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.
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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- Affinity of Protein A/G for IgG Types from Different Species
- Effect of Various Temperatures on Nicking Endonucleases
Selection Tools
- 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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