Data

3D genomics across the tree of life reveals condensin II as a determinant of architecture type

The University of Western Australia
Hoencamp, Claire ; Dudchenko, Olga ; Elbatsh, Ahmed M.O. ; Brahmachari, Sumitabha ; Raaijmakers, Jonne A. ; Schaik, Tom van ; Cacciatore, Ángela Sedeño ; Contessoto, Vinicius ; Heesbeen, Roy G.H.P. van ; Broek, Bram van den ; Mhaskar, Aditya N. ; Teunissen, Hans ; Hilaire, Brian Glenn St ; Weisz, David ; Omer, Arina D. ; Pham, Melanie ; Colaric, Zane ; Yang, Zhenzhen ; Rao, Suhas S.P. ; Mitra, Namita ; Lui, Christopher ; Yao, Weijie ; Khan, Ruqayya ; Moroz, Leonid L. ; Kohn, Andrea ; Leger, Judy St ; Mena, Alexandria ; Holcroft, Karen ; Gambetta, Maria Cristina ; Lim, Fabian ; Farley, Emma ; Stein, Nils ; Haddad, Alexander ; Chauss, Daniel ; Mutlu, Ayse Sena ; Wang, Meng C. ; Young, Neil D. ; Hildebrandt, Evin ; Cheng, Hans H. ; Knight, Christopher J. ; Burnham, Theresa L.U. ; Hovel, Kevin A. ; Beel, Andrew J. ; Mattei, Pierre-Jean ; Kornberg, Roger D. ; Warren, Wesley C. ; Cary, Gregory ; Gómez-Skarmeta, Jose Luis ; Hinman, Veronica ; Maeshima, Kazuhiro ; Multani, Asha S. ; Pathak, Sen ; Nel-Themaat, Liesl ; Behringer, Richard R. ; Kaur, Parwinder ; Medema, René H. ; Steensel, Bas van ; Wit, Elzo de ; Onuchic, José N. ; Pierro, Michele Di ; Aiden, Erez Lieberman ; Rowland, Benjamin D.
Viewed: [[ro.stat.viewed]] Cited: [[ro.stat.cited]] Accessed: [[ro.stat.accessed]]
ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=info:doi10.5281/zenodo.4582361&rft.title=3D genomics across the tree of life reveals condensin II as a determinant of architecture type&rft.identifier=10.5281/zenodo.4582361&rft.publisher=Zenodo&rft.description=GAMinG script (python) and sequence file (.dat) to prepare files to run molecular dynamics in GROMACS (see ndb.rice.edu for more info regarding how to run the simulations). Two .hic maps and two sample trajectory files for high and low lengthwise compaction (binary format, see ndb.rice.edu for the conversion of .cndb to other formats) corresponding to fig 4 in the main text. There are also two aggregate chromosome analysis (ACA) hic maps corresponding to lower (CAPH2) and higher (WT) compaction.&rft.creator=Hoencamp, Claire &rft.creator=Dudchenko, Olga &rft.creator=Elbatsh, Ahmed M.O. &rft.creator=Brahmachari, Sumitabha &rft.creator=Raaijmakers, Jonne A. &rft.creator=Schaik, Tom van &rft.creator=Cacciatore, Ángela Sedeño &rft.creator=Contessoto, Vinicius &rft.creator=Heesbeen, Roy G.H.P. van &rft.creator=Broek, Bram van den &rft.creator=Mhaskar, Aditya N. &rft.creator=Teunissen, Hans &rft.creator=Hilaire, Brian Glenn St &rft.creator=Weisz, David &rft.creator=Omer, Arina D. &rft.creator=Pham, Melanie &rft.creator=Colaric, Zane &rft.creator=Yang, Zhenzhen &rft.creator=Rao, Suhas S.P. &rft.creator=Mitra, Namita &rft.creator=Lui, Christopher &rft.creator=Yao, Weijie &rft.creator=Khan, Ruqayya &rft.creator=Moroz, Leonid L. &rft.creator=Kohn, Andrea &rft.creator=Leger, Judy St &rft.creator=Mena, Alexandria &rft.creator=Holcroft, Karen &rft.creator=Gambetta, Maria Cristina &rft.creator=Lim, Fabian &rft.creator=Farley, Emma &rft.creator=Stein, Nils &rft.creator=Haddad, Alexander &rft.creator=Chauss, Daniel &rft.creator=Mutlu, Ayse Sena &rft.creator=Wang, Meng C. &rft.creator=Young, Neil D. &rft.creator=Hildebrandt, Evin &rft.creator=Cheng, Hans H. &rft.creator=Knight, Christopher J. &rft.creator=Burnham, Theresa L.U. &rft.creator=Hovel, Kevin A. &rft.creator=Beel, Andrew J. &rft.creator=Mattei, Pierre-Jean &rft.creator=Kornberg, Roger D. &rft.creator=Warren, Wesley C. &rft.creator=Cary, Gregory &rft.creator=Gómez-Skarmeta, Jose Luis &rft.creator=Hinman, Veronica &rft.creator=Maeshima, Kazuhiro &rft.creator=Multani, Asha S. &rft.creator=Pathak, Sen &rft.creator=Nel-Themaat, Liesl &rft.creator=Behringer, Richard R. &rft.creator=Kaur, Parwinder &rft.creator=Medema, René H. &rft.creator=Steensel, Bas van &rft.creator=Wit, Elzo de &rft.creator=Onuchic, José N. &rft.creator=Pierro, Michele Di &rft.creator=Aiden, Erez Lieberman &rft.creator=Rowland, Benjamin D. &rft.date=2021&rft.type=dataset&rft.language=English Access the data
Cite Saved to MyRDA Save to MyRDA

Access:

Open

Full description

GAMinG script (python) and sequence file (.dat) to prepare files to run molecular dynamics in GROMACS (see ndb.rice.edu for more info regarding how to run the simulations). Two .hic maps and two sample trajectory files for high and low lengthwise compaction (binary format, see ndb.rice.edu for the conversion of .cndb to other formats) corresponding to fig 4 in the main text. There are also two aggregate chromosome analysis (ACA) hic maps corresponding to lower (CAPH2) and higher (WT) compaction.

Notes

External Organisations
Netherlands Cancer Institute; Baylor College of Medicine; Rice University; Oncode Institute; Shanghai Institute for Advanced Immunochemical Studies; Florida State University; University of Lausanne; University of California Davis; Leibniz Institute of Plant Genetics and Crop Plant Research; National Institute on Aging; University of Melbourne; Stanford University; University of California Los Angeles; University of California San Diego; University of Missouri; Carnegie Mellon University; National Institute of Genetics; University of Texas MD Anderson Cancer Center; Cornell University; Jackson Laboratory; Universidad Pablo de Olavide; SeaWorld San Diego
Associated Persons
Olga Dudchenko (Creator)Claire Hoencamp (Creator); Ahmed M.O. Elbatsh (Creator); Sumitabha Brahmachari (Creator); Jonne A. Raaijmakers (Creator); Tom van Schaik (Creator); Ángela Sedeño Cacciatore (Creator); Vinicius Contessoto (Creator); Roy G.H.P. van Heesbeen (Creator); Bram van den Broek (Creator); Aditya N. Mhaskar (Creator); Hans Teunissen (Creator); Brian Glenn St Hilaire (Creator); David Weisz (Creator); Arina D. Omer (Creator); Melanie Pham (Creator); Zane Colaric (Creator); Zhenzhen Yang (Creator); Suhas S.P. Rao (Creator); Namita Mitra (Creator); Christopher Lui (Creator); Weijie Yao (Creator); Ruqayya Khan (Creator); Leonid L. Moroz (Creator); Andrea Kohn (Creator); Judy St Leger (Creator); Alexandria Mena (Creator); Karen Holcroft (Creator); Maria Cristina Gambetta (Creator); Fabian Lim (Creator); Emma Farley (Creator); Alexander Haddad (Creator); Daniel Chauss (Creator); Ayse Sena Mutlu (Creator); Meng C. Wang (Creator); Neil D. Young (Creator); Evin Hildebrandt (Creator); Hans H. Cheng (Creator); Christopher J. Knight (Creator); Theresa L.U. Burnham (Creator); Kevin A. Hovel (Creator); Andrew J. Beel (Creator); Pierre-Jean Mattei (Creator); Roger D. Kornberg (Creator); Wesley C. Warren (Creator); Gregory Cary (Creator); Jose Luis Gómez-Skarmeta (Creator); Veronica Hinman (Creator); Kazuhiro Maeshima (Creator); Asha S. Multani (Creator); Sen Pathak (Creator); Liesl Nel-Themaat (Creator); Richard R. Behringer (Creator); René H. Medema (Creator); Bas van Steensel (Creator); Elzo de Wit (Creator); José N. Onuchic (Creator); Michele Di Pierro (Creator); Benjamin D. Rowland (Creator)

Issued: 2021-03-04

This dataset is part of a larger collection

Click to explore relationships graph
Help

Related Organisations

Related People

Related Websites

User Contributed Tags    

Login to tag this record with meaningful keywords to make it easier to discover

Identifiers
Similar data you may be interested in: