Data Use Policy for External Users

External data users may freely download, analyze and publish results based on any ENCODE data without restrictions. This applies to all datasets, regardless of type or size, and includes no grace period for ENCODE data producers, either as individual members or as part of the Consortium. Researchers using unpublished ENCODE data are encouraged to contact the data producers to discuss possible coordinated publications; however, this is optional. The Consortium will continue to publish the results of its own analysis efforts in independent publications.

We request that researchers who use ENCODE datasets (published or unpublished) in publications and presentations cite the ENCODE Consortium in all of the following ways: 

  1. Cite the Consortium's most recent publications:
  2. Acknowledge the ENCODE Consortium and the ENCODE production laboratory(s) generating the particular dataset(s)
  3. Reference the ENCODE accession numbers of the datasets (ENCSR...) and files (ENCFF...) used
    • Supplemental table example:
      Kazachenka et al. [1] included a table of ENCODE accessions for datasets and file(s) as Supplementary Table 6.
    • Inline citation example:
      Inoue et al. [2] included a list of the file accessions inline:
      We downloaded the call sets from the ENCODE portal (Sloan et al. 2016) ( with the following identifiers: ENCFF001SWK, ENCFF002CKI, ENCFF002CKJ, ENCFF002CKK, ENCFF002CKN, ENCFF002CKY, ENCFF002CUS, ENCFF002CTX, ENCFF002CUU, ENCFF002CKV, and ENCFF002CUN.

[1] Kazachenka A, Bertozzi TM, Sjoberg-Herrera MK, et al. Identification, Characterization, and Heritability of Murine Metastable Epialleles: Implications for Non-genetic Inheritance. Cell. 2018;175(5):1259-1271.e13. PMID: 30454646; PMCID: PMC6242299

[2] Inoue F, Kircher M, Martin B, et al. A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity. Genome Res. 2017;27(1):38-52. PMID: 27831498; PMCID: PMC5204343

Updated January 30, 2019.