Temporal single cell profiling on biopsies taken from living cells

Temporal single cell profiling on biopsies from living cells: find out more about how the FluidFM technology can support your single cell profiling needs. 

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Introducing new tools for single cell profiling

Recording gene expression changes throughout the lifetime of a single cell.

The true essence of a living organism lies within the uniqueness of its cells. Each cell possesses a distinct personality that expresses itself uniquely throughout its life cycle. To fully comprehend the complexity of such diversity, we must study individual cells rather than generalize their behavior. Although high-throughput single-cell technologies have made significant strides in the study of cellular heterogeneity, it is still challenging to detect relevant cell trajectories due to statistical averaging.

Temporal Single Cell Profiling with Cytoplasmic Biopsies by Cytosurge

However, with the FluidFM OMNIUM platform, we can now take picoliter biopsies that allow us to follow the dynamic changes that occur within living, single cells over time. It's an extraordinary opportunity to witness the evolution of a living organism with spatial and temporal resolution at the single-cell level.

Biopsies without compromising viability.

Gentle, force-controlled extraction keeps your cell alive after taking a biopsy.

Live monitoring of single cells

Take several biopsies of the same cell, while monitoring its development over time.

Temporal Gene Expression Profiling

Biopsies are snapshot representations of a cell’s transcriptome that can be analyzed downstream.

Do you want more information about single-cell biopsies?  

Workflows to support your single cell profiling experiment.

Both workflows are based on our proprietary FluidFM (Fluidic Force Microscopy) technology which uses closed microscopic channels in force sensitive probes. These probes have apertures down to 300 nm and allow to simultaneously sense interaction forces down to pN and to dispense or aspirate femtoliter volumes. This truly unique combination enables novel experimental designs for a wide range of applications in life sciences, biophysics and mechanobiology.

Biopsy Collection Workflow

The single-cell biopsy workflow comprises the extraction of a small volume of the cytoplasm or the nucleus from a single cell without disrupting the cell viability. This workflow was developed based on the work of Chen et al. (2022) who invented the Live-seq approach, combining single-cell biopsies with a low RNA-seq approach to perform temporal transcriptome profiling. [1] With Live-seq approach, two important applications are now possible: 

 Transcriptome before phenotyping: Record transcriptional events over time to reveal how molecular components influence cell behavior.

 Direct Lineage Tracing: Directly link an individual cell’s history and trajectory to unravel past cell states and understand lineage decisions.

Whole Cell Collection Workflow

This whole cell collection workflow consists in extracting the whole content of the cell while maintaining the cell native context for your single-cell analysis. Select the cell you wish to study in its natural environment, and gain access to its complete range of biological information. 

Discuss your single-cell profiling experiment with our experts! 

Impact Areas

This effective workflow can be employed in a broad range of applications areas and shows strong potential for cancer research and drug discovery. 


To investigate cancer cellular heterogeneity where individual cells can show unique differences in gene expression states, sensitivity to drugs, or immune recognition. To identify transcriptional factors for resistance development heterogeneity.

Immuno-microbial genomics

To better understand genetic variations caused by host-pathogen interactions and to identify the microorganisms that are present and the genes involved in their interactions with the host immune system.


To analyze epigenetic changes at the individual cell level. For example, single-cell sequencing can be used to study how changes in DNA methylation patterns affect gene expression in specific cells. Similarly, single-cell profiling can be used to study histone modifications and their effects on gene expression at the individual cell level. Therefore, single-cell profiling and epigenetics are closely linked and can be used together to study various biological phenomena.

Developmental biology

Single-cell profiling can be used to evaluate gene expression changes during embryonic development, identifying different stages of cell differentiation, and understanding the regulatory mechanisms involved in cell lineage differentiation. Most genome-wide profiling methods destroy the cell, which makes follow-up molecular or phenotypic experiments on this same cell impossible. The combination of the FluidFM technology with scRNA-seq may be a game changer for the area of research.

Cellular reprogramming

To identify the molecular signatures of different cell types, including those that can be used to reprogram cells. By understanding the gene expression patterns and epigenetic modifications associated with a specific cell type, researchers can design better reprogramming strategies to convert one cell type to another. In addition, single cell technologies can be used to monitor the success of cell reprogramming, since changes in gene expression and epigenetic modifications can be measured at the single-cell level.


The key to this workflow is its ability to take single-cell extracts without killing the cell. This unique feature is promising for various application areas. For instance, taking a biopsy from cells of a heterogeneous disease before and after exposure to a specific therapeutic to identify molecular signatures for early drug development. Single cell profiling with FluidFM may change drastically the way researchers study cellular heterogeneity and gene expression.


[1] Chen, Wanze, et al. "Live-seq enables temporal transcriptomic recording of single cells." Nature 608.7924 (2022): 733-740.