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Related Concept Videos

Subcellular Fractionation01:32

Subcellular Fractionation

The homogenate obtained after cell lysis contains various membrane-bound organelles that can be further separated into pure fractions by subcellular fractionation. These isolates are used to study specific cellular components, analyze localized protein activity, and are even employed in diagnostics. Fractionation is typically achieved using centrifugation methods, the most common being density-gradient and differential centrifugation.
Differential Centrifugation
Differential centrifugation is...

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Nuclei Isolation from Adult Mouse Kidney for Single-Nucleus RNA-Sequencing
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Single-Cell Nucleus Extraction with Cellular Indexing.

Trinh Lam1, Ana Esmeralda Gomez Martinez1, Alison Su1

  • 1Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720, USA.

Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
|September 30, 2025
PubMed
Summary
This summary is machine-generated.

A new microfluidic device, VacTrap, isolates single nuclei from mammalian cells, preserving their spatial origin for multiomics studies. This technology overcomes limitations in bulk fractionation, enabling detailed single-cell analysis.

Keywords:
hydrogelsmicrofluidicsmultiomicsorganellesproteomicssingle‐cell

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Area of Science:

  • Biotechnology
  • Cell Biology
  • Microfluidics

Background:

  • Bulk organelle fractionation obscures crucial cell-to-cell heterogeneity.
  • Existing microfluidic techniques struggle to link isolated organelles to their parent cells for multiomics.

Purpose of the Study:

  • To develop a high-throughput microfluidic device for isolating and spatially indexing single nuclei from mammalian cells.
  • To enable reliable multiomics readouts by preserving the connection between nuclei and their cellular origin.

Main Methods:

  • The VacTrap device utilizes a three-layer system: a Bis-gel microwell layer with a trapdoor base, a polydimethylsiloxane (PDMS) microwell layer, and a vacuum manifold.
  • Cell lysis via differential detergent fractionation (DDF) releases nuclei, while cytoplasmic proteins are retained in the Bis-gel.
  • Vacuum-assisted trapdoor dissolution synchronizes nuclear transfer to the PDMS layer with 98% efficiency.

Main Results:

  • Successful fractionation of cytoplasmic proteins from individual nuclei was verified by in situ immunoprobing.
  • Morphological analysis confirmed the preservation of intact nuclear features after isolation.
  • The VacTrap device achieved 98% transfer efficiency, preserving nuclear integrity and spatial indexing.

Conclusions:

  • VacTrap provides a robust, automated platform for single-cell preparation in multiomics applications.
  • The device effectively isolates nuclei while retaining spatial information, addressing limitations of bulk fractionation.
  • This technology facilitates advanced single-cell multiomics by enabling precise organelle-to-cell reconnection.