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Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing ChIP-seq
Published on: April 19, 2013
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Purification of nanogram-range immunoprecipitated DNA in ChIP-seq application
Jian Zhong1, Zhenqing Ye2, Samuel W Lenz1
1Epigenomics Development Laboratory, Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
BMC Genomics
|December 23, 2017
Summary
This study evaluated commercial DNA purification reagents for low-input chromatin immunoprecipitation-sequencing (ChIP-seq). Certain reagents offer consistent high performance for nanogram-range DNA, improving ChIP-seq methodology.
Area of Science:
- Epigenetics
- Molecular Biology
- Genomics
Background:
- Chromatin immunoprecipitation-sequencing (ChIP-seq) is crucial for studying genome-wide protein-DNA interactions.
- Current ChIP protocols often yield low nanogram quantities of DNA, necessitating efficient purification.
- Limited data exists on the performance of purification reagents for minute ChIP DNA amounts.
Purpose of the Study:
- To compare the efficacy of commercial DNA purification reagents for nanogram-range ChIP DNA.
- To assess the impact of storage conditions on purified low-input ChIP DNA.
- To evaluate the effect of purification on subsequent ChIP-seq library preparation and data quality.
Main Methods:
- Compared DNA recovery of ten commercial reagents and phenol/chloroform extraction for 1-50 ng ChIP DNA.
- Investigated DNA loss during storage based on polypropylene tube type.
- Evaluated ChIP-seq performance using four selected purification reagents with 1 ng DNA input.
Main Results:
- Significant differences in DNA recovery were observed for 1 ng DNA, but were similar for higher amounts.
- Low nanogram DNA is susceptible to storage loss, influenced by tube material.
- Selected purification kits minimally impacted library preparation efficiency, yielding high-quality, comparable ChIP-seq data.
Conclusions:
- Provides comparative data on DNA purification reagents for low-input ChIP DNA.
- Highlights the critical importance of storage conditions for nanogram-range purified DNA.
- Identifies high-performing reagents to enhance ChIP-seq methodology for low-input applications.
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