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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...

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Updated: Jan 12, 2026

Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples

Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples

Published on: April 7, 2023

High-plex spatial RNA imaging in one round with conventional microscopes using color-intensity barcodes.

Tianyi Chang¹, Shihui Zhao^1,2, Kunyue Deng^1,2

¹Biomedical Pioneering Innovation Center (BIOPIC), Peking University International Cancer Institute, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.

Nature Biotechnology

|October 31, 2025

Summary

This summary is machine-generated.

Profiling of RNA in situ through single-round imaging (PRISM) enables 64-plex RNA imaging using standard microscopes by expanding color capacity. This breakthrough facilitates detailed spatial transcriptomic analysis across diverse biological systems.

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Last Updated: Jan 12, 2026

Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples

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Published on: August 6, 2014

Single Cell Analysis Of Transcriptionally Active Alleles By Single Molecule FISH

Single Cell Analysis Of Transcriptionally Active Alleles By Single Molecule FISH

Published on: September 20, 2020

Area of Science:

Molecular Biology
Genomics
Microscopy

Background:

Conventional fluorescence microscopy limits spatial RNA imaging to few channels.
Sequential fluorescence in situ hybridization requires complex instrumentation for multiplexing.

Purpose of the Study:

Introduce a novel method, PRISM, for high-plex spatial RNA imaging.
Expand RNA coding capacity using color intensity grading.
Enable multiplexed RNA imaging with conventional microscopes.

Main Methods:

Developed PRISM (Profiling of RNA in situ through single-round imaging).
Utilized color intensity grading for expanded coding capacity.
Employed radius vector filtering for codeword distinguishability.
Achieved 64-plex color-barcoded RNA imaging in a single round.

Main Results:

Demonstrated PRISM's versatility across multiple tissues.
Generated a 3D mouse embryonic development atlas (E12.5-E14.5).
Created a quasi-3D human hepatocellular carcinoma tumor-normal transition landscape.
Mapped 3D cell atlas and subcellular RNA localization in mouse brain.
Identified the role of cancer-associated fibroblasts in tumor immune microenvironments.

Conclusions:

PRISM significantly enhances spatial RNA imaging capabilities.
The method supports high-plex analysis with accessible instrumentation.
PRISM provides new insights into developmental biology, cancer, and neuroscience.