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...

You might also read

Related Articles

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

Sort by

Same author

Improving the precision of AAV lung gene therapy for SP-B deficiency using computationally derived lung-specific promoters.

Gene therapy·2026

Same author

Knowledge preservation in the era of big science and AI: strategies for sustainable scientific research.

Nature communications·2026

Same author

Protecting cells at the genetic level and simulating unauthorized access via a biohackathon.

Science advances·2026

Same author

Identification of computationally designed skeletal and cardiac promoters with high specificity across AAV delivery routes.

BMC biotechnology·2026

Same author

Synthetic circuits for cell ratio control.

Nature·2026

Same author

Analysis and control of untemplated DNA polymerase activity for guided synthesis of kilobase-scale DNA sequences.

Nature communications·2026

Same journal

Common xenobiotics modulate gut microbial responses to low‑calorie sweeteners in vitro.

Molecular systems biology·2026

Same journal

ParTIpy: a scalable framework for archetypal analysis and Pareto task inference.

Molecular systems biology·2026

Same journal

Quantitative interactome mapping of skeletal muscle insulin resistance.

Molecular systems biology·2026

Same journal

Interpretable multi-omics integration across mixed-order tensors with MANTRA.

Molecular systems biology·2026

Same journal

To cleave or not to cleave: a systemic evaluation of DSS versus DSSO for cross-linking mass spectrometry analysis.

Molecular systems biology·2026

Same journal

Multiscale learning of gene network-driven phenotypic dynamics of single cells.

Molecular systems biology·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Feb 19, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

Genetic circuit characterization and debugging using RNA-seq.

Thomas E Gorochowski¹, Amin Espah Borujeni¹, Yongjin Park¹

¹Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.

Molecular Systems Biology

|November 11, 2017

Summary

This summary is machine-generated.

This study introduces RNA sequencing (RNA-seq) for debugging complex genetic circuits by simultaneously measuring internal states and part performance. This method identifies unexpected failures and guides improvements in synthetic biology design.

Keywords:

biofab combinatorial logic omics synthetic biology systems biology

More Related Videos

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

Characterization of In Vitro Differentiation of Human Primary Keratinocytes by RNA-Seq Analysis

Characterization of In Vitro Differentiation of Human Primary Keratinocytes by RNA-Seq Analysis

Published on: May 16, 2020

Related Experiment Videos

Last Updated: Feb 19, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

Characterization of In Vitro Differentiation of Human Primary Keratinocytes by RNA-Seq Analysis

Characterization of In Vitro Differentiation of Human Primary Keratinocytes by RNA-Seq Analysis

Published on: May 16, 2020

Area of Science:

Synthetic Biology
Molecular Biology
Genomics

Background:

Genetic circuits perform computations within cells but are challenging to debug due to dynamic, multi-state functions.
Current debugging methods often lack the resolution to identify complex failure modes in intricate circuits.

Purpose of the Study:

To develop and apply RNA sequencing (RNA-seq) methods for comprehensive characterization and debugging of genetic circuits.
To enable simultaneous measurement of internal gate states, genetic part performance, and host gene expression impact.

Main Methods:

Development of RNA-seq protocols for simultaneous measurement of genetic circuit components and host gene expression.
Application to a three-input, one-output genetic circuit with multiple sensors and logic gates.
Analysis of transcription profiles across all input combinations to extract biophysical models of part activities and responses.

Main Results:

Identification of unexpected failure modes, including cryptic antisense promoters, terminator inefficiency, and sensor malfunctions.
Quantification of genetic part activities and the response functions of sensors and gates.
Demonstration of targeted circuit repair using a bidirectional terminator to mitigate antisense transcription.

Conclusions:

RNA-seq is a powerful, scalable method for genetic circuit characterization and debugging, surpassing limitations of traditional reporters.
This approach facilitates the identification of novel failure mechanisms and guides rational design for improved synthetic biology systems.