Published March 4, 2021
| Version v1
Dataset
Open
3D genomics across the tree of life reveals condensin II as a determinant of architecture type
Authors/Creators
- Hoencamp, Claire1
- Dudchenko, Olga2
- Elbatsh, Ahmed M.O.1
- Brahmachari, Sumitabha3
- Raaijmakers, Jonne A.4
- Schaik, Tom van5
- Cacciatore, Ángela Sedeño1
- Contessoto, Vinicius3
- Heesbeen, Roy G.H.P. van4
- Broek, Bram van den6
- Mhaskar, Aditya N.1
- Teunissen, Hans5
- Hilaire, Brian Glenn St2
- Weisz, David2
- Omer, Arina D.2
- Pham, Melanie2
- Colaric, Zane2
- Yang, Zhenzhen7
- Rao, Suhas S.P.2
- Mitra, Namita2
- Lui, Christopher2
- Yao, Weijie2
- Khan, Ruqayya2
- Moroz, Leonid L.8
- Kohn, Andrea8
- Leger, Judy St.9
- Mena, Alexandria10
- Holcroft, Karen11
- Gambetta, Maria Cristina12
- Lim, Fabian13
- Farley, Emma13
- Stein, Nils14
- Haddad, Alexander2
- Chauss, Daniel15
- Mutlu, Ayse Sena16
- Wang, Meng C.16
- Young, Neil D.17
- Hildebrandt, Evin18
- Cheng, Hans H.18
- Knight, Christopher J.19
- Burnham, Theresa L.U.20
- Hovel, Kevin A.21
- Beel, Andrew J.22
- Mattei, Pierre-Jean22
- Kornberg, Roger D.22
- Warren, Wesley C.23
- Cary, Gregory24
- Gómez-Skarmeta, José Luis25
- Hinman, Veronica26
- Maeshima, Kazuhiro27
- Multani, Asha S.28
- Pathak, Sen28
- Nel-Themaat, Liesl28
- Behringer, Richard R.28
- Kaur, Parwinder29
- Medema, René H.4
- Steensel, Bas van5
- Wit, Elzo de5
- Onuchic, José N.3
- Pierro, Michele Di3
- Aiden, Erez Lieberman2
- Rowland, Benjamin D.1
- 1. Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- 2. The Center for Genome Architecture, Baylor College of Medicine, Houston TX 77030, USA
- 3. Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- 4. Division of Cell Biology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- 5. Division of Gene Regulation, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- 6. BioImaging Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- 7. Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China
- 8. Whitney laboratory and Department of Neuroscience, University of Florida, Gainesville, FL 32611, USA
- 9. Department of Biosciences, Cornell University College of Veterinary Medicine, Ithaca, NY 14853, USA
- 10. SeaWorld San Diego, San Diego, CA 92109, USA
- 11. Moody Gardens, Galveston, TX 77554, USA
- 12. Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
- 13. Department of Medicine/Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
- 14. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), 06466 Seeland, Germany
- 15. National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- 16. Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- 17. Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville VIC 3010, Australia
- 18. Avian Diseases and Oncology Laboratory, USDA, ARS, East Lansing, MI 48823, USA
- 19. Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA
- 20. Department of Wildlife, Fish, and Conservation Biology University of California, Davis, Davis, CA 95616, USA
- 21. Coastal and Marine Institute and Department of Biology, San Diego State University, San Diego, CA 92106, USA
- 22. Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- 23. Department of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
- 24. The Jackson Laboratory, Bar Harbor, ME 04609, USA
- 25. Centro Andaluz de Biología del Desarrollo CSIC/ Universidad Pablo de Olavide, 41013 Sevilla, Spain
- 26. Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- 27. National Institute of Genetics, and SOKENDAI, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- 28. Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- 29. Faculty of Science, UWA School of Agriculture and Environment, University of Western Australia, Perth WA 6009, Australia
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.
Files
Files
(1.6 GB)
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md5:396e5179ec9e74c4fa12624f202bc2ce
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md5:50fdf5a18ed2aa7d85726bf598727f34
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771.0 MB | Download |
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md5:31b51e668e36ce06048b53e5fe1fe5ad
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7.6 MB | Download |
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md5:745dda28c153b76c4b1cce9fc6a9f0a5
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34.1 kB | Download |
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md5:cea5addc546a1ff8abbec5efbb545820
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30.9 kB | Download |
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md5:680ab4ae54a23e6535d9ceefd7522077
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890.0 kB | Download |
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md5:ba58fcd2860e521b7386edadec933042
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864.3 kB | Download |
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md5:1c35dc06a0729f2266311abb565c093c
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6.8 MB | Download |