SSBD:database

44-Hihara-NucleosomeDyn

Author reviewed
SSBD:downloads
Project name
44-Hihara-NucleosomeDyn
Release date
2017-10-03
Update date
2018-11-15
Pre-release URL
-
Project title
-
License
CC BY
Method summary
See details in Hihara et al. (2012) Cell Reports, 2(6): 1645-1656.
PubMed URL
https://www.ncbi.nlm.nih.gov/pubmed/23246002
Kind
Quantitative data
Organism
-
Total
9 files / 146.0 MB
Image datasets
zipped 0 files / 0 bytes, raw image 0 files / 0 bytes, total 0 files / 0 bytes
Quantitative datasets
zipped 3 files / 13.1 MB, raw bdml 6 files / 132.9 MB, total 9 files / 146.0 MB
Image datasets
0
Quantitative datasets
3
Strain
-
Datatype
single molecule dynamics
Basedon
Simulation
XYZ-scale
XY: 1 micrometer, Z: 1 micrometer
T-scale
1 microsecond for each time interval
dblink
None
External links
http://www.e-cell.org/ecell4/
Experiment type
-
Microscope type
-
Acquisition mode
-
Contrast method
-
Microscope model
-
Detector model
-
Objective model
-
Filter set
-
Biological Process
-
Cellular Component
nucleuosome ( GO:0000786 )
People
Contact
Kazunari Kaizu
RIKEN
Quantitative Biology Center
Laboratory for Biochemical Simulation
6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
Contributors
Saera Hihara, Chan-Gi Pack, Kazunari Kaizu, Tomomi Tani, Tomo Hanafusa, Tadasu Nozaki, Satoko Takemoto, Tomohiko Yoshimi, Hideo Yokota, Naoko Imamoto, Yasushi Sako, Masataka Kinjo,　Koichi Takahashi, Takeharu Nagai, Kazuhiro Maeshima
downloads
https://ssbd.riken.jp/data/44-Hihara-NucleosomeDyn/

Dataset List

Thumbnail
Dataset
Organism
Kind / Links
nuc_0.1_0
-
Quantitative data BDML
BDML file for the result of the Monte Carlo computer simulation of nucleosome dynamics in EGFP-pentamers (parameters: 13 nm spheres representing EGFP-pentamers in free 0.1mM 10 nm spheres representing a nucleosome)
nuc_0.5_0
-
Quantitative data BDML
BDML file for the result of the Monte Carlo computer simulation of nucleosome dynamics in EGFP-pentamers (parameters: 13 nm spheres representing EGFP-pentamers in fixed 0.5 mM 10 nm spheres representing a nucleosome)
nuc_0.5_20
-
Quantitative data BDML
BDML file for the result of the Monte Carlo computer simulation of nucleosome dynamics in EGFP-pentamers resembling "a dog on a leash" situation (parameters: 13 nm spheres representing EGFP-pentamers in 0.5 mM 10 nm spheres representing a nucleosome with 20 nm as maximum displacement from the initial position)