Spanning two decades, the Encyclopaedia of DNA Elements (ENCODE) is a collaborative research project that aims to identify all the functional elements in the human and mouse genomes. To best serve the scientific community, all data generated by the consortium is shared through a web-portal (https://www.encodeproject.org/) with no access restrictions. The fourth and final phase of the project added a diverse set of new samples (including few associated with human diseases), and a wide range of new assays aimed at detection, characterization and validation of functional genomic elements. The ENCODE data portal hosts results from over 23,000 functional genomics experiments, over 800 functional elements characterization experiments (including in vivo transgenic enhancer assays, reporter assays and CRISPR screens) along with over 60,000 results of computational and integrative analyses (including imputations, predictions and genome annotations). The ENCODE Data Coordination Center (DCC) is responsible for development and maintenance of the data portal, along with the implementation and utilisation of the ENCODE uniform processing pipelines to generate uniformly processed data. Here we report recent updates to the data portal. Specifically, we have completely redesigned the home page, improved search interface, added several new pages to highlight collections of biologically related data (deeply profiled cell lines, immune cells, Alzheimer’s Disease, RNA-Protein interactions, degron matrix and a matrix of experiments organised by human donors), added single-cell experiments, and enhanced the cart interface for visualisation and download of user-selected datasets. Along with this, we also provide a brief summary of data generated using the ENCODE uniform processing pipelines. Finally, we have added extensive help pages, tutorials and documentation to assist researchers from a variety of backgrounds in exploring the universe of ENCODE data.

Encyclopedia of DNA elements consisting of list of functional elements in human genome, including elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Enables scientific and medical communities to interpret role of human genome in biology and disease. Provides identification of common cell types to facilitate integrative analysis and new experimental technologies based on high-throughput sequencing. Genome Browser containing ENCODE and Epigenomics Roadmap data. Data are available for entire human genome.

WGBS - Homo sapiens GM12878 - ENCODE - U54HG006998 - Richard Myers, HAIB

Overview of ENCODE data types.

Experimental assays used by the ENCODE Consortium.

CTCF - TF ChIP-seq - Homo sapiens K562 - ENCODE - U54HG004558 - Michael Snyder, Stanford

aFor full listings and references, see Table S1.

Dataset: Base64 encode version1

This dataset is for improving base64 encoding capabilities. GPT 4o is great at base64 encoding. user: convert this hex data to base64: 880567a1

assistant: The base64 encoding of the hex data 880567a1 is iAVnoQ==.

user: convert this json data representing a byte sequence to base64: [30,41,183]

assistant: The base64 encoding of the JSON data [30,41,183] is Him3.

However llama3 is terrible at base64 encoding. Short examples of what… See the full description on the dataset page: https://huggingface.co/datasets/neoneye/base64-encode-v1.

H3K4me1 - Histone ChIP-seq - Homo sapiens K562 - ENCODE - U54HG004558 - Peggy Farnham, USC

CTCF - TF ChIP-seq - Homo sapiens HepG2 - ENCODE - U54HG004576 - Richard Myers, HAIB

ATAC-seq - Homo sapiens GM12878 - ENCODE - UM1HG009442 - Michael Snyder, Stanford

H3K79me2 - Histone ChIP-seq - Homo sapiens parathyroid adenoma tissue male adult (65 years) - ENCODE - U54HG006991 - Bradley Bernstein, Broad

CTCF - TF ChIP-seq - Mus musculus strain Bruce4 ES-Bruce4 - ENCODE - R01HG003991 - Bing Ren, UCSD

H3K36me3 - Histone ChIP-seq - Homo sapiens K562 - ENCODE - U54HG004592 - John Stamatoyannopoulos, UW

H3K4me3 - Histone ChIP-seq - Homo sapiens K562 - ENCODE - U54HG006991 - Bradley Bernstein, Broad

H3K27ac - Histone ChIP-seq - Mus musculus strain B6NCrl cortical plate tissue male adult (2 months) - ENCODE - R01HG003991 - Bing Ren, UCSD

DNase-seq - Homo sapiens GM12878 - ENCODE - U54HG004592 - John Stamatoyannopoulos, UW

CTCF - TF ChIP-seq - Homo sapiens HeLa-S3 - ENCODE - U54HG004570 - Bradley Bernstein, Broad

ZBTB33 - TF ChIP-seq - Homo sapiens MCF-7 - ENCODE - U54HG006996 - Michael Snyder, Stanford

total RNA-seq - Homo sapiens K562 - ENCODE - U54HG007005 - Brenton Graveley, UConn