The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data

被引：50

作者：

Reiff, Sarah B. ^{[1
]}

Schroeder, Andrew J. ^{[1
]}

Kirli, Koray ^{[1
]}

Cosolo, Andrea ^{[1
]}

Bakker, Clara ^{[1
]}

Lee, Soohyun ^{[1
]}

Veit, Alexander D. ^{[1
]}

Balashov, Alexander K. ^{[1
]}

Vitzthum, Carl ^{[1
]}

Ronchetti, William ^{[1
]}

Pitman, Kent M. ^{[1
]}

Johnson, Jeremy ^{[1
]}

Ehmsen, Shannon R. ^{[1
]}

Kerpedjiev, Peter

Abdennur, Nezar ^{[2
]}

Imakaev, Maxim ^{[2
]}

Ozturk, Serkan Utku ^{[3
]}

Camoglu, Ugur ^{[3
]}

Mirny, Leonid A. ^{[2
,4
]}

Gehlenborg, Nils ^{[1
]}

Alver, Burak H. ^{[1
]}

Park, Peter J. ^{[1
]}

机构：

[1] Harvard Med Sch, Dept Biomed Informat, Boston, MA 02115 USA

[2] MIT, Inst Med Engn & Sci, Cambridge, MA 02139 USA

[3] Karya SMD Software Solut, TR-35040 Izmir, Turkey

[4] MIT, Dept Phys, Cambridge, MA 02139 USA

来源：

NATURE COMMUNICATIONS | 2022年 / 13卷 / 01期

关键词：

CHROMATIN INTERACTIONS; ENCODE DATA; CONTACTS;

D O I：

10.1038/s41467-022-29697-4

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The 4D Nucleome (4DN) Network aims to elucidate the complex structure and organization of chromosomes in the nucleus and the impact of their disruption in disease biology. We present the 4DN Data Portal (https://dataAdnucleome.org/), a repository for datasets generated in the 4DN network and relevant external datasets. Datasets were generated with a wide range of experiments, including chromosome conformation capture assays such as HiC and other innovative sequencing and microscopy-based assays probing chromosome architecture. All together, the 4DN data portal hosts more than 1800 experiment sets and 36000 files. Results of sequencing-based assays from different laboratories are uniformly processed and quality-controlled. The portal interface allows easy browsing, filtering, and bulk downloads, and the integrated HiGlass genome browser allows interactive visualization and comparison of multiple datasets. The 4DN data portal represents a primary resource for chromosome contact and other nuclear architecture data for the scientific community.

引用

页数：11

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