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Related Experiment Video

Updated: Oct 3, 2025

Genetic Engineering of Primary Mouse Intestinal Organoids Using Magnetic Nanoparticle Transduction Viral Vectors for Frozen Sectioning

Genetic Engineering of Primary Mouse Intestinal Organoids Using Magnetic Nanoparticle Transduction Viral Vectors for Frozen Sectioning

Published on: May 10, 2019

Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition.

Johannes Bues^1,2, Marjan Biočanin^1,2, Joern Pezoldt^1,2

¹Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

|February 15, 2022

Summary

DisCo technology enables efficient single-cell RNA sequencing for small tissue samples. This new method reveals extensive cellular heterogeneity in intestinal organoids and crypts, uncovering novel stem cell populations.

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Last Updated: Oct 3, 2025

Genetic Engineering of Primary Mouse Intestinal Organoids Using Magnetic Nanoparticle Transduction Viral Vectors for Frozen Sectioning

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Published on: May 10, 2019

Author Spotlight: The 3D Culturing of Organoids from Murine Intestinal Crypts and a Single Stem Cell for Organoid Research

Author Spotlight: The 3D Culturing of Organoids from Murine Intestinal Crypts and a Single Stem Cell for Organoid Research

Published on: April 7, 2023

Author Spotlight: Integrating Organoid Models with Single-Cell and Spatial Transcriptomics Technologies

Author Spotlight: Integrating Organoid Models with Single-Cell and Spatial Transcriptomics Technologies

Published on: March 29, 2024

Area of Science:

Biotechnology
Genomics
Cell Biology

Background:

Single-cell RNA sequencing (scRNA-seq) is powerful but typically requires large cell inputs, making it inefficient for small tissue samples.
Processing small samples in bulk confounds cellular readouts, limiting detailed analysis of tissue heterogeneity.

Purpose of the Study:

To develop a novel system for deterministic, low-input single-cell encapsulation and analysis.
To enable high-throughput scRNA-seq on individual small tissue samples like organoids and crypts.

Main Methods:

Developed DisCo, a microfluidic system for precise co-encapsulation of cells and mRNA-capture beads.
Utilized machine vision and multilayer microfluidics for controlled particle and cell positioning.
Achieved high capture efficiency (>70%) and processing speeds up to 350 cells/hour for low-input suspensions.

Main Results:

Analyzed 31 individual intestinal organoids, revealing significant heterogeneity and identifying a fetal-like Ly6a+ stem cell subtype.
Discovered an uncharacterized 'gobloid' subtype enriched in goblet cell precursors and mature Muc2+ cells.
Examined individual mouse intestinal crypts, finding structures similar to spheroids composed of regenerative stem cells.

Conclusions:

DisCo provides a robust solution for analyzing cellular heterogeneity in low-input biological samples.
The technology enables high-resolution cellular snapshots from individual organoids and crypts.
Findings highlight the potential of DisCo for uncovering novel cell populations and understanding tissue development and homeostasis.