Table 2.
Table summarising all the ENCODE collections
| Collection | Description | Total numbers* | Link |
|---|---|---|---|
| ENCORE matrix | The ENCORE matrix summarises assays performed to study protein-RNA interactions of RNA-binding proteins (RBPs) encoded in the human genome. | 1832 | http://tinyurl.com/encore-matrix |
| Immune cells matrix | Immune cells matrix summarises epigenomic profiling of human immune cells at different cellular fates and states, including activation, stimulation, and disease (MS). | 1736 | http://tinyurl.com/Immune-matrix |
| Stem cells differentiation matrix | Stem cells differentiation matrix summarises assays performed on 3 different stem cells (H1, H9, PGP) and their in vitro differentiated derivatives. | 781 | http://tinyurl.com/stem-cell-matrix |
| Deeply profiled cell lines matrix | The deeply profiled cell lines matrix represents data from cell lines that have been extensively studied within the ENCODE project. | 6474 | http://tinyurl.com/deeply-profiled |
| Protein Knockdown/Degron matrix | This matrix displays experiments that were performed on transformed HCT116 cell lines, utilising the auxin-inducible Degron (AID) system. | 252 | http://tinyurl.com/degron-matrix |
| Human donor matrix | The Human Donor Matrix provides a matrix view of assays performed on biosamples derived from individual human donors. | 6978 | http://tinyurl.com/human-donor-matrix |
| ENTEx matrix | The ENTEx matrix displays approximately 30 overlapping tissues from four individual donors, which were sampled in a collaborative effort with the GTEx Consortium. | 1567 | http://tinyurl.com/entex-matrix |
| Rush Alzheimer’s Disease Study Matrix | Human brain samples collection page that includes data from multiple brain regions collected from individuals with various levels of cognitive impairment. | 664 | http://tinyurl.com/brain-matrix |
| Reference Epigenomes matrix | Project data from human tissue, cell line, primary cell, and in vitro differentiated cell biosamples, organised as reference epigenomes following guidelines set out by IHEC. | 4145 | http://tinyurl.com/reference-epigenome-matrix |
| Mouse development matrix | The mouse development matrix displays embryonic to postnatal mouse developmental time course data across several tissues, organised as reference epigenomes. | 1934 | http://tinyurl.com/mouse-development-matrix |
*Note: Refer to Fig. 5 for a more comprehensive breakdown of the total number of datasets within each category.