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DNase-seq (purpose)
identifies open regions of chromatin
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DNase-seq (description)
- relies on preferential digestion of chromatin regions unprotected by bound proteins, which are hypersensitive to DNase I
- following digestion, run on a gel
- prep you library
- deep sequencing
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FAIRE-seq (purpose)
identifies crosslinked chromatin interacting with proteins
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FAIRE-seq (description)
- relies on cross-linked chromatin, assisted by treatment with formaldhyde
- sonication
- extraction of the naked DNA fragments, the naked DNA left behind is purified and sequenced
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Proximity Ligation Assay (PLA) (purpose)
to find protein-protein interactions that might otherwise be difficult to quantify
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MNase-seq (describe)
Nuclei are isolated and chromatin is crosslinked and digested with Micrococcal Nuclease that in the presence of Ca2+ digests all exposed DNA
- Nucleosomes and TFs shield DNA “footprints” from digestion and protected DNA fragments are purified, adapted, next-gen sequenced
- and the reads are mapped to the genome
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MNase-seq (purpose)
profiles nucleosome occupancy and position
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ATAC-seq (purpose)
accessible regions of the genome are accessed by adapters
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