index

ChIP-Seq:

ChIP-Seq combines chromatin immunoprecipitation with DNA sequencing, to obtain the DNA sequences which are able to interact with the immunoprecipitated proteins. This is very useful to identify transcription factors and nucleosome-associated sequences. Workflow is very simple: first, the cells need to be treated with formaldehyde, to create cross-link between the proteins and the DNA. Then, DNA is extracted fragmented with sonication and an antibody against the protein of interest is added. Precipitation could be achieved via beads associated to A/G proteins and centrifugation. Subsequently the pellet needs to be treated with an high ionic force and high temperature, to resolve the cross-links and dissociate DNA fragments from the protein of interest. Finally, linkers have to be added at the ends of the fragments: specific primers for PCR (able to recognize these linkers) will be used to amplify and sequence each fragments. Also, a libraries can be created.

(Samuele Irudal)

ATAC-Seq

DNase-seq

FAIRE

Nucleosome positioning

other