In silico nanoscope to study the interplay of genome organization and transcription regulation 
Soundhararajan Gopi, Giovanni B Brandani, Cheng Tan, Jaewoon Jung, Chenyang Gu,
Azuki Mizutani, Hiroshi Ochiai, Yuji Sugita, and Shoji Takada
Nuc. Acids Res. 2025
https://doi.org/10.1101/2024.10.22.619557


The original data are deposited to the Zenodo repository
(https://zenodo.org/records/13958906?preview=1&token=eyJhbGciOiJIUzUxMiIsImlhdCI6MTcyOTQ
5NTQzOSwiZXhwIjoxNzkxNjc2Nzk5fQ.eyJpZCI6Ijg5ODliNWFmLTEyM2ItNDY3ZC1iZDJiLTNhYzY5NzljYzl
hOSIsImRhdGEiOnt9LCJyYW5kb20iOiI0YjdmNjIyMTllMjhkOTg1N2Q1ZjFiZWNmMDJlODQ3NSJ9.aps).

Details of the uploaded data:
================================================================================================
200kb_Nanog_CG_models
	Equilibrated 200kb Nanog models at a residue-level resolution in mmCIF format
	   - Coordinates are in Angstrom
	   - File names : Eq_struct_Cluster(1-5).cif
	   - Eq_struct_Cluster1_.cif correcsponds to Model 1* in the manuscript
	   - Chain information
		chain A-B: DNA		:grey
		chain C-J: Core Histone		:pink
		chain K  : Linker Histone (H1)		:orange
		chain L  : BRD4		:purple
		chain S  : SOX2 	:light green
		chain O  : OCT4		:green
		chain N  : NANOG	:light green
		chain Q  : KLF4		:light green
		chain P  : P300		:yellow
		chain W  : RNA pol. II and Mediator complex (Pre-Initiation Complex - PIC)	:black
	   - Files are available in .cif, pse (PyMol) and .gro (CGDYN GENESIS) format

================================================================================================	   
Please contact the authors for any additional information on the data. The scripts include paths to relevant files used as input to reproduce the data presented in the work.