ArticleScientific data2018
ChIP-seq and ChIP-exo profiling of Pol II, H2A.Z, and H3K4me3 in human K562 cells.
Article in Scientific data, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Zfp462 Is a Key Mediator of Osteoblast Differentiation and Might Contribute to Age-Related Bone Loss.Aging cell · 2026Article
- ssG4-seq for global profiling of strand-specific G-quadruplex structures in mammalian genomes.Nature communications · 2025Article
- Identification of human RNA Polymerase II interactors at early stages of transcription.bioRxiv : the preprint server for biology · 2025Article
- The Dynamics of Histone Modifications during Mammalian Zygotic Genome Activation.International journal of molecular sciences · 2024Review
- Synergising single-cell resolution and 4sU labelling boosts inference of transcriptional bursting.Genome biology · 2023Article
- CTCF-CTCF loops and intra-TAD interactions show differential dependence on cohesin ring integrity.Nature cell biology · 2022Article
- A comparison of experimental assays and analytical methods for genome-wide identification of active enhancers.Nature biotechnology · 2022Article
- SAFA facilitates chromatin opening of immune genes through interacting with anti-viral host RNAs.PLoS pathogens · 2022Article
- Enhancers predominantly regulate gene expression during differentiation via transcription initiation.Molecular cell · 2021Article
- Reducing the structure bias of RNA-Seq reveals a large number of non-annotated non-coding RNA.Nucleic acids research · 2020Article
- ChIP-seq and ChIP-exo profiling of Pol II, H2A.Z, and H3K4me3 in human K562 cells.Scientific data · 2018Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The human K562 chronic myeloid leukemia cell line has long served as an experimental paradigm for functional genomic studies. To systematically and functionally annotate the human genome, the ENCODE consortium generated hundreds of functional genomic data sets, such as chromatin immunoprecipitation coupled to sequencing (ChIP-seq). While ChIP-seq analyses have provided tremendous insights into gene regulation, spatiotemporal insights were limited by a resolution of several hundred base pairs. ChIP-exonuclease (ChIP-exo) is a refined version of ChIP-seq that overcomes this limitation by providing higher precision mapping of protein-DNA interactions. To study the interplay of transcription initiation and chromatin, we profiled the genome-wide locations for RNA polymerase II (Pol II), the histone variant H2A.Z, and the histone modification H3K4me3 using ChIP-seq and ChIP-exo. In this Data Descriptor, we present detailed information on parallel experimental design, data generation, quality control analysis, and data validation. We discuss how these data lay the foundation for future analysis to understand the relationship between the occupancy of Pol II and nucleosome positions at near base pair resolution.
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