Published March 4, 2021 | Version v1
Dataset Open

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

Creators

  • 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)

Name Size Download all
md5:396e5179ec9e74c4fa12624f202bc2ce
771.0 MB Download
md5:50fdf5a18ed2aa7d85726bf598727f34
771.0 MB Download
md5:31b51e668e36ce06048b53e5fe1fe5ad
7.6 MB Download
md5:745dda28c153b76c4b1cce9fc6a9f0a5
34.1 kB Download
md5:cea5addc546a1ff8abbec5efbb545820
30.9 kB Download
md5:680ab4ae54a23e6535d9ceefd7522077
890.0 kB Download
md5:ba58fcd2860e521b7386edadec933042
864.3 kB Download
md5:1c35dc06a0729f2266311abb565c093c
6.8 MB Download