Streamlined cytoplasmic extraction with the FluidFM OMNIUM Platform

Sequence your cells while keeping them alive.

FluidFM biopsy solution for cytoplasmic extraction of single cells

A FluidFM Nanosyringe, akin to a regular biopsy needle for patients, collects cytoplasmic samples from living cells.

A biopsy is a cytoplasmic extract from a living cell, which comprises RNA that that is representative of a cell’s transcriptome at a given point in time.

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.

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.

The streamlined FluidFM biopsy workflow provides a delicate procedure to systematically collect a small portion of a chosen cell’s cytoplasm.

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.

The integrated microscope and environmental conditions control enable experimentation under full visual control using epifluorescence or brightfield. Cell selection and precise biopsy volume are controlled and monitored via the custom FluidFM ARYA software.

The FluidFM OMNIUM platform is a single-cell manipulation system designed to streamline the use of FluidFM probes in life-science applications.

Sequence your cells
& keep them alive

Gentle and controlled cytoplasmic extraction workflow with high cell viability.

Unveil real-time cell fate decisions

Record both slow and fast cell state transitions in real-time instead of pseudo-time.

Match gene expression to a specific cell & phenotype

Visual feedback enables correlation of gene expression to cell traits within a 2D environment

Learn more about the Biopsy solution with the FluidFM OMNIUM Platform

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FluidFM Biopsy Workflow & Features

Cytoplasmic Biopsy Collection Solution _Cytosurge

1. Biopsy Collection

The cytoplasmic biopsy is collected with a FluidFM Nanosyringe from a cell within 2D cultures of adherent mammalian cells. The cells are selected in the FluidFM ARYA software, followed by automatic insertion of the Nanosyringe into the cytoplasm of the chosen cell. Extraction is then initiated by the application of a gentle negative pressure through the microchannel of the Nanosyringe. The extraction can be monitored live and stopped once the desired biopsy volume is reached.

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.

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.

Use Cases

Pinpoint the drivers of cell fate decisions.

Take a biopsy from a specific cell that has been exposed to external stimuli such as mechanical stress, changes to the microenvironment or drug treatment and assess the impact this has on the single-cell transcriptome.

Select a specific cell for extraction.

Live imaging with the integrated microscope of the FluidFM OMNIUM platform enables you to take a Biopsy from a specific cell based on its phenotype or specific cell environment.

Record state transitions of the same cell through consecutive biopsies.

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. Learn more.

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

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The FluidFM biopsy solution in detail

Cytoplasmic biopsies with high cell viability

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.

Precise control of the biopsy volume

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.

Read our latest post "LUTHOR HD: Pushing the boundaries of single cell transcriptome analysis by in vitro mRNA amplification."

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Live-cell imaging to record morphological changes of individual cells after biopsies.

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.

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.

Easy collection of single cell biopsies for further downstream processing.

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.

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

How can you analyze cytoplasmic biopsies?

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:

Read the blog post - LUTHOR HD: Pushing the Boundaries of Single Cell Transcriptome Analysis by in vitro mRNA Amplification.
Download directly the blog post PDF version here.

[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

What makes the FluidFM biopsy solution so gentle to cells?

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.

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