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

You might also read

Related Articles

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

Sort by
Same author

Laccase as a green biocatalyst for xenobiotic degradation: integrative insights from molecular docking and bibliometric analysis.

3 Biotech·2026
Same author

Optimization of OSCC spheroid generation for high-throughput drug screening.

In vitro models·2026
Same author

Bioactivity-Guided Isolation of Cytotoxic Compounds From Curcuma caesia: In Vitro and In Silico Investigation for Oral Cancer.

Chemistry & biodiversity·2025
Same author

Discovery of a fluorinated squaramide as a potential CXCR2- autophagy signalling modulator in chemo-resistant oral squamous cell carcinoma and polyploid giant cancer cells.

European journal of medicinal chemistry·2025
Same author

Disrupting microtubule dynamics to rewire apoptosis, differentiation, and EMT programs in oral squamous cell carcinoma through indenamine derivatives.

Bioorganic & medicinal chemistry·2025
Same author

Advancing oral squamous cell carcinoma research: the evolving role of patient-derived cell lines, xenografts, and organoid models.

3 Biotech·2025

Related Experiment Video

Updated: May 9, 2025

Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers
10:28

Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers

Published on: September 20, 2018

6.4K

Chromatin Shearing in Suspension Cell Line: A Guide for Optimization.

Ambika Chamoli1, Priyanka Patel Vatsa1, Vinal Upadhyay1

  • 1Department of Biotechnology, National Institute of Pharmaceutical Education and Research, (An Institute of National Importance, Government of India, Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers), Ahmedabad, Gujrat, India.

DNA and Cell Biology
|May 5, 2025
PubMed
Summary

Optimizing chromatin shearing is crucial for successful chromatin immunoprecipitation (ChIP) experiments. This study standardized sonication parameters for Kasumi-1 cells, yielding DNA fragments of 250-600 bp.

Keywords:
chromatin immunoprecipitationchromatin sonicationshearing

More Related Videos

Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells
08:34

Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells

Published on: December 10, 2014

18.6K
Chromatin Extraction from Frozen Chimeric Liver Tissue for Chromatin Immunoprecipitation Analysis
09:26

Chromatin Extraction from Frozen Chimeric Liver Tissue for Chromatin Immunoprecipitation Analysis

Published on: March 23, 2021

2.6K

Related Experiment Videos

Last Updated: May 9, 2025

Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers
10:28

Repressing Gene Transcription by Redirecting Cellular Machinery with Chemical Epigenetic Modifiers

Published on: September 20, 2018

6.4K
Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells
08:34

Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells

Published on: December 10, 2014

18.6K
Chromatin Extraction from Frozen Chimeric Liver Tissue for Chromatin Immunoprecipitation Analysis
09:26

Chromatin Extraction from Frozen Chimeric Liver Tissue for Chromatin Immunoprecipitation Analysis

Published on: March 23, 2021

2.6K

Area of Science:

  • Molecular Biology
  • Genomics
  • Epigenetics

Background:

  • Chromatin immunoprecipitation (ChIP) is vital for studying DNA-protein interactions and protein binding sites.
  • The chromatin fragmentation step is a critical and sensitive stage in the ChIP protocol.
  • Experimental variability in ChIP can arise from suboptimal chromatin shearing.

Purpose of the Study:

  • To optimize chromatin shearing parameters for the Kasumi-1 cell line.
  • To identify key variables influencing chromatin fragmentation efficiency and reproducibility.
  • To standardize a robust protocol for generating DNA fragments of a specific size range for ChIP.

Main Methods:

  • Cells (Kasumi-1) were fixed with formaldehyde, lysed, and nuclei were isolated.
  • Chromatin shearing was performed using sonication with varied buffers and parameters.
  • Sonication settings optimized: 150 W peak incident power, 7.0% duty factor, 200 cycles/burst, water fill level 8, for 7 minutes.

Main Results:

  • Optimal sonication yielded DNA fragments of approximately 250-600 bp.
  • Standardized sonication buffer composition: 0.15% SDS and 0.05% DOC.
  • Successful chromatin fragmentation was achieved within 7 minutes under optimized conditions.

Conclusions:

  • The quality of chromatin shearing directly impacts the success of ChIP experiments.
  • Optimized sonication parameters and buffer composition provide a standardized protocol for Kasumi-1 cells.
  • This standardization reduces experimental variability and improves the reliability of ChIP assay results.