Published July 6, 2018 | Version v1
Dataset Open

Single-particle tracking data for "CTCF sites display cell cycle dependent dynamics in factor binding and nucleosome positioning"

Creators

  • 1. Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
  • 2. Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA 94720, USA
  • 3. Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 208156789, USA

Description

This dataset contains all the raw SPT data reported in "­­­­CTCF sites display cell cycle dependent dynamics in factor binding and nucleosome positioning" in the form of SPT trajectories. The SPT trajectories are provided in two different formats for convenience: a CSV format and a Matlab format. Both formats are readable by Spot-On: https://spoton.berkeley.edu/

The SPT data contains "fast tracking" spaSPT data and this data was analyzed using the Matlab version of Spot-On which can be found and downloaded at: https://gitlab.com/tjian-darzacq-lab/spot-on-matlab

 

Full details about the Matlab and CSV formats are provided in the ReadMe files in the associated zip files.

Please see the associated manuscript for a detailed description of how the data was acquired and analyzed.

Notes

Acknowledgements: We thank Sarah Hainer and Tom Fazzio for advice on ATAC-seq data interpretation and providing reagents. We thank Sheila Teves and all current and former Dekker lab members for helpful discussions; especially Betul Akgol Oksuz, Bryan Lajoie, Ankita Nand and Hakan Ozadam for advice on computational analysis. This work was supported by grants from the National Human Genome Research Institute (HG003143) and the NIH Common Fund (DK107980) to J.D. and by NIH grants UO1-EB021236 and U54-DK107980 (X.D.), the California Institute of Regenerative Medicine grant LA1-08013 (X.D.). This work was performed in part at the UC Berkeley CRL Molecular Imaging Center, supported by the Gordon and Betty Moore Foundation. A.S.H. is a postdoctoral fellow of the Siebel Stem Cell Institute. J.D. is an investigator of the Howard Hughes Medical Institute.

Files

fastSPT_raw_data.zip

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