Table 1.
The full complement of ENCODE data sets summarized by cell type [types annotated as cancer are marked with asterisk (*)]
| Cell type | Tissue | Description | Data sets |
|||
|---|---|---|---|---|---|---|
| TF/His | RNA | Other | Total | |||
| Tier 1 initial | ||||||
| GM12878 | Blood | Lymphoblastoid | 137 | 27 | 49 | 213 |
| K562* | Blood | Leukemia | 247 | 45 | 80 | 372 |
| Tier 1 added in 2011 | ||||||
| H1-hESC | Embryonic stem | Embryonic stem | 96 | 14 | 23 | 133 |
| Tier 2 initial | ||||||
| HeLa-S3* | Uterine cervix | Cervical carcinoma | 93 | 14 | 30 | 137 |
| HepG2* | Liver | Liver carcinoma | 118 | 19 | 26 | 163 |
| HUVEC | Umbilical endothelium | Umbilical vein endothelial | 37 | 13 | 16 | 66 |
| Tier 2 added in 2011 | ||||||
| A549* | Lung | Lung carcinoma | 89 | 22 | 12 | 123 |
| CD14+ | Blood | Monocyte | 17 | 4 | 4 | 25 |
| IMR90 | Lung | Lung fibroblast | 11 | 16 | 10 | 37 |
| MCF-7* | Breast | Breast carcinoma | 50 | 15 | 32 | 97 |
| SK-N-SH* | Brain | Neuroblastoma | 36 | 16 | 7 | 59 |
| Tier 2 added in 2012 | ||||||
| CD20+ | Blood | B cell | 11 | 5 | 4 | 20 |
| H1-neuron | Neuron | H1ES-derived neuron | 5 | 3 | 1 | 9 |
| LHCN-M2 | Muscle | Myoblast | 7 | 2 | 4 | 13 |
| Human: totals | ||||||
| Tier1 + Tier2 (14) | 954 | 215 | 298 | 1467 | ||
| Tier 3 (274) | 591 | 94 | 734 | 1419 | ||
| All (288) | 1545 | 309 | 1032 | 2886 | ||
| Mouse | ||||||
| All (81) | 381 | 102 | 100 | 583 | ||
Studies in the human genome focused on common cell types in designated ‘tiers’, with Tier1 most intensively studied, followed by Tier 2. A total of 10 292 files have been released referenced to the human (hg19/GRCh37) genome. For mouse (mm9/NCBI37), the comparable number is 8952 files. Data are available for download from the UCSC download server; for access see http://encodeproject.org/ENCODE/downloads.html and http://encodeproject.org/ENCODE/downloadsMouse.html. File formats are described on the ENCODE Portal File Formats page.