PUBLICATION
Highly quantitative measurement of differential protein-genome binding with PerCell chromatin sequencing
- Authors
- Tallan, A., Kucinski, J., Sunkel, B., Taslim, C., LaHaye, S., Liu, Q., Qi, J., Wang, M., Kendall, G.C., Stanton, B.Z.
- ID
- ZDB-PUB-250521-7
- Date
- 2025
- Source
- Cell reports methods : 101052101052 (Journal)
- Registered Authors
- Kendall, Genevieve
- Keywords
- CP: molecular biology, CP: systems biology, Nextflow, chromatin sequencing, cross-species epigenomics, genomics normalization, quantitative epigenomics, sarcoma, transcription factor
- MeSH Terms
-
- Animals
- Protein Binding
- Zebrafish/genetics
- Genome*
- Chromatin Immunoprecipitation Sequencing*/methods
- Humans
- Chromatin*/genetics
- Chromatin*/metabolism
- Computational Biology/methods
- Epigenomics/methods
- Cell Line, Tumor
- PubMed
- 40393455 Full text @ Cell Rep Methods
Citation
Tallan, A., Kucinski, J., Sunkel, B., Taslim, C., LaHaye, S., Liu, Q., Qi, J., Wang, M., Kendall, G.C., Stanton, B.Z. (2025) Highly quantitative measurement of differential protein-genome binding with PerCell chromatin sequencing. Cell reports methods. :101052101052.
Abstract
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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping