Table 2.
The full complement of ENCODE data sets summarized by assay
| Data type/assay | Experiments |
|---|---|
| Chromatin interactions | |
| 5C | 14 |
| ChIA-PET | 8 |
| DNA methylation | |
| Methyl array | 125 |
| Methyl RRBS | 95 |
| Methyl-seq | 20 |
| Histone modifications | |
| ChIP-seq | 315 |
| ChIP-seq (MOUSE) | 179 |
| Open chromatin | |
| DNase-DGF | 56 |
| DNase-DGF (MOUSE) | 22 |
| DNase-seq | 221 |
| Dnase-seq (MOUSE) | 55 |
| FAIRE-seq | 39 |
| RNA profiling | |
| CAGE | 78 |
| Exon array | 158 |
| RNA-chip | 26 |
| RNA-PET | 31 |
| RNA-seq | 245 |
| RNA-seq (MOUSE) | 102 |
| Transcription factor binding sites | |
| ChIP-seq | 1229 |
| ChIP-seq (MOUSE) | 202 |
| Other | |
| DNA cleavage | 1 |
| DNA-PET | 6 |
| GENCODE genes | 7 |
| Genotype | 64 |
| Negative regulatory elements | 2 |
| Nucleosome positioning | 2 |
| Proteogenomics | 14 |
| Replication timing | 24 |
| Replication timing (MOUSE) | 18 |
| RNA binding proteins | 47 |
| Short read mapability | 13 |
| Short read mapability (MOUSE) | 5 |
Descriptive overviews along with methods and references are included in the description page that accompanies all data sets.