Sequence your cells while keeping them alive 

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Record state transitions on the same cell through consecutive cytoplasmic biopsies retrieved with the FluidFM OMNIUM Platform.

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FluidFM biopsy solution for cytoplasmic extraction of single cells

A FluidFM Nanosyringe, akin to a regular biopsy needle for patients, can consecutively collect cytoplasmic samples from a specifically selected living cell. Supported by Live imaging, the FluidFM OMNIUM platform enables you to take a sample from a specific cell based on its phenotype or specific cell environment.


FluidFM biopsy solution for cytoplasmic extraction of single cells

The cytoplasmic sample collected from a living cell is called a “biopsy”. A cytoplasmic biopsy comprises RNA, that is representative of a cell’s transcriptome at a given point in time.



FluidFM biopsy solution for cytoplasmic extraction of single cells

A biopsy can be collected while the cell stays alive and therefore makes it possible to correlate the transcriptome of a specific, living cell to its future phenotype as represented here, in the case of an osteocyte.

The biopsy solution on the FluidFM OMNIUM platform, supports a streamlined workflow that uses a FluidFM Nanosyringe to collect cytoplasmic biopsies for Live-cell sequencing or Live-seq. Live-seq with the biopsy solution, matches gene expression to a specific cell and phenotype: the visual feedback enables correlation of gene expression to cell traits within a 2D environment.

Each biopsy contains a snapshot of a cell’s transcriptome at a specific time point. Because the biopsy keeps the cell alive, the transcriptome of a given cell can be directly linked to its phenotype. Subsequent biopsies can be taken to track state transitions in real-time.

Live-seq with the biopsy solution, unveils real-time cell fate decisions by recording both slow and fast cell state transitions in real-time instead of pseudo-time. It is now possible to take a biopsy from a specific cell that has been exposed to external stimuli and assess the impact this has on the single-cell transcriptome.

Discover Now: How to sequence a cell while keeping it alive. 

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The FluidFM Biopsy Workflow

The workflow is facilitated through the FluidFM technology: a combination between atomic force microscopy (AFM) and microfluidics. Through the FluidFM OMNIUM platform, it is possible to regulate the force exerted on the cell when the Nanosyringe is gently inserted, and precisely control the biopsy volume to ensure high cell viability.

FluidFM biopsy solution for cytoplasmic extraction of single cells

A. The FluidFM OMNIUM platform is a single-cell manipulation system designed to streamline the use of FluidFM probes in life-science applications. B. SEM picture of the FluidFM Nanosyringe - The sharp apex of the FluidFM Nanosyringe enables gentle probe insertion into a cell to collect a small portion of cytoplasm.

The integrated microscope and environmental conditions control enable experimentation under full visual control using epifluorescence or brightfield. The cell selection, automated FluidFM Nanosyringe insertion into the cytoplasm of the chosen cell, and precise biopsy volume collection, are controlled and monitored with the FluidFM ARYA software.

1. Biopsy Collection

The cytoplasmic biopsy is collected with a FluidFM Nanosyringe from a cell within 2D cultures of adherent mammalian cells. Extraction is then initiated by applying a negative pressure through the microchannel of the Nanosyringe. The extraction can be monitored live and stopped once the desired biopsy volume has been reached. 

Cytoplasmic Biopsy Collection Solution _Cytosurge

2. Biopsy Ejection

After the extraction is completed, the system automatically inserts the FluidFM Nanosyringe into a 1μL droplet of buffer and ejects the biopsy. The buffer contains RNA inhibitors to prevent RNA degradation.

Cytoplasmic Biopsy Collection Solution _Cytosurge

3. Buffer Droplet Transfer

The droplet that contains the cytoplasmic Biopsy, can be easily transferred into a tube and snap frozen for downstream analysis with a low input RNA-seq protocol such as Luthor HD or the enhanced Smart-Seq2 protocol as used in Live-seq approach.

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Further reading

The gentle nature of the FluidFM biopsy solution comes from the use of force sensitive FluidFM Nanosyringes, that provide force feedback when interacting with a cell’s membrane. The FluidFM Nanosyringe has a sharp tip that facilitates gentle insertion into the cell membrane. The microchannel and nanometric opening provide fluidic access to the intracellular environment through which the cytoplasm from the cell can be extracted. Throughout the extraction process the Nanosyringe is accurately kept in place by the FluidFM OMNIUM platform, thereby minimizing physical perturbation of the cell and maximizing viability. 

In this video, a picoliter biopsy is taken from a specific HeLa cell with a FluidFM Nanosyringe. 

The FluidFM Nanosyringes, leveraging advanced microfabrication techniques akin to those employed in microchip production, boast unparalleled reproducibility in both the shape and size of their integrated microchannels. This precise geometry, when paired with the ARYA software volume control and quantification module, facilitates exact control and precise quantification of biopsy volumes.

The FluidFM biopsy solution allows collecting biopsies from individual cells and tracking them over time by recording the coordinates of each cell in the ARYA software. This allows the researcher to study the response of an individual cell to a stimulus without disturbing the cell and correlate the response to the previously collected transcriptome. Furthermore, it enables repetitive sampling of the same cell to generate time-resolved transcriptional trajectories.

FluidFM biopsy solution for cytoplasmic extraction of single cells

Microscopic view of Panc-1 cells. The precision point & click selection allows selecting the cell of interest based on morphological or other phenotypical traits, for cytoplasmic extraction.


The FluidFM biopsy solution comes with a custom single-cell biopsy kit for an easy collection of cytoplasmic biopsies. The picoliter extracts are ejected from the FluidFM Nanosyringe into a 1μL droplet of buffer on the droplet slide. From there, the droplet can conveniently be transferred to vials for snap freezing or direct library preparation for transcriptomic analysis.

FluidFM biopsy solution for cytoplasmic extraction of single cells

After the biopsy collection, the buffer droplet filled with the picoliter cytoplasm extract is deposited on the droplet slide coated with a hydrophobic surface. 

The single-cell biopsy kit contains:

  • 35mm Ibidi® dish with an imprinted grid to support alignment and position recovery of the platform. 
  • Droplet slide and holder, with hydrophobic surface, for precise positioning of the buffer droplet and sample collection.
  • Drying station for automatically removing the droplet around the Nanosyringe, before and after taking the biopsy.
  • Coating containers


Our collaborators from ETH Zurich and EPFL Lausanne successfully demonstrated that using a FluidFM Nanosyringe, it is possible to take an extract from a cell’s cytoplasm without killing it (Cell, 2016 [1]) and that this “single-cell Biopsy” is a representable snapshot of a cell’s transcriptome at a given point in time (Nature, 2022 [2]). Learn more about their findings when pioneering Live-seq using FluidFM cytoplasmic biopsies. 


Additional resources available: 


[1] 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.

[2] W. Chen, O. Guillaume-Gentil, P. Yde Rainer, C. G. Gäbelein, W. Saelens, V. Gardeaux, A. Klaeger, R. Dainese, M. Zachara, T. Zambelli, J. A. Vorholt & B. Deplancke. Live-seq enables temporal transcriptomic recording of single cells. (Aug 2022) Nature, doi:10.1038/s41586-022-050

The total RNA content of a cell ranges between 1pg up to 50pg per cell, depending on the cell type. This comes down to an RNA content of a few pg of RNA per biopsy. Live-Seq as published by Chen et al. (Nature, 2022 [1]) is a combination of a cytoplasmic biopsy taken with a FluidFM Nanosyringe, and a low-input RNA sequencing protocol that is an enhanced version of SmartSeq2. Together with Lexogen, Cytosurge is developing a streamlined, commercially available workflow for biopsy collection and analysis using Lexogen’s LUTHOR HD kit. LUTHOR HD is a high-definition single-cell 3’ mRNA-seq library prep kit based on their proprietary THOR technology for direct RNA amplification. 


Related resources:

[1] W. Chen, O. Guillaume-Gentil, P. Yde Rainer, C. G. Gäbelein, W. Saelens, V. Gardeaux, A. Klaeger, R. Dainese, M. Zachara, T. Zambelli, J. A. Vorholt & B. Deplancke. Live-seq enables temporal transcriptomic recording of single cells. (Aug 2022) Nature, doi:10.1038/s41586-022-05046-9

Our proprietary FluidFM (Fluidic Force Microscopy) technology integrates the best features of force microscopy and micro-channeled probes. The FluidFM probes, of which the FluidFM Nanosyringe is one example, “senses” the surface which enables highly gentle interactions with cells. The FluidFM Nanosyringe has a sharp tip and an aperture of 600nm that allows to simultaneously sense interaction forces with the cell membrane and to aspirate exact femtoliters.

Find out more about:

[1] 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.

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