Table 1.
Summary of ENCODE datasets, as of 15 September 2009
| Data type | Description | Investigators | Number of experiments |
|---|---|---|---|
| BiP | Bi-directional promoters | NHGRI | 2 |
| CAGE | 5′ cap analysis gene expression | Riken | 11 |
| ChIP-seq | TF and polymerase binding, histone marks by ChIP | Yale, UC Davis, HudsonAlpha, Broad, UW, UNC | 185 |
| DNA-seq | DNA fragment sequencing | Genome Inst Singapore | 5 |
| DNase-seq | DNaseI hypersensitivity | UW, Duke | 20 |
| Exon-array | Gene expression by all-exon microarray | Affymetrix/CSHL | 10 |
| FAIRE-seq | Formaldehyde Assisted Isolation of Regulatory Elements | U. Texas | 5 |
| Genes | High-quality gene annotations | Gencode/Sanger | 3 |
| Mapability | Uniqueness of short read nmers | Broad, Duke, UMass | 5 |
| Methyl27 | DNA methylation by Illumina 27K | HudsonAlpha | 3 |
| Methyl-seq | DNA methylation by restriction enzymes | HudsonAlpha | 15 |
| NRE | Negative regulatory elements | NHGRI | 6 |
| PET | 5′- and 3′-paired-end tags | Genome Inst. Singapore | 13 |
| RIP-chip | RNA-binding proteins | SUNY Albany | 7 |
| RNA-chip | RNA microarray | Affymetrix/CSHL | 25 |
| RNA-seq | RNA sequencing | Caltech, CSHL, GIS, Yale | 23 |
| TbaAlign | Multi-species alignment with TBA | NHGRI | 1 |
| CNV | Copy number variation | HudsonAlpha | 3 |
| DHS-5C | Chromatin interactions: DHS versus TSS | U Washington | 2 |
| 5C | Chromatin interactions: pilot region | U Mass | 2 |
| Total | 341 |