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Chromatin Analysis

NEB has validated enzymes for methods to profile chromatin accessibility and functional interactions using native, fixed, and fresh frozen paraffin-embedded (FFPE) cell or tissue samples.


Overview of the NicE-view seq

Chromatin analysis accessibility profiling in cells or tissues with NicE-seq
NEB developed Nicking Enzyme-assisted viewing and sequencing (NicE-viewSeq) to enable profiling chromatin accessibility with fixed cells or tissues.


Tools to study chromatin structure and function

  • Nicking Enzyme assisted sequencing (NicE-seq) incorporates Nt.CviPII (NEB #R0626) for profiling chromatin accessibility using 4% formaldehyde fixed cells with high dynamic range of 100K to 1000 cells.

  • Micrococcal Nuclease (NEB # M0247) can be used in Protect-seq to identify inaccessible chromatin domains or Chromatin Immunoprecipitation (ChIP) assays

  • Protein A (NEB # S1425) or Protein G (NEB #S1430) Magnetic Beads can be used in Protect-seq, ChIP, and other affinity-based epigenetics assays.

  • NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB #E7645) can be used to prepare chromatin immunoprecipitated DNA samples for next-generation sequencing.

  • DNase I (NEB #M0303) can be used for footprinting, DNase-seq, or Protect-seq.

  • AluI (NEB #R0137), MseI (NEB #R0525), and Haeiii (NEB #R0108) can be used to digest protein complexes from formaldehyde-fixed chromatin, which can then be used in Chromatin Immunoprecipitation (ChIP) or chromatin conformation capture (3C).

  • GpC Methyltransferase (M.CviPI) (NEB # M0227) is useful for chromatin accessibility studies, and nucleosome and chromatin-associated protein (CAP) footprinting.

  • 5-methyl-dCTP (NEB # N0356) nucleotides can be used in NicE-seq as a component of the labeling mixture.  

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FAQs for Chromatin Analysis
Protocols for Chromatin Analysis
    Publications related to Chromatin Analysis
    • Spracklin, G., Yang, L., Pradhan, S., Dekker, J. (2023) Measuring Inaccessible Chromatin Genome-Wide Using Protect-seq Methods in molecular biology; 2611: 53–61, PubMedID: 36807063, DOI: https://doi.org/10.1007/978-1-0716-2899-7_4
    • Sunitha Kumary et al. (2024) Emerging Approaches to Profile Accessible Chromatin from Formalin-Fixed Paraffin-Embedded Section. Epigenomes; DOI: 10.3390/epigenomes8020020
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This product is intended for research purposes only. This product is not intended to be used for therapeutic or diagnostic purposes in humans or animals.


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