Irvine – January 29th, 2021 - Fixstars Solutions Inc., a global leader in acceleration technologies, announced that a research paper on expansion sequencing -- which is one of the in situ sequencing (ISS) methods -- was published online in the journal of science today.
ISS is a new sequencing method which, unlike conventional DNA/RNA methods, is able to simultaneously profile sequences of bases and their locations in a cell. This paper developed expansion sequencing based on the expansion microscopy technology and enabled high resolution mapping of RNAs within tissue context on conventional microscopes.
Fixstars has contributed to accelerating the analysis and image processing of expansion sequencing with its software acceleration technologies and its high-speed storage. With Fixstars' help, the analysis software performance should be able to achieve a 35-fold speed increase (6-month analysis per 10TB data to 5-day analysis).
"The method of in situ RNA sequencing with expansion microscopy is one of the most revolutionary technologies which allows researchers to understand what sequences of RNA express with their spatial information in biological tissues. We extend our sincere congratulations to the authors and colleagues on the publication of their paper. It is a great honor for us to be involved with it. We continuously strive to provide ever-better services.", said one of co-authors, Atsushi Kajita, Ph.D., Manager, Software Engineering of Fixstars Solutions, Inc.
Fixstars will continue to accelerate life sciences through the provision of technical expertise in parallel processing.
- Research paper title:
- Expansion Sequencing: Spatially Precise In Situ Transcriptomics in Intact Biological Systems
- Authors (Fixstars Solutions, Inc. members only):
Atsushi Kajita (Manager, Software Engineering)
Karl Marrett (Software Engineer)
Robert Prior (Software Engineer)
- Methods for highly multiplexed RNA imaging are limited in spatial resolution, and thus in their ability to localize transcripts to nanoscale and subcellular compartments. We adapt expansion microscopy, which physically expands biological specimens, for long-read untargeted and targeted in situ RNA sequencing. We applied untargeted expansion sequencing (ExSeq) to mouse brain, yielding readout of thousands of genes, including splice variants and novel transcripts. Targeted ExSeq yielded nanoscale-resolution maps of RNAs throughout dendrites and spines in neurons of the mouse hippocampus, revealing patterns across multiple cell types; layer-specific cell types across mouse visual cortex; and the organization and position-dependent states of tumor and immune cells in a human metastatic breast cancer biopsy. Thus ExSeq enables highly multiplexed mapping of RNAs, from nanoscale to system scale.
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