Table 1.
Table summarising all the ENCODE series
| Series | Description | Total numbers | Link |
|---|---|---|---|
| Organism Development series | Set of related functional genomics datasets performed to study the changes that occur within the genomic landscape of a particular biosample type during the developmental stages of an organism. | 433 | https://tinyurl.com/Organism-DevelopmentSeries |
| Treatment time series | Set of functional genomics assays that were performed on the same biosample but sampled at different treatment durations | 82 | http://tinyurl.com/TreatmentTimeSeries |
| Treatment concentration series | Set of functional genomics datasets that were assayed on a particular biosample for a fixed time but treated with different concentrations of the same chemical. | 2 | http://tinyurl.com/TreatmentConcentrationSeries |
| Replication timing series | Set of functional genomics datasets that assayed different primary cells and cell lines sampled at various cell cycle phases, including early S, late S, G1b, S1, S2, S3, S4 and G2. | 22 | http://tinyurl.com/ReplicationTimingSeries |
| Gene silencing series | Two types: (A) Pair of functional genomics datasets performed on biosamples that contain either a normal copy or a silenced copy of a target gene using either siRNA, shRNA, or CRISPR editing (B) Pair of control and experimental datasets that are depleted of a particular target protein using an auxin-inducible degron (AID) method. | 1196 | http://tinyurl.com/GeneSilencingSeries |
| Differentiation series | Set of related functional genomics datasets wherein assays were performed on in vitro differentiated cells or organoids that were derived from embryonic stem cells (such as H9) or pluripotent stem cells (such as GM23338 and WTC11). | 41 | http://tinyurl.com/Differentiation-Series |
| Disease series | Two types: (A) Groups assays performed on brain samples that have been collected from the Rush Institute from patients diagnosed with different levels of cognitive impairments, and (B) Pair of assays performed on tissues derived from non-cancerous and cancerous samples from the same patient. | 132 | http://tinyurl.com/DiseaseSeries |
| Reference epigenome series | Collection of datasets profiling all the epigenomic marks of a particular biosample, ideally collected from the same individual donor. | 325 | https://tinyurl.com/ReferenceEpigenomeSeries |
| Multiomics series | Set of paired multiomics assays (snATAC-seq and snRNA-seq) performed on a particular biosample. | 160 | https://tinyurl.com/encode-multiomics-series |