====== Protocols ======

This page serves as a repository of protocols used in 4DN projects. All teams are encouraged to post your protocols as sub-pages to this Wiki page.

1. [[https://docs.google.com/document/d/1N8ZgdQen2VFO30vyk4fHlpKko18bZIaYfQdbtordhnU/edit|Genomic technologies currently in use or being developed in the 4DN network]] (10/17/2016).

  - 3C-seq ([[http://download.springer.com/static/pdf/909/chp:10.1007/978-1-60327-461-6_7.pdf?originUrl=http://link.springer.com/protocol/10.1007/978-1-60327-461-6_7&token2=exp=1478559619~acl=/static/pdf/909/chp%3A10.1007%2F978-1-60327-461-6_7.pdf?originUrl=http://link.springer.com/protocol/10.1007/978-1-60327-461-6_7*~hmac=eb2a0496e877ac93bc53ff29375c9a27fe2ada021c8f91470c0a85d883ae10f0|Dekker lab]])

  - 4C-seq ([[https://docs.google.com/a/eng.ucsd.edu/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDoyZTQ0ZDU1NDE0YTRjZGMy|Harmen J.G. van Werken et al. 2012]])

  - 5C ([[http://www.nature.com/nprot/journal/v2/n4/pdf/nprot.2007.116.pdf|J. Dostie & J. Dekker]][[http://www.nature.com/nprot/journal/v2/n4/pdf/nprot.2007.116.pdf|http://www.nature.com/nprot/journal/v2/n4/pdf/nprot.2007.116.pdf]]. 2007)

  - Hi-C ([[https://docs.google.com/a/eng.ucsd.edu/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDozOTVjOGZkYjNlZmJhNTdj|Dekker. lab, supp data]])

  - ChIA-PET ([[https://docs.google.com/a/eng.ucsd.edu/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDoyZWY2OWFkY2Y4ZWZkMQ|Y. Goh & Ruan et al 2012]])

  - Capture-Hi-C ([[http://www.nature.com/articles/ncomms7178#methods|Houlston lab, 2015]])

  - Tethered Conformation Capture (TCC)- ([[http://www.nature.com/nbt/journal/v30/n1/extref/nbt.2057-S1.pdf|R. Kalhor & L. Chen et al Nat 2012]], supp data p38)

  - In situ Hi-C ([[http://www.cell.com/cms/attachment/2033493464/2049506921/mmc1.pdf|Rao and Erez-Lieberman A. 2014]], methods p18)

  - Dnase Hi-C ([[https://docs.google.com/a/eng.ucsd.edu/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo1M2ZkZTRhODJkNjg5N2Zm|Ramani et al 2016)]]

  - Micro-C ([[http://www.nature.com/protocolexchange/protocols/5105#/procedure|Rando Lab, Procedure]])

  - Genome Architecture Mapping (GAM) (2017 [[https://www.nature.com/articles/nature21411|research paper]])

  - COLA ([[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4064277/pdf/1751-0473-9-12.pdf|Grabherr lab, 2014]] (full paper), [[http://scfbm.biomedcentral.com/articles/10.1186/1751-0473-9-12#Sec2|methods]]

  - Single-cell Hi-C ([[http://www.nature.com/nprot/journal/v10/n12/pdf/nprot.2015.127.pdf|Frazer Lab, 2013]])

  - Combinatorial single-cell Hi-C ([[https://docs.google.com/a/eng.ucsd.edu/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDoyMGFmMDNjNTQ1Zjg2MTgz|Shendure Lab, 2015]] (paper), [[http://science.sciencemag.org/content/sci/suppl/2015/05/06/science.aab1601.DC1/Cusanovich-SM.pdf|methods ]](supp data))

  - Split-pool Barcoding ([[http://www.cell.com/cms/attachment/2032378908/2048933656/mmc7.pdf|McCarroll Lab, 2015]])

  - RICh-PET(Ruan Lab, Unpublished)

  - ChIP RICh-PET (Ruan Lab, Unpublished)

  - Distance Hi-C (Zipfeld Lab, Unpublished)

  - [[https://sites.google.com/a/4dnucleome.org/4d-nucleome-wiki/protocols/damid|DamID]] (Bas van Steensel, 2000 ([[http://www.nature.com/nbt/journal/v18/n4/pdf/nbt0400_424.pdf|research paper]]), 2007 ([[http://www.nature.com/nprot/journal/v2/n6/pdf/nprot.2007.148.pdf|Protocol]]) and Single-Cell DamID (van Steensel Lab, 2013 ([[http://www.sciencedirect.com/science/article/pii/S0092867413002171|extended experimental pro]]cedures)

  - TSA-Seq ([[https://www.ncbi.nlm.nih.gov/genbank/tsa/|U]]npublished)

  - Repli-Seq ([[http://www.biorxiv.org/content/early/2017/03/01/104653|Marchal et. al., Nature Protocols, in press 2017]])

  - TRIP ([[http://www.nature.com/nprot/journal/v9/n6/pdf/nprot.2014.072.pdf|Bas van Steensel & Maarten van Lohuizen, 2014]], Protocol)

  - [[https://docs.google.com/a/eng.ucsd.edu/viewer?a=v&pid=sites&srcid=NGRudWNsZW9tZS5vcmd8NGQtbnVjbGVvbWUtd2lraXxneDo1OGFkMTRkYmY5ZjI0NzQw|CUT&RUN (Steven Henikoff 2017)]]

2. Imaging technologies currently in use or being developed in the 4DN network (being compiled by Clodagh O'Shea).

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{{medialist>4dn:protocols:}}