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Epigenomics
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CUT&RUN

CUT&RUN (Cleavage Under Targets and Release Using Nuclease) is a chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing (Skene P.J. et al., 2017). It is an alternative approach to chromatin immunoprecipitation (ChIP-seq) to explore protein-DNA bindings at the genome-wide level.
Required material:
~2,000-5,000 cells for histone modification
~10,000 cells for transcription factors



High throughput ChIP-seq

High throughput ChIP-seq (Chromatin Immunoprecipitation sequencing), is an automated method for systematic mapping of in vivo protein-DNA binding that increases the throughput and sensitivity, while reducing the labor and cost required for conventional ChIP-seq. (Garber M. et al., 2013)
Required material:
105-106 cells / 10-50mg tissue sample



ATAC-seq (Bulk ATAC and Single Cell ATAC)

Bulk ATAC
ATAC (Assay for Transposase-Accessible Chromatin)-seq is a method for mapping chromatin accessibility genome-wide. This method probes DNA accessibility with hyperactive Tn5 transposase, which inserts sequencing adapters into accessible regions of chromatin. Sequencing reads can then be used to infer regions of increased accessibility, as well as to map regions of transcription factor binding and nucleosome position. The method is a fast and sensitive alternative to DNase-seq for assaying chromatin accessibility genome-wide, or to MNase for assaying nucleosome positions in accessible regions of the genome (Buenrostro J. et al., 2015)
Required material:
50,000 viable cells

Single Cell ATAC Single-cell ATAC (Assay for Transposase Accessible Chromatin) is a method to map chromatin accessibility at the single cell level. The chromatin profiling of thousands of single cells allows us to explore how chromatin compaction and DNA-binding proteins regulate gene expression at high resolution. It can be used to study cellular heterogeneity, to identify cell subpopulations and to perform single-cell trajectory analysis.
Required material:
10,000-100,000 viable cells



Low-C

Hi-C comprehensively detects chromatin interactions in the mammalian nucleus. This method is based on Chromosome Conformation Capture, in which chromatin is crosslinked with formaldehyde, then digested, and re-ligated in such a way that only DNA fragments that are covalently linked together form ligation products. The ligation products contain the information of not only where they originated from in the genomic sequence but also where they reside, physically, in the 3D organization of the genome. In Hi-C, a biotin-labeled nucleotide is incorporated at the ligation junction, enabling selective purification of chimeric DNA ligation junctions followed by deep sequencing (Belton J.M. et al., 2012) Low-C is an improved in situ Hi-C method that allows the generation of high-quality genome-wide chromatin conformation maps using very low amounts of starting tissue material (Díaz N et al., 2018).
Required material:
103-106 cells


Capture methyl-seq

Targeted methylation sequencing (Capture methyl-seq) is a balanced, cost-effective choice between whole-genome bisulfite sequencing and methylation arrays. It can be used for both screening and biomarker discovery studies. This method targets over 3.3 million CpGs.
Required material:
500 ng input DNA



Contact: Dr. Elias Orouji