Data & Resources
Selected published datasets, atlases, and computational resources
PRIME predictions
Genome-wide predictions of active regulatory elements generated using PRIME across 141 FANTOM5 cell type and tissue facets.
- Paper: Einarsson H, et al. Mapping active cis-regulatory elements from transcription initiation events. bioRxiv. 2026.
- Interactive browser: PRIME Atlas
- Download: PRIME predictions
Enhancer–gene regulatory interactions
Genome-wide scE2G predictions of enhancer–gene regulatory interactions across seven 10x Genomics multiome datasets, including K562, GM12878, PBMC, BMMC, and pancreatic islets.
- Paper: Sheth, Qiu, et al. Mapping enhancer–gene regulatory interactions from single-cell data. Nature Genetics. 2026.
- Download: scE2G predictions (files named
[Dataset]/scE2G/scE2G_multiome.[CellType].predictions.tsv.gz)
FANTOM5 enhancers
Divergently transcribed enhancers identified from CAGE data generated by the FANTOM consortium.
- Paper: Andersson R, et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014.
- Original data (hg19 and mm9)
- Reprocessed human CAGE data aligned to GRCh38 (hg38)
- Reprocessed mouse CAGE data aligned to GRCm38 (mm10)
CAGE data across 108 lymphoblastoid cell lines
CAGE profiles from 108 Epstein–Barr virus-transformed lymphoblastoid cell lines (89 YRI and 19 LWK) generated to investigate promoter architecture and regulatory variation.
- Paper: Einarsson H, et al. Promoter sequence and architecture determine expression variability and confer robustness to genetic variants. eLife. 2022.
- Data: NCBI Gene Expression Omnibus GSE188131