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Related Experiment Video

Updated: Jun 3, 2025

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing

Published on: July 28, 2017

Single-cell Organelle Extraction with Cellular Indexing.

Trinh Lam¹, Alison Su¹, Ana E Gomez Martinez¹

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

Biorxiv : the Preprint Server for Biology

|January 7, 2025

Summary

This summary is machine-generated.

VacTrap isolates and spatially indexes single nuclei from mammalian cells using a novel microfluidic device. This breakthrough enables precise mapping of nuclei to their cell of origin for advanced multiomics studies.

Keywords:

hydrogel microfluidics multiomics organelle proteomics single-cell

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An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

Published on: May 23, 2018

Area of Science:

Cell biology
Biotechnology
Microfluidics

Background:

Bulk organelle fractionation methods lack single-cell resolution.
Existing microfluidic techniques fail to link fractionated organelles to their cell of origin.
Single-cell multiomics requires precise mapping of cellular components back to their source cell.

Purpose of the Study:

To develop a high-throughput microfluidic device for isolating and spatially indexing single nuclei.
To enable the mapping of individual nuclei to their original mammalian cell.
To provide a tool for advancing single-cell multiomics applications.

Main Methods:

Development of VacTrap, a three-layer microfluidic device utilizing Bis-gel microwells with 'trapdoors' (BAC-gel) and a vacuum manifold.
Cell lysis using DDF to release nuclei, followed by electrophoretic separation of cytoplasmic proteins.
Vacuum-assisted, synchronized nuclei transfer from Bis-gel to PDMS microwells with trapdoor dissolution.

Main Results:

VacTrap achieves 98% efficiency in synchronized nuclei transfer across 80% of a 256-microwell array.
Nuclei transfer efficiency surpasses 1% compared to passive methods (<1%).
Morphological analysis confirms preservation of organelle integrity during the VacTrap process.

Conclusions:

VacTrap offers a robust, high-throughput solution for spatial indexing of single nuclei.
The device enables precise mapping of nuclei to their cell of origin, crucial for multiomics.
VacTrap advances the field of single-cell analysis by preserving cellular context.