ENCODE2

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.

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.