In situ FUNseq integrates (live-cell) phenotypes, spatial context, and omics to reveal rare cell types and interactions through high-depth profiling of selected single-cell regions.
What is the name of the methodology?
In situ functional sequencing (in situ FUNseq): a multiplexed live-to-fixed spatial transcriptomic profiling method
OI Name
Miao-Ping Chien
What is the methodology good for?
It is a spatial transcriptomics method that enables the capture of transcriptomes from user-defined regions at single-cell resolution in fixed cell or tissue samples, with higher sequencing depth than current sequencing-based spatial omics methods. The method is compatible with live-cell imaging prior to fixation and is non-destructive to the sample, allowing immunostaining both before and after the in situ FUNseq pipeline.
What is/are the main advantages of this methodology over related technologies (1-3 sentences)?
The method is a cost-effective and more sensitive spatial omics alternative to currently available approaches. It enables live-to-fixed spatial profiling by allowing live-cell imaging prior to fixation and subsequent library preparation, making it compatible with capturing complex cellular dynamics and interactions. Immunostaining can also be performed either before or after the pipeline.
“It took us 2.5 years to get here; now the real fun starts!” – Lars van Roemburg
What are the most important limitations of the methodology (1-3 sentences)?
Performing the assay requires a specialized microscope with a light-patterning modality; therefore, it may be best to collaborate with us. Furthermore, the conditions for final optimization for tissue profiling are still being developed.
What type of samples are compatible with methodology (yes, no, possibly)
Cancer cell lines | Primary cells in culture | Organoids | Primary tissue |
Yes | Yes | Possibly | Yes |
What future develops to the methodology are you planning, in any?
We aim to expand the in situ FUNseq methodology to spatial proteomics to develop a multi-omics approach. In addition, we will explore a microfluidics-based method to automate the whole pipeline.
If someone outside your lab wants to use the methodology, what is the best option?
The protocol is quite complex and requires a specialized microscope or imaging modality; therefore, it is best to contact and collaborate with us.
Name one or more people in your lab that are experienced with the methodology
Lars van Roemburg
Who originally developed the methodology (provide reference if applicable)?
In situ FUNseq is developed by the Miao-Ping Chien group, led by Lars van Roemburg. It is still unpublished.