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...

Southern Blot

Southern Blot

Agarose gel electrophoresis is very useful in separating DNA fragments by size. Running a DNA ladder containing fragments of the known length alongside the sample helps determine the approximate length of the sample DNA fragments. However, additional steps are needed to verify the sequence identity of the sample DNA fragments.
Denatured DNA fragments must be transferred onto a carrier membrane from the gel to make it accessible to a probe - a small ssDNA fragment complementary to the target DNA...

In-situ Hybridization

In-situ Hybridization

In situ hybridization (ISH) is a technique used to detect and localize specific DNA or RNA molecules in cells, tissue, or tissue sections using a labeled probe. The technique was first used in 1969 for the investigation of nucleic acids. It is currently an essential tool in scientific research and clinical settings, especially for diagnostic purposes.
Types of probes and labels
A probe is a complementary strand of DNA or RNA that binds to corresponding nucleotide sequences in a cell. Many...

You might also read

Related Articles

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

Sort by

Same author

Non-canonical histone H3.3 and its chaperones HIRA and DAXX participate in the regulation of KSHV latency.

bioRxiv : the preprint server for biology·2026

Same author

Herpesvirus-encoded lncRNA targets host splicing by interacting with splicing factors.

PLoS pathogens·2026

Same author

Cross-Species Insights Into Gamma Herpesvirus Transcriptomes: Long-Read and Multi-Omics Perspectives.

Journal of medical virology·2026

Same author

A viral circular RNA in Kaposi's sarcoma-associated herpesvirus modulates viral and host gene expression during latent and lytic replication.

Exploration of targeted anti-tumor therapy·2025

Same author

High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing.

Nucleic acids research·2024

Same author

The model student: GPT-4 performance on graduate biomedical science exams.

Scientific reports·2024

Same journal

Probabilistic RNA designability via interpretable ensemble approximation and dynamic decomposition.

Bioinformatics (Oxford, England)·2026

Same journal

Quantifying domain-specific relevance of computational biology Wikipedia articles using TF-IDF and cosine similarity.

Bioinformatics (Oxford, England)·2026

Same journal

GATSBI: improving context-aware protein embeddings through biologically motivated data splits.

Bioinformatics (Oxford, England)·2026

Same journal

BiMba: using Vision Mamba to predict protein sites that bind other proteins.

Bioinformatics (Oxford, England)·2026

Same journal

ProMeta: a meta-learning framework for robust disease diagnosis and prediction from plasma proteomics.

Bioinformatics (Oxford, England)·2026

Same journal

Is a Win-Win possible? Achieving pareto-optimal privacy-utility balance in fine-tuned genome language model embeddings against embedding reconstruction attacks.

Bioinformatics (Oxford, England)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jul 10, 2025

Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data

Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data

Published on: December 1, 2023

Hybkit: a Python API and command-line toolkit for hybrid sequence data from chimeric RNA methods.

Daniel Stribling^1,2,3, Lauren A Gay¹, Rolf Renne^1,2,3

¹Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, United States.

Bioinformatics (Oxford, England)

|November 25, 2023

Summary

This summary is machine-generated.

Hybkit is a new Python toolkit for analyzing hybrid RNA sequences generated by microRNA/target ligation experiments. It offers customizable analysis, plotting, and integration of predicted interactions for deeper insights into microRNA function.

More Related Videos

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion

Published on: June 25, 2017

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

Published on: July 10, 2020

Related Experiment Videos

Last Updated: Jul 10, 2025

Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data

Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data

Published on: December 1, 2023

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion

Published on: June 25, 2017

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

Published on: July 10, 2020

Area of Science:

Bioinformatics
Molecular Biology
Computational Biology

Background:

MicroRNA (miRNA) research relies on experimental methods like miRNA/target ligation to understand gene regulation.
These methods generate chimeric (hybrid) RNA sequences, providing valuable data on miRNA interactions.
Analyzing these hybrid sequences is crucial for elucidating miRNA function.

Purpose of the Study:

To introduce Hybkit, a novel Python 3 API and command-line toolkit.
To enable customizable analysis and annotation of hybrid sequence data.
To facilitate the evaluation of hybrid characteristics and miRNA/target interactions.

Main Methods:

Development of a Python 3 API and command-line toolkit named Hybkit.
Implementation of objects for custom analysis of hybrid sequence data.
Inclusion of miRNA-specific analysis, built-in plotting, and integration of predicted miRNA/target interactions in Vienna format.

Main Results:

Hybkit provides a flexible platform for analyzing hybrid RNA sequences.
The toolkit supports customizable evaluation and annotation of hybrid characteristics.
Analysis includes miRNA-specific methods and visualization of results.

Conclusions:

Hybkit enhances the analysis of experimental data from miRNA/target ligation studies.
The toolkit offers a powerful resource for researchers investigating miRNA function.
Hybkit is freely available, promoting accessibility in bioinformatics research.