Highly quantitative measurement of differential protein-genome binding with PerCell chromatin sequencing
Quantitative comparison of ChIP-seq profiling between experimental conditions or samples remains technically challenging for the epigenetics field. Here, we report a strategy combining the use of well-defined cellular spike-in ratios of orthologous species' chromatin and a bioinformatic analysis pipeline to facilitate highly quantitative comparisons of 2D chromatin sequencing across experimental conditions. We find that the PerCell methodology results in efficient and consistent levels of spike-in vs. experimental genomic reads. We demonstrate use of the method and pipeline to enable quantitative, internally normalized chromatin sequencing on zebrafish embryos and human cancer cells. Overall, we propose the PerCell method to enable cross-species comparative epigenomics and promote uniformity of data analyses and sharing across labs.
Authors
- Genevieve C. Kendall (ORCID: https://orcid.org/0000-0003-3775-2006)
- Jack Kucinski (ORCID: https://orcid.org/0000-0002-1788-1305)
- Stephanie LaHaye (ORCID: https://orcid.org/0000-0001-8625-4199)
- Alexi Tallan (ORCID: https://orcid.org/0000-0002-6043-3233)
- Benjamin Z. Stanton (ORCID: https://orcid.org/0000-0002-2613-2955)
- Benjamin D. Sunkel (ORCID: https://orcid.org/0000-0003-1376-9567)
- Cenny Taslim (ORCID: https://orcid.org/0000-0003-3302-9099)
- Meng Wang (ORCID: https://orcid.org/0000-0002-3457-5908)
- Qi Liu (ORCID: https://orcid.org/0000-0002-0084-6482)
- Jun Qi (ORCID: https://orcid.org/0000-0003-2995-7650)
Institutions
- Nationwide Children's Hospital (US)
- Dana-Farber Cancer Institute (US)
Publication Details
- Journal
- Cell Reports Methods
- Published
- 2025-05-19
- DOI
- https://doi.org/10.1016/j.crmeth.2025.101052
- Citations
- 1
- Primary Topic
- Genomics and Chromatin Dynamics
- Type
- article
- Field-Weighted Citation Impact
- 0.81
Funders
- American Cancer Society
- V Foundation for Cancer Research
- Alex's Lemonade Stand Foundation for Childhood Cancer
- St. Baldrick's Foundation
- Ohio State University
- Nationwide Children's Hospital
- CancerFree KIDS
- National Institutes of Health
- Research Institute, Nationwide Children's Hospital
- National Heart, Lung, and Blood Institute
- National Cancer Institute
- National Institute of General Medical Sciences