TABLE 1.
ENCODE data types, as of January 2012
| Data type | Description |
|---|---|
| 5C | Chromatin conformation capture |
| BIP | Bi-directional promoters, identified informatically |
| CAGE | 5′ cap analysis of gene expression |
| ChIA-pet | Chromatin interaction analysis with paired-end tags |
| ChIP-seq | DNA fragments from ChIP purifications, measured by sequencing |
| Genotype | CNV and SNP as determined by the Illumina Human 1M-Duo Infinium HD BeadChip assay and circular binary segmentation (CBS) |
| DNase-DGF | Digital DNase genomic footprinting |
| DNA PET | DNA fragments measured by paired-end di-tag sequencing |
| DNase-seq | Sequencing of DNase-digested DNA |
| Exon-array | RNA expression measured by Affymetrix exon microarrays |
| FAIRE-seq | Formaldehyde-assisted isolation of regulatory elements |
| Gencode | Curated gene annotation |
| Integ Cluster | Element cluster by integrative analysis |
| Mapability | Level of sequence uniqueness within the genome |
| Methyl27 | DNA methylation, measured by Illumina bead arrays |
| Methyl-RRBS | DNA methylation, measured by reduced representation bisulfite sequencing |
| Methyl-seq | DNA methylation, measured by sequencing |
| NRE | Negative regulatory elements |
| Nucleosome | Nucleosome positioning data |
| ORChID | Predicted hydroxyl radical cleavage intensity on naked DNA |
| Proteogenomics | Mass Spectrometry Proteogenomic Mapping |
| RIP-chip | RNA-protein interactions, measured by microarrays |
| RIP-chip Gene ST | RIP-chip on Affymetrix GeneChip (R) Human Gene 1.0 ST Arrays |
| RIP-chip Tiling Array | RIP-chip on Affymetrix GeneChip ENCODE 2.0R Tiling Arrays |
| RIP-seq | RNA-protein interactions, measured by sequencing |
| RNA PET | RNA expression measured by paired-end di-tag sequencing |
| RNA-chip | Tiling arrays measuring expression in various cell compartments |
| RNA-seq | RNA expression measured by sequencing |
| SwitchGear | SwitchGear Genomics 3′ UTR reporter assay |
