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

Sample Preparation for Analysis: Overview01:21

Sample Preparation for Analysis: Overview

252
Sample preparation is an essential step in the analytical process. It involves preparing a sample so that it can be analyzed accurately. The goal is to extract the analyte, the substance you want to measure, from the sample while removing any components that may interfere with the analysis. Sample preparation techniques vary depending on the physical state of the sample.
Bulk or large solid samples are typically reduced in size using grinding, crushing, or milling techniques to increase the...
252
Sample Preparation for Analysis: Advanced Techniques01:08

Sample Preparation for Analysis: Advanced Techniques

388
Accurate analysis of complex samples often requires advanced preparation techniques to achieve reliable and reproducible results. Samples containing inorganic or organic materials can be challenging to dissolve or decompose effectively. Standard sample preparation methods include acid digestion, fusion, dry ashing, and wet digestion.
Acid digestion with strong acids is commonly used to dissolve inorganic materials that are insoluble (do not dissolve) in water. This method can be useful for...
388

You might also read

Related Articles

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

Sort by
Same author

Intermittent hypoxia ameliorates behavioral deficits and exerts neurorestoration in a mouse photothrombotic stroke model.

Theranostics·2026
Same author

Biology-aligned cervical cancer screening: target-centric biomarkers and next-generation diagnostic platforms.

Biomarker research·2026
Same author

Molecular characterisation of telitacicept response phenotypes in systemic lupus erythematosus: an exploratory integrated transcriptome and B-cell receptor repertoire profiling study.

Journal of translational medicine·2026
Same author

Maternal trans-vaccenic acid shapes neonatal T cell development and early-life immune imprinting.

Science (New York, N.Y.)·2026
Same author

Nonlinear association between serum insulin, visceral fat area, and kidney function in female with type 2 diabetes: a retrospective study.

Frontiers in endocrinology·2026
Same author

Spatially resolved m<sup>6</sup>A profiling using m<sup>6</sup>A-ARTR-DBiT.

Nature methods·2026
Same journal

Correction to: Pathogenicity patterns in cytochrome P450 family.

Bioinformatics advances·2026
Same journal

Region-aware bridge modeling enables interpretable mesoscale representation of spatial transcriptomic tissue sections.

Bioinformatics advances·2026
Same journal

Microbiome differential abundance methodologies to detect relevant taxa associated with chemotherapy toxicity rate in colorectal cancer.

Bioinformatics advances·2026
Same journal

maldipickr dereplicates microbial MALDI-TOF spectra to facilitate multiplexed isolation.

Bioinformatics advances·2026
Same journal

RAM-MSA: an anytime memory-bounded method for exact multiple sequence alignment using path finding.

Bioinformatics advances·2026
Same journal

Interpretable machine learning for low-sample multi-omics: a case study of ferret vaccine response.

Bioinformatics advances·2026
See all related articles

Related Experiment Video

Updated: Jul 15, 2025

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

2.5K

KAS-Analyzer: a novel computational framework for exploring KAS-seq data.

Ruitu Lyu1,2, Tong Wu1,2, Gayoung Park3

  • 1Department of Chemistry, The University of Chicago, IL 60637, United States.

Bioinformatics Advances
|September 25, 2023
PubMed
Summary
This summary is machine-generated.

KAS-Analyzer is a new computational tool that simplifies the analysis of KAS-seq and spKAS-seq data, enabling deeper insights into transcription and R-loop structures. This framework enhances the study of dynamic transcriptional regulation.

More Related Videos

3' End Sequencing Library Preparation with A-seq2
12:01

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

10.6K
High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

10.3K

Related Experiment Videos

Last Updated: Jul 15, 2025

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

2.5K
3' End Sequencing Library Preparation with A-seq2
12:01

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

10.6K
High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

10.3K

Area of Science:

  • Genomics and Molecular Biology
  • Computational Biology and Bioinformatics

Background:

  • Kethoxal-assisted ssDNA sequencing (KAS-seq) is a powerful method for studying transcriptionally engaged RNA polymerases by profiling single-stranded DNA (ssDNA).
  • Strand-specific KAS-seq (spKAS-seq) enables genome-wide mapping of R-loop structures by detecting ssDNA imbalances.
  • A lack of user-friendly, open-source computational tools hinders the widespread adoption and comprehensive analysis of KAS-seq data.

Purpose of the Study:

  • To introduce KAS-Analyzer, the first comprehensive computational framework for KAS-seq and spKAS-seq data analysis.
  • To streamline and enhance the interpretation of KAS-seq and spKAS-seq data, facilitating broader research applications.
  • To provide novel tools for detailed analysis, including transcription metrics, enhancer identification, R-loop mapping, and differential polymerase activity.

Main Methods:

  • Development of KAS-Analyzer, a computational framework integrating standard and novel analysis tools for KAS-seq and spKAS-seq data.
  • Implementation of specific modules for calculating transcription-related metrics, identifying single-stranded transcribing (SST) enhancers, and high-resolution R-loop mapping.
  • Application of KAS-Analyzer to time-course KAS-seq datasets to analyze dynamic transcriptional responses to UVB radiation.

Main Results:

  • KAS-Analyzer provides a comprehensive suite of tools for analyzing KAS-seq and spKAS-seq data, addressing the current computational gap.
  • The framework enables detailed investigation of transcriptional dynamics, including the identification of SST enhancers and precise R-loop mapping.
  • Demonstrated robust capabilities in analyzing dynamic transcriptional regulatory programs using time-course data, showcasing its utility in response to stimuli like UVB radiation.

Conclusions:

  • KAS-Analyzer significantly enhances the accessibility and analytical power for KAS-seq and spKAS-seq data.
  • The tool facilitates a deeper understanding of genome-wide transcription, R-loop formation, and dynamic regulatory processes.
  • KAS-Analyzer is an open-source resource available for the research community to advance studies in molecular biology and genomics.