Encyclopedia of DNA Elements (ENCODE)

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

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

fs.listdir("s3://encode-public")

Description:

The Encyclopedia of DNA Elements (ENCODE) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. ENCODE investigators employ a variety of assays and methods to identify functional elements. The discovery and annotation of gene elements is accomplished primarily by sequencing a diverse range of RNA sources, comparative genomics, integrative bioinformatic methods, and human curation. Regulatory elements are typically investigated through DNA hypersensitivity assays, assays of DNA methylation, and immunoprecipitation (IP) of proteins that interact with DNA and RNA, i.e., modified histones, transcription factors, chromatin regulators, and RNA-binding proteins, followed by sequencing.

Contact:

The Encyclopedia of DNA Elements (ENCODE) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. ENCODE investigators employ a variety of assays and methods to identify functional elements. The discovery and annotation of gene elements is accomplished primarily by sequencing a diverse range of RNA sources, comparative genomics, integrative bioinformatic methods, and human curation. Regulatory elements are typically investigated through DNA hypersensitivity assays, assays of DNA methylation, and immunoprecipitation (IP) of proteins that interact with DNA and RNA, i.e., modified histones, transcription factors, chromatin regulators, and RNA-binding proteins, followed by sequencing.

Update Frequency:

Daily

Managed By:

ENCODE Data Coordinating Center

Resources:

1. resource:
   • Description: Released and archived ENCODE data
   • ARN: arn:aws:s3:::encode-public
   • Region: us-west-2
   • Type: S3 Bucket

Tags:

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

Tutorials:

1. tutorial:

   • Title: Exploring ENCODE data from EC2 with Jupyter notebook
   • URL: https://github.com/ENCODE-DCC/encode-data-usage-examples/blob/master/mount_s3_bucket_and_run_jupyter_on_ec2.ipynb
   • AuthorName: Keenan Graham
   • AuthorURL: https://github.com/keenangraham

2. tutorial:

   • Title: ENCODE CTCF ChIP-seq data correlation across different cell types
   • URL: https://github.com/ENCODE-DCC/encode-data-usage-examples/blob/master/ctcf_chip_seq_cross_cell_type_correlation.ipynb
   • AuthorName: Paul Sud
   • AuthorURL: https://github.com/p-sud

3. tutorial:

   • Title: Ingesting ENCODE data into TileDB with S3 backend
   • URL: https://github.com/ENCODE-DCC/encode-data-usage-examples/blob/master/ingest_encode_data_tile_db_with_s3_backend.ipynb
   • AuthorName: Otto Jolanki
   • AuthorURL: https://github.com/ottojolanki

Publication:

1. publication:
   • Title: New developments on the Encyclopedia of DNA Elements (ENCODE) data portal
   • URL: https://academic.oup.com/nar/article/48/D1/D882/5622708#190992715
   • AuthorName: Luo et al 2020
   • AuthorURL: http://orcid.org/0000-0001-6948-2042