Table 1 Table summarising all the ENCODE series

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