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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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Related Experiment Video

Updated: Apr 15, 2026

Optimization of a Multiplex RNA-based Expression Assay Using Breast Cancer Archival Material

Optimization of a Multiplex RNA-based Expression Assay Using Breast Cancer Archival Material

Published on: August 1, 2018

Protocol optimization improves the performance of multiplexed RNA imaging.

Josh J Luce¹, Christian A Reardon-Lochbaum^1,2, Paolo Cadinu^1,3

¹Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA.

Scientific Reports

|August 31, 2025

Summary

This summary is machine-generated.

Multiplexed error robust fluorescence in situ hybridization (MERFISH) protocol optimizations significantly enhance RNA detection quality. These MERFISH improvements apply to both cell culture and tissue samples, aiding spatial transcriptomics research.

Keywords:

Fluorescence in situ hybridization Multiplexed error robust in situ hybridization (MERFISH)RNA Spatial transcriptomics

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Last Updated: Apr 15, 2026

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Published on: April 7, 2023

Area of Science:

Molecular Biology
Genomics
Biotechnology

Background:

Spatial transcriptomics enables detailed cellular structure analysis in tissues.
Multiplexed error robust fluorescence in situ hybridization (MERFISH) is a key spatial transcriptomics technique.
MERFISH relies on sequential single-molecule fluorescence in situ hybridization (smFISH) for RNA identification.

Purpose of the Study:

To systematically investigate the impact of protocol variations on MERFISH performance.
To identify optimal choices for MERFISH probe design, hybridization, and buffer conditions.
To provide empirical guidance for improving MERFISH quality and applicability.

Main Methods:

Exploration of MERFISH protocol parameters including probe design and hybridization conditions.
Systematic testing of buffer storage and composition effects on RNA detection.
Implementation of protocol modifications to enhance MERFISH performance.

Main Results:

Specific protocol modifications were identified that demonstrably improve MERFISH performance.
Optimized protocols led to enhanced MERFISH quality in both cell culture and tissue samples.
The study provides a comprehensive analysis of factors influencing MERFISH accuracy.

Conclusions:

Systematic optimization of MERFISH protocols can significantly improve RNA detection sensitivity and specificity.
The findings offer practical guidance for researchers using MERFISH and related RNA FISH techniques.
Enhanced MERFISH protocols are valuable for advancing spatial transcriptomics and understanding tissue architecture.