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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: Aug 17, 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

Multiplexed evaluation of mouse wound tissue using oligonucleotide barcoding with single-cell RNA sequencing.

Michael Januszyk¹, Michelle Griffin¹, Shamik Mascharak¹

¹Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA.

|December 16, 2022

Summary

This study introduces a cost-effective single-cell RNA sequencing protocol using oligonucleotide barcoding for analyzing complex tissues like healing wounds. This method enhances scalability for large-scale biological studies.

Keywords:

Gene Expression Model Organisms RNAseq Single Cell

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Last Updated: Aug 17, 2025

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

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Using R, Seurat, and CellChat to Analyze a Single-Cell Transcriptomics Dataset of Mouse Skin Wound Healing

Using R, Seurat, and CellChat to Analyze a Single-Cell Transcriptomics Dataset of Mouse Skin Wound Healing

Published on: August 1, 2025

Area of Science:

Molecular Biology
Genomics
Tissue Engineering

Background:

Single-cell RNA sequencing (scRNA-seq) offers deep insights into complex tissues.
High costs of scRNA-seq limit its application in large-scale studies.
Healing wounds present unique challenges for current scRNA-seq protocols.

Purpose of the Study:

To develop a cost-effective protocol for single-cell RNA sequencing of challenging tissues.
To enable large-scale studies of complex biological processes like wound healing.
To adapt oligonucleotide barcoding for pooled sample analysis in scRNA-seq.

Main Methods:

Protocol development for oligonucleotide barcoding and sample pooling.
Application of the protocol to mouse models of skin wound healing.
Tissue harvest and barcoding procedures detailed for reproducibility.

Main Results:

Successful implementation of oligonucleotide barcoding for pooled scRNA-seq.
Demonstration of the protocol's applicability to challenging healing wound tissues.
Adaptability of the protocol across different species including rats, pigs, and humans.

Conclusions:

The developed protocol significantly reduces the cost of scRNA-seq for complex tissues.
This method provides a scalable solution for large-scale single-cell studies.
The protocol is a valuable tool for advancing research in wound healing and other complex biological systems.