Summary: University of Michigan researchers have developed FICTURE, a groundbreaking algorithm that, combined with their Seq-Scope technology, allows scientists to visualize gene expression at sub-micrometer resolution. This innovative approach reduces the cost of spatial transcriptome profiling from $10,000 to approximately $500, making advanced genetic research more accessible to laboratories worldwide.
Journal: Nature Methods, 2024
Reading time: 4 minutes
Hacking DNA Sequencers for Better Results
“Basically, we are hacking DNA sequencing machines and letting them do all of the hard work,” explains Hyun Min Kang, professor of biostatistics at U-M School of Public Health. This innovative approach transforms standard DNA sequencing equipment into powerful tools for studying gene expression at unprecedented detail.
To put the resolution in perspective, the technology can analyze areas smaller than a human hair, which ranges from 20 to 200 micrometers in width.
Breaking Through Data Barriers
Traditional methods have struggled with the vast amount of genetic information present in cells. “The problem is traditionally, there are no computational methods that allow us to understand this data set at microscopic resolution,” notes Jun Hee Lee, professor of Molecular & Integrative Physiology at U-M Medical School.
The new FICTURE algorithm solves this problem by pooling surrounding data to make accurate inferences at the micrometer level, providing clear, unbiased views of cellular activity.
Democratizing Advanced Research
Perhaps most significantly, the team has made this technology more accessible by dramatically reducing costs. The price for high-resolution spatial transcriptome profiling has dropped from about $10,000 to around $500, opening new possibilities for researchers worldwide.
“We’re getting a lot of emails from companies and other investigators who previously assumed they wouldn’t be able to do such experiments and analyses. Now they are in the realm of possibility,” says Lee.
Glossary
- Transcriptome: The collection of all RNA transcribed from genes within a cell or tissue
- Spatial transcriptomics: Technology that allows researchers to see where genes are active within tissue
- Seq-Scope: Method to analyze gene expression at sub-micrometer resolution
- FICTURE: Algorithm for analyzing high-resolution spatial genetic data
Reader Quiz
- Q: What is the new cost of high-resolution spatial transcriptome profiling with this technology?
A: Approximately $500 - Q: How does the resolution of this technology compare to a human hair?
A: It can analyze areas smaller than a human hair (which is 20-200 micrometers wide) - Q: What does FICTURE do to improve data analysis?
A: It pools surrounding data together to make accurate inferences at the micrometer level - Q: What type of machines are being “hacked” for this technique?
A: DNA sequencing machines
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