Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

RNA-seq03:21

RNA-seq

10.8K
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...
10.8K
Ribosome Profiling02:24

Ribosome Profiling

3.7K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.7K

You might also read

Related Articles

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

Sort by
Same author

Single-cell DNA methylation analysis uncovers epigenetic pathways in the transformation of MDS to AML.

Leukemia·2026
Same author

Author Correction: CAF-derived GLUT1 and its role in modulating ovarian cancer progression: a multi-dimensional analysis of the tumor microenvironment.

Communications biology·2026
Same author

Longitudinal changes in DNA methylation in IDH-mutant glioma fuel disease progression through altered cell state differentiation.

Nature genetics·2026
Same author

Recent Advances of Atomic/Molecular Layer Deposition Engineering Silicon Interface for Lithium-Ion Batteries.

Nano-micro letters·2026
Same author

Discovery of furan-trimethoxyphenyl hybrids as novel colchicine-binding site inhibitors that induce mitotic catastrophe with potent anti-acute myeloid leukemia effect.

Bioorganic chemistry·2026
Same author

L1CAM signaling through planar cell polarity drives SOX2 expression and lung adenocarcinoma metastasis.

Nature communications·2026
Same journal

An assay to quantify sexual commitment and stage conversion in the human malaria parasite Plasmodium falciparum.

Nature protocols·2026
Same journal

Author Correction: Direct inoculation of bioreactor-controlled stirred suspension culture with cryopreserved human pluripotent stem cells.

Nature protocols·2026
Same journal

High-throughput measurements of protein domain functions using magnetic separation.

Nature protocols·2026
Same journal

Inducing physiological polarity and performing gene editing using CRISPR-Cas9 in human trophoblast organoids.

Nature protocols·2026
Same journal

Photocatalytic low-temperature defluorination of PTFE.

Nature protocols·2026
Same journal

Multimodal imaging and quantification of lanthanide chelate-labeled micro- and nanoplastics in plants.

Nature protocols·2026
See all related articles

Related Experiment Video

Updated: Oct 29, 2025

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
10:12

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

18.8K

Smart-RRBS for single-cell methylome and transcriptome analysis.

Hongcang Gu1,2, Ayush T Raman3, Xiaoxue Wang4

  • 1Broad Institute of MIT and Harvard, Cambridge, MA, USA. gu_hongcang@hotmail.com.

Nature Protocols
|July 10, 2021
PubMed
Summary
This summary is machine-generated.

This study introduces Smart-RRBS, a novel method for simultaneously profiling DNA methylation and gene expression in single cells. This approach aids in understanding cellular heterogeneity and epigenetic regulation in cancer research.

More Related Videos

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
13:47

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

25.8K
Isolation of Region-specific Microglia from One Adult Mouse Brain Hemisphere for Deep Single-cell RNA Sequencing
09:49

Isolation of Region-specific Microglia from One Adult Mouse Brain Hemisphere for Deep Single-cell RNA Sequencing

Published on: December 3, 2019

11.2K

Related Experiment Videos

Last Updated: Oct 29, 2025

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
10:12

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

18.8K
Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
13:47

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

25.8K
Isolation of Region-specific Microglia from One Adult Mouse Brain Hemisphere for Deep Single-cell RNA Sequencing
09:49

Isolation of Region-specific Microglia from One Adult Mouse Brain Hemisphere for Deep Single-cell RNA Sequencing

Published on: December 3, 2019

11.2K

Area of Science:

  • Genomics
  • Epigenetics
  • Single-cell biology

Background:

  • Investigating cellular heterogeneity requires methods that capture multiple molecular layers within individual cells.
  • Understanding the interplay between DNA methylation and gene expression is crucial for deciphering epigenetic regulation.
  • Previous methods have limitations in simultaneously profiling both epigenetic modifications and transcriptional states at a single-cell level.

Purpose of the Study:

  • To present a detailed protocol for Smart-RRBS, a method for dual DNA methylation and transcriptome profiling in single cells.
  • To guide researchers on the utility of Smart-RRBS for cancer research and the study of cellular heterogeneity.
  • To enable in-depth analysis of rare cell populations and the regulatory consequences of epigenetic modifications.

Main Methods:

  • The Smart-RRBS protocol combines Smart-seq2 for RNA profiling and reduced representation bisulfite sequencing (RRBS) for DNA methylation analysis.
  • It involves the physical separation of messenger RNA (mRNA) from genomic DNA within individual cells.
  • The method is applicable to both isolated single cells and micro-dissected tissue samples.

Main Results:

  • Smart-RRBS generates paired epigenetic promoter and RNA-expression measurements for approximately 24% of protein-coding genes per cell.
  • The protocol is effective for analyzing samples ranging from single cells to hundreds of cells from micro-dissected tissues.
  • Manual processing of up to 192 samples takes approximately 3 days, excluding cell sorting and sequencing.

Conclusions:

  • Smart-RRBS provides a robust method for paired epigenetic and transcriptomic profiling at the single-cell level.
  • This technique facilitates the study of cellular heterogeneity and the functional impact of DNA methylation.
  • The protocol is accessible with basic molecular biology expertise and standard laboratory equipment.