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Protocols

CUT&RUN specifications

Information


Unique identifier OMICS_31955
Name CUT&RUN
Alternative name AutoCUT&RUN
Software type Application/Script
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Steven Henikoff

Publication for CUT&RUN

CUT&RUN citations

 (9)
call_split

Non B Form DNA Is Enriched at Centromeres

2018
Mol Biol Evol
PMCID: 5889037
PMID: 29365169
DOI: 10.1093/molbev/msy010
call_split See protocol

[…] CUT&RUN was performed as described (, ). In brief, K562 or Cos-7 cells were gently washed twice in room temperature Wash buffer [20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and a Roche complete […]

library_books

A cut above

2017
eLife
PMCID: 5310838
PMID: 28199181
DOI: 10.7554/eLife.25000

[…] se enzyme. Due to lower sample and sequencing requirements, CUT&RUN might be applicable to a number of real-world situations, where cost and sample availability are often an issue.As a new technique, CUT&RUN will require further evaluation to determine whether it could replace (or at least complement) ChIP-seq and its variants at the same scale. For example, it is not clear if CUT&RUN can be appli […]

library_books

An efficient targeted nuclease strategy for high resolution mapping of DNA binding sites

2017
eLife
PMCID: 5310842
PMID: 28079019
DOI: 10.7554/eLife.21856.033

[…] tocol (Appendix 1), and achieved near-complete protein extraction with no evidence of protein redistribution (). Under native conditions, we identified 2298 sites with high motif scores. In contrast, CUT&RUN mapping of CTCF detected ~22,000 sites that were also present in X-ChIP (), with a diverse range of motif scores (). As expected, all sites identified by native ChIP also were robustly detecte […]

library_books

Protecting western redcedar from deer browsing—with a passing reference to TRP channels

2015
PMCID: 4843894
PMID: 27227013
DOI: 10.1080/23328940.2015.1047078

[…] life more sustainable? – received only limited coverage.If one thinks about the greenest concepts of the past century, the concept of tree farming immediately comes to mind. Tree farming replaced the cut-and-run timber-harvesting approach with sustainable tree growing (farming) in a perpetual cycle: planting – active management (which often includes intermediate harvests) – final harvest – plantin […]

call_split

Rad51–Rad52 Mediated Maintenance of Centromeric Chromatin in Candida albicans

2014
PLoS Genet
PMCID: 3998917
PMID: 24762765
DOI: 10.1371/journal.pgen.1004344
call_split See protocol

[…] DNA to enrich for single stranded DNA. The enriched DNA was loaded onto 0.4% agarose gel in 1X TBE buffer and run for 15–16 h at 15–20 volts. After run in the first dimension, the desired lanes were cut and run in the second dimension (at 90° to the first) in 1.1% agarose gel in 1X TBE for 2–4 h at 100–125 volts in presence of EtBr (0.3 mg/ml). After that, Southern blotting was done under alkalin […]

library_books

The Mitochondrial Chaperone TRAP1 Promotes Neoplastic Growth by Inhibiting Succinate Dehydrogenase

2013
PMCID: 3677096
PMID: 23747254
DOI: 10.1016/j.cmet.2013.04.019

[…] xperiments were carried out on isolated mitochondria in order to identify ETC complexes. After a first electrophoresis in nondenaturing conditions, bands were visualized with Coomassie blue staining, cut, and run on SDS-PAGE for the identification of protein components by western immunoblot. Crosslinking assays were performed on isolated mitochondria incubated with the membrane-permeable, homobifu […]


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CUT&RUN institution(s)
Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, USA; Cancer and Blood Disorders, Seattle Children’s Hospital, Seattle, WA, USA; Clinical Research Division Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
CUT&RUN funding source(s)
Supported by a grant from the ChanZuckerberg Initiative, by the Howard Hughes Medical Institute and by a Damon Runyon-Sohn Foundation Fellowship.

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