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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: Jun 2, 2025

Author Spotlight: High-Throughput Image-Based Quantification of Mitochondrial DNA Synthesis and Distribution

Author Spotlight: High-Throughput Image-Based Quantification of Mitochondrial DNA Synthesis and Distribution

Published on: May 5, 2023

Protocol for mitochondrial variant enrichment from single-cell RNA sequencing using MAESTER.

Jonathan D Good¹, Ksenia R Safina¹, Tyler E Miller²

¹Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.

|January 16, 2025

Summary

This study introduces a new method combining single-cell RNA sequencing with mitochondrial DNA analysis to simultaneously reveal cell states and tissue clonal structures. This approach offers deeper insights into cellular dynamics and tissue organization.

Keywords:

Genetics RNA-seq Sequence analysis Single Cell

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Simultaneous Mapping and Quantitation of Ribonucleotides in Human Mitochondrial DNA

Published on: November 14, 2017

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Last Updated: Jun 2, 2025

Author Spotlight: High-Throughput Image-Based Quantification of Mitochondrial DNA Synthesis and Distribution

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Published on: May 5, 2023

Author Spotlight: Two-Step Tag-Free Isolation of Mitochondria for Improved Protein Discovery and Quantification

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Simultaneous Mapping and Quantitation of Ribonucleotides in Human Mitochondrial DNA

Simultaneous Mapping and Quantitation of Ribonucleotides in Human Mitochondrial DNA

Published on: November 14, 2017

Area of Science:

Genomics
Molecular Biology
Cell Biology

Background:

Single-cell RNA sequencing (scRNA-seq) provides high-resolution cell state information.
Current scRNA-seq methods often fail to capture tissue clonal structures.
Understanding clonal architecture is crucial for tissue development and disease progression.

Purpose of the Study:

To develop a protocol for simultaneously analyzing cell states and clonal information.
To integrate mitochondrial DNA (mtDNA) variant analysis with scRNA-seq.
To enable simultaneous probing of cell states and clonal dynamics in primary human tissues.

Main Methods:

Protocol development for enriching mitochondrial DNA (mtDNA) variants from 3'-barcoded full-length cDNA.
Detailed steps for library preparation, mtDNA enrichment, PCR cleanup, and paired-end sequencing.
Computational analysis including maegatk, variant calling, and data integration.

Main Results:

Successful integration of cell state and clonal information from primary human tissues.
Demonstration of a protocol to simultaneously assess cellular heterogeneity and tissue lineage.
Illumination of cell states and clonal dynamics through combined scRNA-seq and mtDNA variant analysis.

Conclusions:

The presented protocol effectively combines cell state and clonal information.
This method enhances the characterization of cellular heterogeneity and tissue architecture.
The approach provides novel insights into cell states and clonal dynamics in complex tissues.