Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

Ribosome Profiling

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Differential assembly of mouse and human tumor microenvironments.

Nature immunology·2026

Same author

NCOR2 represses MHC class I molecule expression to drive metastatic progression of breast cancer.

Nature communications·2026

Same author

Clinical cure of chronic hepatitis B is associated with priming and perpetuation of hepatic CD4<sup>+</sup> T cell responses.

Science translational medicine·2026

Same author

Submicrometre sampling of living cells by macrophages.

Nature·2026

Same author

Functions and features of circulating memory T cells.

Immunity·2026

Same author

STEVE: Single-cell Transcriptomics Expression Visualization and Evaluation.

bioRxiv : the preprint server for biology·2026

Same journal

ClairS: a deep-learning method for long-read tumor-normal pair somatic small variant calling.

Nature methods·2026

Same journal

RNAbpFlow: base pair-augmented SE(3) flow matching for conditional RNA 3D structure generation.

Nature methods·2026

Same journal

Spatio-DARLIN enables robust and efficient in situ lineage tracing in mice at single-cell resolution.

Nature methods·2026

Same journal

EasyGrid: a versatile platform for automated cryo-EM sample preparation and quality control.

Nature methods·2026

Same journal

Cloud-based microscope enables live neuroimaging for 24 h and beyond with worldwide access.

Nature methods·2026

Same journal

Deep molecular profiling in three dimensions.

Nature methods·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Dec 15, 2025

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells

Published on: January 7, 2020

ZipSeq: barcoding for real-time mapping of single cell transcriptomes.

Kenneth H Hu¹, John P Eichorst^1,2, Chris S McGinnis³

¹Department of Pathology, University of California San Francisco, San Francisco, CA, USA.

|July 8, 2020

Summary

This summary is machine-generated.

ZipSeq enables real-time spatial transcriptomics in live tissues by printing unique barcodes onto cells. This new method reveals novel gene expression patterns linked to tissue structures, advancing our understanding of biological processes.

More Related Videos

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

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

Related Experiment Videos

Last Updated: Dec 15, 2025

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells

Published on: January 7, 2020

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

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:

Molecular Biology
Genomics
Cell Biology

Background:

Spatial transcriptomics integrates gene expression with cellular location.
Existing methods for live tissue analysis have limitations.

Purpose of the Study:

To develop a novel method for real-time spatial transcriptomics in live tissues.
To map gene expression patterns in relation to histological structures.

Main Methods:

Developed ZipSeq, utilizing patterned illumination and photocaged oligonucleotides.
Serially printed unique barcodes ('zipcodes') onto live cells in intact tissues.
Applied ZipSeq to in vitro wound healing, lymph node sections, and tumor microenvironments.

Main Results:

Discovered novel gene expression patterns associated with histological structures across all tested settings.
Revealed myeloid and T cell differentiation trajectories within the tumor microenvironment.
Demonstrated ZipSeq's scalability for comprehensive live tissue mapping.

Conclusions:

ZipSeq offers a powerful tool for real-time, high-resolution spatial transcriptomics in live biological systems.
The method facilitates the discovery of spatially resolved gene expression dynamics.
ZipSeq provides a pathway for complete mapping of live tissues, enabling further imaging and perturbation studies.