Biopsy Solution for Cytoplasmic Extraction

Gentle & accurate cytoplasmic biopsies collected with the FluidFM OMNIUM Platform.

Cytoplasmic Extraction Solution Adapted To Your Needs

Based on the FluidFM OMNIUM - a semi-automated single-cell manipulation system developed for the non-destructive injection and extraction of individual cells, the single-cell biopsy solution was created to perform the extraction of controlled volume of cytoplasm with the FluidFM Nanosyringe, directly from an individual selected cell within 2D cultures of adherent mammalian cells. The platform allows you to collect RNA, metabolites or proteins - any cytoplasmic extract you need to record the intricate dynamic evolution throughout the whole lifetime of a single cell. The volume of such biopsies can be precisely controlled during the collection process, to ensure cell viability.

  • Controlled nano-extraction of pL subcellular content for downstream analysis from the very same cell.
  • Selection, spatial and visual control of individual cells.
  •  The biopsy is transferred into 1 µL buffer droplet for an easy transfer in a pcr tube for snap freezing and, further downstream analysis.

  • The force-controlled extraction performed with the FluidFM nanosyringe, preserves the cell throughout the whole extraction process.

  • The streamlined workflow based on the FluidFM OMNIUM allows for direct feedback on profiled cells.
  • An intuitive software (ARYA) to save time on your experiment. With a user-friendly, point-and-click interface, obtain an easy cell selection - target the nucleus or cytoplasm.
  • Precisely (re-) locate your cells with the recording of XY-coordinates of the edited cells.
Biopsy Platform for Cytoplasmic Extraction by Cytosurge

Preserve cell viability.

Get reliable results without altering gene expression, cell phenotype, or cell-cell interactions.

Sequential sampling

Extract consecutively from the same cell within the same run or periodically over time.

Temporal gene expression profiling

Sequential analysis of the single-cell’s transcriptome

Contextual integrity

Ensure spatial and visual preservation.

'Interested in Cytoplasmic Extraction?

Cytoplasmic Collection Workflow

Picture the single-cell cytoplasmic collection workflow as a delicate procedure that collects a small portion of a chosen cell’s cytoplasm, without inflicting any harm on the cell itself.


What can you do with the cytoplasmic collection workflow? One of the first application of the workflow is the Live-seq approach. It uses single-cell cytoplasmic biopsies to provide snapshot representations of a cell’s transcriptome that can be analyzed downstream. More specifically, it gives access to two important information: transcriptome recordings prior to phenotyping and sequential transcriptome readouts from the very same cell. This approach offers promising outcomes in epigenetics, cellular reprogramming, immuno-oncology and host-pathogen interactions studies.

Biopsy Platform for Cytoplasmic Extraction by Cytosurge


Biopsy Platform for Cytoplasmic Extraction by Cytosurge

Cell Lineage Tracing

Biopsy Platform for Cytoplasmic Extraction by Cytosurge

Single-Cell Profiling

Biopsy Platform for Cytoplasmic Extraction by Cytosurge


Do you need help or technical information?

Knowledge Center

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.

[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

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. 

[2] 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.

[3] 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.

Mitochondria Transplantation with FluidFM - Story featuring Christoph Gäbelein.