Projects ENCODE

ENCODE flagship paper: integrated encyclopedia of DNA elements in the human genome. Used 1,640 data sets from 147 cell types to systematically catalogue RNA transcription, transcription factor binding, chromatin structure, and histone modifications. Defined 80.4% of the genome as participating in at least one biochemical event. One of the most cited papers in genomics history.

Comprehensive RNA-seq analysis of the human transcriptome across multiple cell lines, revealing pervasive transcription with 62% of the genome covered by processed transcripts, thousands of novel non-coding RNAs, and extensive RNA processing complexity.

DNase I hypersensitivity mapping across 125 cell types, defining the accessible chromatin landscape of the human genome. Identified 2.9 million DNase I hypersensitive sites, 97% of which fell in non-coding regions, providing the most comprehensive view of regulatory DNA.

Comparative encyclopedia of DNA elements in the mouse genome, enabling cross-species analysis of regulatory element conservation and divergence. Provided the foundation for understanding which functional elements are evolutionarily constrained.

Major update of the ENCODE data portal supporting ENCODE 3 data, including new data types (ChIP-seq, RNA-seq, WGBS, DNase-seq, Hi-C), improved metadata standards, and the Registry of candidate cis-Regulatory Elements (cCREs) for genome annotation.

Expanded ENCODE encyclopedias of DNA elements in human and mouse genomes (ENCODE 4). Included data from 1,178 human and 439 mouse biosamples with new assays for chromatin conformation, RNA-binding proteins, and DNA methylation. The Registry of cCREs now covers over 1 million human and 300,000 mouse candidate regulatory elements.

ENCODE Pilot Project launched by NHGRI to identify functional elements in 1% (30 Mb) of the human genome. 35 research groups across 80 institutions used multiple experimental and computational approaches to annotate genes, regulatory elements, and chromatin features.

Landmark ENCODE pilot results demonstrating that the majority of the human genome is biochemically functional, with pervasive transcription, abundant regulatory elements, and complex chromatin landscapes. Challenged the traditional view of 'junk DNA' and established ENCODE as a foundational genomics resource.

Comprehensive guide to the ENCODE resource, describing data types, experimental protocols, analysis pipelines, and data access tools. Provided the framework for understanding the full-genome ENCODE project and the upcoming 2012 Nature publications.