad for future projects—the same code could be used to generate a database for other genes and cell types. The code is openly available on the Ciernia Lab Github.
Dr. Ciernia says the COVID-19 pandemic provided the perfect opportunity to work on this project, as her lab wasn’t initially able to generate any new data. Instead, they decided to work with previously collected data to develop a tool that will likely benefit many researchers.
“I hope people use our tool to inform their own experiments and to interpret how genes they’ve identified in a particular model or disease might be related to other disorders or other processes that happen naturally in development,” says Dr. Ciernia. “The other use is really in hypothesis generation. If you have a disorder you’re interested in, you can use our tool to help narrow down which microglial genes might be good candidates to go into the lab and test.”
Access the tool here: https://ciernialab.shinyapps.io/MGEnrichmentApp/