All of the Epigenetic sequencing methods are collected together under this heading

High-Resolution Crosslinking Chromatin Immunoprecipitation Sequencing Crosslinking chromatin immunoprecipitation (X-ChIP) is a foundational technique in chromatin research (Breiling et al., 2001) (Negre et al., 2001). With the advent of NGS this simple technique, now called X-ChIP-seq, is able produce high-resolution results (Skene et al., 2015). The […]

Circular Chromosome Conformation Capture with Unique Molecular Identifiers This variation on the 4C approach uses UMIs to derive high-complexity quantitative chromosome contact profiles with controlled signal-to-noise ratios (Schwartzman et al., 2016). It is an efficient and accurate method for analyzing targeted loci. The method is […]

Transposome Hypersensitive Sites Sequencing THS-seq is a method for highly sensitive characterization of chromatin accessibility. This variation on ATAC-seq uses linear amplification of accessible DNA ends, in vitro transcription, and an engineered Tn5 super-mutant (Sos et al., 2016)Advantages: Requires very little input material Can detect […]

Systematic Evolution of Ligands by Exponential Enrichment / High-Throughput Systematic Evolution of Ligands by Exponential Enrichment From the time that the first SELEX experiments were described by 3 independent groups in 1990 (Ellington et al., 1990) (Tuerk et al., 1990) (Sullenger et al., 1990), the […]

Protein/DNA Binding Followed by High-Throughput Sequencing PB_seq is a DNA-binding assay that allows the DNA-protein binding energy landscape to be characterized genome-wide, in the absence of chromatin (Guertin et al., 2012). It belongs to the family of methods more commonly known as systematic evolution of […]

Pathology Tissue Chromatin Immunoprecipitation PAT-ChIP is a variation of ChIP-Seq, optimized for the analysis of chromatin derived from FFPE samples. The distinguishing features of this method are dewaxing with a xylene substitute (Histolemon, Carlo Erba) followed by both MNase digestion and sonication (Fanelli et al., […]

Occupied Regions of Genomes from Affinity-Purified Naturally Isolated Chromatin ORGANIC is a gentle protocol that avoids crosslinking and sonication (Kasinathan et al., 2014). The method is a combination of MNase-Seq and native ChIP that provides accurate maps of chromatin-occupied regions in complex eukaryotic genomes.Advantages: Avoids […]

Nucleosome Occupancy Methylome-Sequencing NOMe-Seq is a single-molecule, high-resolution nucleosome positioning assay (Han et al., 2011). This method is based on the ability of the GpC methyltransferase M.CviPI to methylate GpC sites that are not bound by nucleosomes, to create a digital footprint of nucleosome positioning. […]

Next-Generation Capture-C NG Capture-C is a refinement of 3C-Seq (Duan et al., 2012) and Hi-C (Lieberman-Aiden et al., 2009). It represents a family of methods used to analyze chromatin interactions. NG Capture-C adds multiple pull-down steps of the biotinylated fragments with magnetic beads to the […]