4D Nucleome (4DN)

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

fs = DagsHubFilesystem(".", repo_url="https://dagshub.com/DagsHub-Datasets/4dnucleome-dataset")

fs.listdir("s3://4dn-open-data-public")

Description:

The goal of the National Institutes of Health (NIH) Common Fund’s 4D Nucleome (4DN) program is to study the three-dimensional organization of the nucleus in space and time (the 4th dimension). The nucleus of a cell contains DNA, the genetic “blueprint” that encodes all of the genes a living organism uses to produce proteins needed to carry out life-sustaining cellular functions. Understanding the conformation of the nuclear DNA and how it is maintained or changes in response to environmental and cellular cues over time will provide insights into basic biology as well as aspects of human health and disease. The 4DN is an international consortium of researchers who generate data that include results from a variety of genomics and imaging assays with a focus on, but not exclusive to, those that demonstrate close contact between chromatin loci that are non-adjacent on the linear DNA sequence of chromosomes. Additional assays probe the nuclear landscape in the context of interactions of chromatin with specific proteins, RNAs and epigenetic changes.

Contact:

The goal of the National Institutes of Health (NIH) Common Fund’s 4D Nucleome (4DN) program is to study the three-dimensional organization of the nucleus in space and time (the 4th dimension). The nucleus of a cell contains DNA, the genetic “blueprint” that encodes all of the genes a living organism uses to produce proteins needed to carry out life-sustaining cellular functions. Understanding the conformation of the nuclear DNA and how it is maintained or changes in response to environmental and cellular cues over time will provide insights into basic biology as well as aspects of human health and disease. The 4DN is an international consortium of researchers who generate data that include results from a variety of genomics and imaging assays with a focus on, but not exclusive to, those that demonstrate close contact between chromatin loci that are non-adjacent on the linear DNA sequence of chromosomes. Additional assays probe the nuclear landscape in the context of interactions of chromatin with specific proteins, RNAs and epigenetic changes.

Update Frequency:

Daily

Managed By:

4DN-DCIC

Resources:

1. resource:
   • Description: Released and archived 4DNucleome data
   • ARN: arn:aws:s3:::4dn-open-data-public
   • Region: us-east-1
   • Type: S3 Bucket

Tags:

biology, bioinformatics, genetic, genomic, imaging, life sciences, aws-pds

Tutorials:

1. tutorial:

   • Title: Finding and Downloading 4DN Data files
   • URL: https://data.4dnucleome.org/help/user-guide/downloading-files
   • AuthorName: 4DN-DCIC
   • AuthorURL: data.4dnucleome.org

2. tutorial:

   • Title: Using jupyterhub on the 4DN data portal
   • URL: https://data.4dnucleome.org/tools/jupyterhub
   • AuthorName: 4DN-DCIC
   • AuthorURL: data.4dnucleome.org