Since 2007, ENCODE has developed methods and performed a large number of sequence-based studies to map functional elements across the human genome3. The elements mapped (and approaches used) include RNA transcribed regions (RNA-seq, CAGE, RNA-PET, and manual annotation), protein-coding regions (mass spectrometry), TF-binding sites (ChIP-seq and DNase-seq), chromatin structure (DNase-seq, FAIRE-seq, histone ChIP-seq and MNase-seq), and DNA methylation sites (RRBS assay) (Box 1 itemizes methods and abbreviations, Supplementary Table P1 details production statistics)3. To compare and integrate results across the different laboratories, data production efforts focused on two selected sets of cell lines, designated “Tier 1” and “Tier 2” (Box 1). To capture a broader spectrum of biological diversity, selected assays were also executed on a third tier comprising more than 100 cell types including primary cells. All data and protocol descriptions are available at http://www.encodeproject.org/, and a “User’s Guide” including details of cell type choice and limitations was recently published3.
