Description: Assay for transposase-accessible chromatin using sequencing (ATAC-seq), based on direct in vitro transposition of sequencing adaptors into native chromatin, is a rapid (<24 hr) and sensitive(<50,000 cells) method for integrative epigenomic analysis.

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Description: Assay of Transposase-Accessible Chromatin with visualization is a transposase-mediated imaging technology that enables direct imaging of the accessible genome in situ, cell sorting, and deep sequencing to reveal the identity of the imaged elements.

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Description: Domain-specific chromatin isolation by RNA purification (dChIRP) is a technique for dissecting the functional domains of a target RNA in situ. dChIRP can identify domain-level intramolecular and intermolecular RNA-RNA, RNA-protein, and RNA-DNA interactions, and map the RNA’s genomic binding sites with high precision. 

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Description: Genome conformation is central to gene control but challenging to interrogate. HiChIP is a protein-centric chromatin conformation method. HiChIP improves the yield of conformation-informative reads by over 10-fold and lowers the input requirement over 100-fold relative to that of ChIA-PET. HiChIP of cohesin reveals multiscale genome architecture with greater signal-to-background ratios than those of in situ Hi-C.

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Description: Omni-ATAC is an improved ATAC-seq protocol that provides improved data quality across all cell types and cell contexts tested. This protocol reduces the number of reads coming from mitochondrial DNA, increases the library complexity, and increases the signal-to-background ratio of the data. We recommend this protocol for all ATAC-seq applications.

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Description: PARIS (Psoralen Analysis of RNA Interactions and Structures) is a method used to directly determine transcriptome-wide base pairing interactions. It combines four critical steps, in vivo cross-linking, 2D gel purification, proximity ligation, and high-throughput sequencing to achieve high-throughput and near-base pair resolution determination of the RNA structurome and interactome in living cells

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Description: icSHAPE (in vivo CLICK selective 2’-hydroxyl acylation and profiling experiment) is a method that produces one-dimensional reactivity profiles at flexible, single-stranded regions of RNA to predict RNA secondary structure. Leveraging deep sequencing and a novel electrophilic structural probe, NAI-N3, we can measure all four nucleobases at single-base resolution across the transcriptome of any organism.

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