Single cell omics with FluidFM®

Single cell biopsies while keeping the cell alive. 

Non-destructive single cell omics with FluidFM.

The growing interest in single cell omics, i.e. analyzing endogenous molecules from single cells, is based on the understanding that cellular heterogeneity has implications in nearly all fields of biology and medicine and is widespread even within isogenic populations. Whereas technological development was mainly focused on analyzing high numbers of single cells by e.g., sorting and clustering, these technologies were not able to provide molecular signatures at single cell resolution or to analyze single cells in a physiological context without destruction of the cell.

FluidFM provides a fascinating solution for non-destructive and live single cell omics. Thanks to its gentle cell manipulation technology FluidFM allows to extract sub-picoliter volumes from the cytoplasm or nucleus of a single cell and to isolate the extract for further analysis. This cytoplasmic biopsy is so gentle that the cells survive, and sequential biopsies can be performed on the very same cell. By avoiding the destructive cell lysis, trajectory instead of end-point analysis become possible, whether in transcriptomics, metabolomics, proteomics, or any other omics studies.

Non-destructive extraction

Gently extract from cytoplasm or nucleus while keeping the cell alive and fully viable.

Save the physiological context

During extraction, keep the targeted cell in its context next to its neighboring cells and conserve established cell-cell interactions.

Time course biopsy

Repeat the gentle extraction several times on the same cell, e.g. before and after stimulation by a specific drug.

Pick & Place

If full cell content is required, isolate the cell directly from an adherent or suspension culture without affecting neighboring cells.

Discuss your single cell omics experiments with our experts 

Extraction of cellular content with FluidFM


Empower your omics research with FluidFM

Selected FluidFM publications

Genome-wide molecular recording using Live-seq

Chen et al. show the establishment of Live-seq, an approach for single-cell transcriptome profiling that preserves cell viability during RNA extraction using FluidFM. By using a model involving exposure of macrophages with lipopolysaccharide (LPS), they were able to apply a genome-wide ranking of genes based on their ability to impact macrophage LPS response heterogeneity.  Furthermore, they show that Live-seq can be used to sequentially profile the transcriptomes of individual macrophages before and after stimulation with LPS. This enables the direct mapping of a cell’s trajectory and transforms scRNA-seq from an end-point to a temporal analysis approach.

W. Chen, O. Guillaume-Gentil, R. Dainese, P. Yde Rainer, M. Zachara, C. G. Gäbelein, J. A. Vorholt & B. Deplancke. Genome-wide molecular recording using Live-seq. (March 2021) bioRxiv 2021.03.24.436752

Single-Cell Mass Spectrometry

In this publication Guillaume-Gentil et al. show non-destructive and quantitative withdrawal of intracellular fluid with sub-picoliter resolution using FluidFM, followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. By this method they detected and identified several metabolites from the cytoplasm of individual HeLa cells. Validated by 13C-Glucose feeding experiments, this showed that metabolite sampling combined with mass spectrometry analysis was possible while preserving the physiological context and the viability of the analyzed cell. Thus, enabling complementary analysis of the cell. 

O. Guillaume-Gentil, T. Rey, P. Kiefer, A.J. Ibáñez, R. Steinhoff, R. Brönnimann, L. Dorwling-Carter, T. Zambelli, R. Zenobi & J.A. Vorholt. Single-Cell Mass Spectrometry of Metabolites Extracted from Live Cells by Fluidic Force Microscopy. (May 2017) Anal Chem., 89(9), 5017-5023. doi:10.1021/acs.analchem.7b00367

Tunable Single-Cell Extraction for Molecular Analyses

Guillaume-Gentil et al. demonstrate the use of FluidFM for quantitative sampling of cytoplasmic and nucleoplasmic fractions from single cells at a sub-picoliter resolution followed by a comprehensive analysis of the soluble molecules withdrawn from the cytoplasm or the nucleus and dispensed adaptable to a broad range of analytical methods, including the detection of enzyme activities and transcript abundances.

O. Guillaume-Gentil, R.V. Grindberg, R. Kooger, L. Dorwling-Carter, V. Martinez, D. Ossola, M. Pilhofer, T. Zambelli & J.A. Vorholt. Tunable Single-Cell Extraction for Molecular Analyses. (Jul 2016) Cell, 166(2), 506-516. doi: 10.1016/j.cell.2016.06.025.

80+ publications with FluidFM

How it works

Based on hollow force-controlled FluidFM probes

The core principle of FluidFM enabling single cell omics are our patented, hollow force-controlled probes. The variety of available probe tips and aperture sizes enables distinct experimental designs as described above.
More on FluidFM probes & technology

FluidFM probes can be used with the FluidFM ADD-ON in combination with an existing AFM or with our standalone FluidFM OMNIUM system.
More on the two systems

Find out more about our systems