We offer four approaches for epigenomics

ChIP-Seq

Chromatin ImmunoPrecipitation sequencing (ChIP-Seq) is a powerful method for identifying genome-wide DNA binding sites for transcription factors and other proteins. Following ChIP protocols, DNA-bound protein is immunoprecipitated using a specific anti

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ChIP-exo

ChIP-exo is a chromatin immunoprecipitation based method for mapping the locations at which a protein of interest (transcription factor) binds to the genome. It is a modification of the ChIP-seq protocol, improving the resolution of binding sites from hundreds of base pairs to almost one base pair. It employs the use of exonucleases to degrade strands of the protein-bound DNA in the 5′-3′ direction to within a small number of nucleotides of the protein binding site. Locations on the genome at which the protein binds are identified by Next-Generation Sequencing.

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ATAC-Seq

ATAC-seq Assay for transposase-accessible chromatin sequencing (ATAC-seq) has been used extensively in a wide range of organisms to map functional elements using Tn5 transposase’s ability to enrich for open (actively regulated) chromatin regions irrespective of the unique aspects of the organism’s genome. ATAC-seq can identifyactive regulatory elements including but not limited to gene promoters, enhancer elements, and insulators. ATAC-seq operates on minimal cell input (<50K cells), is a simple assay (~2 hrs), and does not suffer from many of the issues present in other genome-wide epigenomic assays (RNA-degradation, target specific affinity reagents, etc.).

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High-throughput ATACseq workflows using open-source protocols are also being developed in the Genomics innovation Hub

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Single-cell ATAC-Seq

Assay for transposase-accessible chromatin sequencing (ATAC-seq) builds on a process called tagmentation: the simultaneous fragmentation and tagging of a genome with sequencing adaptors without the need to use antibodies. ATAC-Seq identifies accessible regions of the genome. Using 10X Genomics technology, you can identify open chromatin regions at the level of a single cell, and compare variation among cells in a cell population.

ORDER Single-cell ATAC-Seq from the Genomics Facility

Single-cell ATAC-Seq workflows using open-source protocols are also being developed in the Genomics innovation Hub

Contact the Genomics Innovation Hub about Collaboration Opportunities